Phosphorus in PDB 145d: Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
Protein crystallography data
The structure of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg), PDB code: 145d
was solved by
G.P.Schroth,
T.F.Kagawa,
P.Shing Ho,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
8.00 /
1.25
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
17.865,
30.822,
44.797,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Phosphorus atom in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
(pdb code 145d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the
Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg), PDB code: 145d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 1 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:11.9
occ:0.65
|
P
|
A:DG2
|
0.0
|
11.9
|
0.7
|
|
OP2
|
C:DG14
|
0.9
|
7.7
|
0.3
|
|
P
|
C:DG14
|
1.0
|
7.5
|
0.3
|
|
OP1
|
A:DG2
|
1.5
|
12.1
|
0.7
|
|
OP2
|
A:DG2
|
1.5
|
12.2
|
0.7
|
|
O3'
|
C:MCY13
|
1.5
|
7.1
|
0.3
|
|
O3'
|
A:MCY1
|
1.6
|
11.2
|
0.7
|
|
O5'
|
A:DG2
|
1.6
|
12.2
|
0.7
|
|
O5'
|
C:DG14
|
2.2
|
7.2
|
0.3
|
|
OP1
|
C:DG14
|
2.3
|
7.5
|
0.3
|
|
C5'
|
C:DG14
|
2.7
|
7.1
|
0.3
|
|
C3'
|
A:MCY1
|
2.7
|
10.3
|
0.7
|
|
H5'
|
C:DG14
|
2.7
|
0.0
|
0.3
|
|
H5''
|
C:DG14
|
2.7
|
0.0
|
0.3
|
|
C5'
|
A:DG2
|
2.7
|
12.6
|
0.7
|
|
H3'
|
A:MCY1
|
2.8
|
0.0
|
0.7
|
|
H5''
|
A:DG2
|
2.9
|
0.0
|
0.7
|
|
C3'
|
C:MCY13
|
2.9
|
6.6
|
0.3
|
|
H5'
|
A:DG2
|
3.0
|
0.0
|
0.7
|
|
H1
|
A:HOH70
|
3.2
|
0.0
|
1.0
|
|
H4'
|
A:MCY1
|
3.2
|
0.0
|
0.7
|
|
H3'
|
C:MCY13
|
3.3
|
0.0
|
0.3
|
|
H1
|
C:HOH26
|
3.3
|
0.0
|
1.0
|
|
H4'
|
C:MCY13
|
3.4
|
0.0
|
0.3
|
|
C4'
|
A:MCY1
|
3.5
|
10.0
|
0.7
|
|
H2
|
C:HOH26
|
3.7
|
0.0
|
1.0
|
|
C4'
|
C:MCY13
|
3.8
|
6.4
|
0.3
|
|
H2''
|
C:MCY13
|
3.8
|
0.0
|
0.3
|
|
C2'
|
A:MCY1
|
3.9
|
9.8
|
0.7
|
|
C2'
|
C:MCY13
|
3.9
|
6.3
|
0.3
|
|
C4'
|
A:DG2
|
3.9
|
12.8
|
0.7
|
|
H2''
|
A:MCY1
|
4.0
|
0.0
|
0.7
|
|
H1'
|
C:MCY13
|
4.0
|
0.0
|
0.3
|
|
O
|
C:HOH26
|
4.0
|
16.6
|
1.0
|
|
O
|
A:HOH70
|
4.0
|
38.8
|
1.0
|
|
C4'
|
C:DG14
|
4.1
|
6.9
|
0.3
|
|
H5''
|
A:MCY1
|
4.1
|
0.0
|
0.7
|
|
H1'
|
A:MCY1
|
4.2
|
0.0
|
0.7
|
|
O4'
|
A:DG2
|
4.3
|
12.8
|
0.7
|
|
H4'
|
A:DG2
|
4.3
|
0.0
|
0.7
|
|
C1'
|
C:MCY13
|
4.4
|
6.1
|
0.3
|
|
H2
|
A:HOH70
|
4.4
|
0.0
|
1.0
|
|
C1'
|
A:MCY1
|
4.5
|
9.4
|
0.7
|
|
C5'
|
A:MCY1
|
4.5
|
10.2
|
0.7
|
|
O4'
|
A:MCY1
|
4.5
|
9.6
|
0.7
|
|
O4'
|
C:MCY13
|
4.5
|
6.2
|
0.3
|
|
H4'
|
C:DG14
|
4.6
|
0.0
|
0.3
|
|
O4'
|
C:DG14
|
4.7
|
6.7
|
0.3
|
|
H2'
|
A:MCY1
|
4.7
|
0.0
|
0.7
|
|
H3'
|
C:DG14
|
4.7
|
0.0
|
0.3
|
|
H2'
|
C:MCY13
|
4.8
|
0.0
|
0.3
|
|
H1
|
A:HOH71
|
4.9
|
0.0
|
1.0
|
|
H5''
|
C:MCY13
|
4.9
|
0.0
|
0.3
|
|
C3'
|
C:DG14
|
5.0
|
6.8
|
0.3
|
|
C5'
|
C:MCY13
|
5.0
|
6.4
|
0.3
|
|
Phosphorus binding site 2 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 2 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:14.5
occ:0.65
|
P
|
A:DG3
|
0.0
|
14.5
|
0.7
|
|
OP2
|
A:DG3
|
1.5
|
14.4
|
0.7
|
|
OP1
|
A:DG3
|
1.5
|
14.6
|
0.7
|
|
O3'
|
A:DG2
|
1.6
|
13.8
|
0.7
|
|
O5'
|
A:DG3
|
1.6
|
13.7
|
0.7
|
|
O3'
|
C:DG14
|
1.7
|
7.0
|
0.3
|
|
O5'
|
C:DC15
|
1.8
|
7.0
|
0.3
|
|
P
|
C:DC15
|
1.9
|
6.9
|
0.3
|
|
OP1
|
C:DC15
|
2.4
|
7.1
|
0.3
|
|
C3'
|
C:DG14
|
2.6
|
6.8
|
0.3
|
|
H2''
|
C:DG14
|
2.6
|
0.0
|
0.3
|
|
C5'
|
A:DG3
|
2.6
|
12.8
|
0.7
|
|
C3'
|
A:DG2
|
2.7
|
13.1
|
0.7
|
|
C5'
|
C:DC15
|
2.8
|
6.9
|
0.3
|
|
H5'
|
C:DC15
|
2.8
|
0.0
|
0.3
|
|
H5''
|
A:DG3
|
2.9
|
0.0
|
0.7
|
|
C2'
|
C:DG14
|
2.9
|
6.7
|
0.3
|
|
H5'
|
A:DG3
|
3.0
|
0.0
|
0.7
|
|
H2'
|
C:DG14
|
3.0
|
0.0
|
0.3
|
|
H3'
|
A:DG2
|
3.1
|
0.0
|
0.7
|
|
H3'
|
C:DG14
|
3.2
|
0.0
|
0.3
|
|
H2''
|
A:DG2
|
3.2
|
0.0
|
0.7
|
|
H5''
|
C:DC15
|
3.3
|
0.0
|
0.3
|
|
OP2
|
C:DC15
|
3.3
|
7.1
|
0.3
|
|
C2'
|
A:DG2
|
3.4
|
12.9
|
0.7
|
|
H2'
|
A:DG2
|
3.5
|
0.0
|
0.7
|
|
H6
|
C:DC15
|
3.7
|
0.0
|
0.3
|
|
H4'
|
C:DG14
|
3.8
|
0.0
|
0.3
|
|
H8
|
A:DG3
|
3.8
|
0.0
|
0.7
|
|
C4'
|
C:DG14
|
3.8
|
6.9
|
0.3
|
|
H4'
|
A:DG2
|
3.8
|
0.0
|
0.7
|
|
H2'
|
A:DG3
|
3.9
|
0.0
|
0.7
|
|
C4'
|
A:DG2
|
3.9
|
12.8
|
0.7
|
|
C4'
|
A:DG3
|
3.9
|
12.2
|
0.7
|
|
H3'
|
A:DG3
|
3.9
|
0.0
|
0.7
|
|
H2'
|
C:DC15
|
4.0
|
0.0
|
0.3
|
|
H2
|
C:HOH39
|
4.0
|
0.0
|
1.0
|
|
C4'
|
C:DC15
|
4.1
|
6.9
|
0.3
|
|
H1
|
C:HOH48
|
4.1
|
0.0
|
1.0
|
|
H5'
|
A:DG2
|
4.1
|
0.0
|
0.7
|
|
O4'
|
C:DC15
|
4.2
|
6.7
|
0.3
|
|
C1'
|
C:DG14
|
4.4
|
6.5
|
0.3
|
|
C3'
|
A:DG3
|
4.4
|
12.0
|
0.7
|
|
O4'
|
A:DG3
|
4.4
|
11.7
|
0.7
|
|
H5'
|
C:DG14
|
4.5
|
0.0
|
0.3
|
|
O
|
C:HOH39
|
4.5
|
52.4
|
1.0
|
|
C5'
|
A:DG2
|
4.6
|
12.6
|
0.7
|
|
C2'
|
A:DG3
|
4.6
|
11.7
|
0.7
|
|
C6
|
C:DC15
|
4.6
|
6.5
|
0.3
|
|
H2
|
C:HOH48
|
4.6
|
0.0
|
1.0
|
|
H3'
|
C:DC15
|
4.7
|
0.0
|
0.3
|
|
C8
|
A:DG3
|
4.7
|
10.9
|
0.7
|
|
O4'
|
C:DG14
|
4.7
|
6.7
|
0.3
|
|
C5'
|
C:DG14
|
4.7
|
7.1
|
0.3
|
|
C1'
|
A:DG2
|
4.7
|
12.5
|
0.7
|
|
H1'
|
C:DG14
|
4.8
|
0.0
|
0.3
|
|
H4'
|
A:DG3
|
4.8
|
0.0
|
0.7
|
|
H5
|
C:DC16
|
4.8
|
0.0
|
0.3
|
|
C2'
|
C:DC15
|
4.8
|
6.8
|
0.3
|
|
C5
|
C:DC16
|
4.8
|
6.3
|
0.3
|
|
C3'
|
C:DC15
|
4.8
|
6.9
|
0.3
|
|
H4'
|
C:DC15
|
4.9
|
0.0
|
0.3
|
|
O
|
C:HOH48
|
4.9
|
37.9
|
1.0
|
|
H5''
|
A:DG2
|
4.9
|
0.0
|
0.7
|
|
O4'
|
A:DG2
|
4.9
|
12.8
|
0.7
|
|
Phosphorus binding site 3 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 3 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:12.0
occ:0.65
|
P
|
A:DG4
|
0.0
|
12.0
|
0.7
|
|
OP1
|
C:DC16
|
1.1
|
7.4
|
0.3
|
|
P
|
C:DC16
|
1.2
|
7.2
|
0.3
|
|
OP1
|
A:DG4
|
1.5
|
12.3
|
0.7
|
|
OP2
|
A:DG4
|
1.5
|
12.2
|
0.7
|
|
O3'
|
A:DG3
|
1.6
|
12.1
|
0.7
|
|
O5'
|
C:DC16
|
1.6
|
7.2
|
0.3
|
|
O5'
|
A:DG4
|
1.6
|
11.7
|
0.7
|
|
O3'
|
C:DC15
|
2.0
|
7.2
|
0.3
|
|
H3'
|
C:DC15
|
2.1
|
0.0
|
0.3
|
|
C3'
|
C:DC15
|
2.5
|
6.9
|
0.3
|
|
OP2
|
C:DC16
|
2.6
|
7.3
|
0.3
|
|
C3'
|
A:DG3
|
2.7
|
12.0
|
0.7
|
|
C5'
|
A:DG4
|
2.7
|
11.0
|
0.7
|
|
H3'
|
A:DG3
|
2.8
|
0.0
|
0.7
|
|
C5'
|
C:DC16
|
3.0
|
7.0
|
0.3
|
|
H5'
|
A:DG4
|
3.0
|
0.0
|
0.7
|
|
H5''
|
A:DG4
|
3.0
|
0.0
|
0.7
|
|
H4'
|
A:DG3
|
3.2
|
0.0
|
0.7
|
|
H4'
|
C:DC15
|
3.3
|
0.0
|
0.3
|
|
H5''
|
C:DC16
|
3.3
|
0.0
|
0.3
|
|
C4'
|
C:DC15
|
3.4
|
6.9
|
0.3
|
|
C4'
|
A:DG3
|
3.5
|
12.2
|
0.7
|
|
H5'
|
C:DC16
|
3.6
|
0.0
|
0.3
|
|
H5''
|
C:DC15
|
3.6
|
0.0
|
0.3
|
|
C2'
|
C:DC15
|
3.8
|
6.8
|
0.3
|
|
C2'
|
A:DG3
|
3.8
|
11.7
|
0.7
|
|
C4'
|
C:DC16
|
3.8
|
6.8
|
0.3
|
|
H2
|
A:HOH37
|
3.9
|
0.0
|
1.0
|
|
H2''
|
A:DG3
|
3.9
|
0.0
|
0.7
|
|
C4'
|
A:DG4
|
3.9
|
10.5
|
0.7
|
|
O4'
|
C:DC16
|
3.9
|
6.6
|
0.3
|
|
O
|
C:HOH64
|
4.0
|
51.3
|
1.0
|
|
H4'
|
C:DC16
|
4.1
|
0.0
|
0.3
|
|
C5'
|
C:DC15
|
4.1
|
6.9
|
0.3
|
|
H2''
|
C:DC15
|
4.1
|
0.0
|
0.3
|
|
H1
|
C:HOH64
|
4.1
|
0.0
|
1.0
|
|
H5''
|
A:DG3
|
4.2
|
0.0
|
0.7
|
|
H2
|
C:HOH64
|
4.2
|
0.0
|
1.0
|
|
H4'
|
A:DG4
|
4.2
|
0.0
|
0.7
|
|
O4'
|
A:DG4
|
4.3
|
10.2
|
0.7
|
|
H1'
|
A:DG3
|
4.3
|
0.0
|
0.7
|
|
H2'
|
C:DC15
|
4.4
|
0.0
|
0.3
|
|
C1'
|
A:DG3
|
4.5
|
11.5
|
0.7
|
|
C5'
|
A:DG3
|
4.5
|
12.8
|
0.7
|
|
O4'
|
A:DG3
|
4.5
|
11.7
|
0.7
|
|
H2
|
C:HOH27
|
4.6
|
0.0
|
1.0
|
|
H1'
|
C:DC15
|
4.6
|
0.0
|
0.3
|
|
O4'
|
C:DC15
|
4.6
|
6.7
|
0.3
|
|
H2'
|
A:DG3
|
4.6
|
0.0
|
0.7
|
|
C1'
|
C:DC15
|
4.7
|
6.7
|
0.3
|
|
O
|
A:HOH37
|
4.8
|
40.1
|
1.0
|
|
OP2
|
C:DC15
|
4.8
|
7.1
|
0.3
|
|
O5'
|
C:DC15
|
4.8
|
7.0
|
0.3
|
|
H1
|
A:HOH37
|
4.9
|
0.0
|
1.0
|
|
H5'
|
C:DC15
|
4.9
|
0.0
|
0.3
|
|
Phosphorus binding site 4 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 4 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:10.9
occ:0.65
|
P
|
A:5CM5
|
0.0
|
10.9
|
0.7
|
|
OP1
|
A:5CM5
|
1.5
|
11.0
|
0.7
|
|
OP2
|
A:5CM5
|
1.5
|
11.3
|
0.7
|
|
P
|
C:5CM17
|
1.6
|
7.5
|
0.3
|
|
O3'
|
A:DG4
|
1.6
|
10.8
|
0.7
|
|
O5'
|
A:5CM5
|
1.6
|
10.5
|
0.7
|
|
OP1
|
C:5CM17
|
1.7
|
7.4
|
0.3
|
|
O5'
|
C:5CM17
|
1.7
|
7.2
|
0.3
|
|
O3'
|
C:DC16
|
1.7
|
7.2
|
0.3
|
|
C5'
|
C:5CM17
|
2.6
|
6.6
|
0.3
|
|
H5'
|
C:5CM17
|
2.6
|
0.0
|
0.3
|
|
C3'
|
A:DG4
|
2.7
|
10.5
|
0.7
|
|
C5'
|
A:5CM5
|
2.8
|
9.3
|
0.7
|
|
C3'
|
C:DC16
|
2.9
|
6.8
|
0.3
|
|
H2''
|
A:DG4
|
2.9
|
0.0
|
0.7
|
|
H5'
|
A:5CM5
|
2.9
|
0.0
|
0.7
|
|
H3'
|
A:DG4
|
3.0
|
0.0
|
0.7
|
|
H5''
|
C:5CM17
|
3.0
|
0.0
|
0.3
|
|
OP2
|
C:5CM17
|
3.1
|
7.5
|
0.3
|
|
H2
|
A:HOH41
|
3.1
|
0.0
|
1.0
|
|
C2'
|
A:DG4
|
3.1
|
10.2
|
0.7
|
|
H1
|
A:HOH58
|
3.1
|
0.0
|
1.0
|
|
H5''
|
A:5CM5
|
3.2
|
0.0
|
0.7
|
|
H2'
|
A:DG4
|
3.2
|
0.0
|
0.7
|
|
H3'
|
C:DC16
|
3.3
|
0.0
|
0.3
|
|
H2''
|
C:DC16
|
3.5
|
0.0
|
0.3
|
|
C2'
|
C:DC16
|
3.6
|
6.6
|
0.3
|
|
O
|
A:HOH58
|
3.7
|
35.9
|
1.0
|
|
H6
|
A:5CM5
|
3.7
|
0.0
|
0.7
|
|
H2'
|
C:DC16
|
3.7
|
0.0
|
0.3
|
|
H1
|
A:HOH41
|
3.8
|
0.0
|
1.0
|
|
O
|
A:HOH41
|
3.9
|
23.9
|
1.0
|
|
H6
|
C:5CM17
|
3.9
|
0.0
|
0.3
|
|
C4'
|
C:5CM17
|
3.9
|
6.3
|
0.3
|
|
C4'
|
A:DG4
|
4.0
|
10.5
|
0.7
|
|
H4'
|
A:DG4
|
4.0
|
0.0
|
0.7
|
|
C4'
|
A:5CM5
|
4.0
|
8.7
|
0.7
|
|
H4'
|
C:DC16
|
4.0
|
0.0
|
0.3
|
|
H5'
|
C:DC16
|
4.0
|
0.0
|
0.3
|
|
C4'
|
C:DC16
|
4.0
|
6.8
|
0.3
|
|
H2'
|
A:5CM5
|
4.1
|
0.0
|
0.7
|
|
H2'
|
C:5CM17
|
4.2
|
0.0
|
0.3
|
|
H3'
|
A:5CM5
|
4.2
|
0.0
|
0.7
|
|
O4'
|
C:5CM17
|
4.2
|
6.1
|
0.3
|
|
O4'
|
A:5CM5
|
4.2
|
8.2
|
0.7
|
|
H3'
|
C:5CM17
|
4.4
|
0.0
|
0.3
|
|
H2
|
A:HOH58
|
4.5
|
0.0
|
1.0
|
|
C3'
|
A:5CM5
|
4.5
|
8.7
|
0.7
|
|
H5'
|
A:DG4
|
4.5
|
0.0
|
0.7
|
|
C1'
|
A:DG4
|
4.6
|
10.0
|
0.7
|
|
C5'
|
C:DC16
|
4.6
|
7.0
|
0.3
|
|
C3'
|
C:5CM17
|
4.7
|
6.4
|
0.3
|
|
C6
|
A:5CM5
|
4.7
|
6.8
|
0.7
|
|
H4'
|
C:5CM17
|
4.7
|
0.0
|
0.3
|
|
H5A1
|
A:5CM5
|
4.8
|
0.0
|
0.7
|
|
C2'
|
A:5CM5
|
4.8
|
8.3
|
0.7
|
|
C5'
|
A:DG4
|
4.8
|
11.0
|
0.7
|
|
H4'
|
A:5CM5
|
4.8
|
0.0
|
0.7
|
|
C2'
|
C:5CM17
|
4.9
|
6.2
|
0.3
|
|
C6
|
C:5CM17
|
4.9
|
5.5
|
0.3
|
|
H5''
|
C:DC16
|
4.9
|
0.0
|
0.3
|
|
O4'
|
A:DG4
|
4.9
|
10.2
|
0.7
|
|
C1'
|
C:DC16
|
5.0
|
6.4
|
0.3
|
|
Phosphorus binding site 5 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 5 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:9.8
occ:0.65
|
P
|
A:DG6
|
0.0
|
9.8
|
0.7
|
|
OP1
|
C:DG18
|
0.9
|
6.9
|
0.3
|
|
P
|
C:DG18
|
1.1
|
6.9
|
0.3
|
|
OP2
|
A:DG6
|
1.5
|
9.8
|
0.7
|
|
OP1
|
A:DG6
|
1.5
|
9.7
|
0.7
|
|
O3'
|
A:5CM5
|
1.6
|
9.1
|
0.7
|
|
O5'
|
A:DG6
|
1.6
|
9.6
|
0.7
|
|
O5'
|
C:DG18
|
1.6
|
6.7
|
0.3
|
|
O3'
|
C:5CM17
|
2.3
|
6.6
|
0.3
|
|
OP2
|
C:DG18
|
2.3
|
6.8
|
0.3
|
|
H3'
|
C:5CM17
|
2.5
|
0.0
|
0.3
|
|
C3'
|
A:5CM5
|
2.6
|
8.7
|
0.7
|
|
C5'
|
A:DG6
|
2.6
|
9.5
|
0.7
|
|
H3'
|
A:5CM5
|
2.7
|
0.0
|
0.7
|
|
H5'
|
A:DG6
|
2.9
|
0.0
|
0.7
|
|
C3'
|
C:5CM17
|
2.9
|
6.4
|
0.3
|
|
H5''
|
A:DG6
|
3.0
|
0.0
|
0.7
|
|
C5'
|
C:DG18
|
3.0
|
6.7
|
0.3
|
|
H4'
|
A:5CM5
|
3.1
|
0.0
|
0.7
|
|
C4'
|
A:5CM5
|
3.4
|
8.7
|
0.7
|
|
H5'
|
C:DG18
|
3.4
|
0.0
|
0.3
|
|
H5''
|
C:DG18
|
3.6
|
0.0
|
0.3
|
|
H4'
|
C:5CM17
|
3.7
|
0.0
|
0.3
|
|
H1
|
A:HOH72
|
3.8
|
0.0
|
1.0
|
|
H2
|
C:HOH61
|
3.8
|
0.0
|
1.0
|
|
C4'
|
C:5CM17
|
3.8
|
6.3
|
0.3
|
|
H2
|
C:HOH54
|
3.8
|
0.0
|
1.0
|
|
C2'
|
A:5CM5
|
3.8
|
8.3
|
0.7
|
|
H5''
|
C:5CM17
|
3.9
|
0.0
|
0.3
|
|
C4'
|
A:DG6
|
3.9
|
9.4
|
0.7
|
|
H4'
|
C:DG18
|
3.9
|
0.0
|
0.3
|
|
H5''
|
A:5CM5
|
3.9
|
0.0
|
0.7
|
|
H2''
|
A:5CM5
|
3.9
|
0.0
|
0.7
|
|
C4'
|
C:DG18
|
4.0
|
6.6
|
0.3
|
|
H4'
|
A:DG6
|
4.0
|
0.0
|
0.7
|
|
C2'
|
C:5CM17
|
4.2
|
6.2
|
0.3
|
|
O4'
|
A:DG6
|
4.2
|
9.3
|
0.7
|
|
C5'
|
A:5CM5
|
4.3
|
9.3
|
0.7
|
|
O4'
|
C:DG18
|
4.3
|
6.4
|
0.3
|
|
H2''
|
C:5CM17
|
4.3
|
0.0
|
0.3
|
|
H1'
|
A:5CM5
|
4.3
|
0.0
|
0.7
|
|
C5'
|
C:5CM17
|
4.4
|
6.6
|
0.3
|
|
O
|
A:HOH72
|
4.5
|
52.1
|
1.0
|
|
C1'
|
A:5CM5
|
4.5
|
7.8
|
0.7
|
|
O4'
|
A:5CM5
|
4.5
|
8.2
|
0.7
|
|
H2
|
A:HOH67
|
4.5
|
0.0
|
1.0
|
|
O
|
C:HOH54
|
4.5
|
37.4
|
1.0
|
|
O
|
B:HOH52
|
4.6
|
54.4
|
1.0
|
|
H2'
|
A:5CM5
|
4.6
|
0.0
|
0.7
|
|
H1
|
C:HOH54
|
4.7
|
0.0
|
1.0
|
|
O
|
C:HOH61
|
4.7
|
22.3
|
1.0
|
|
H2'
|
C:5CM17
|
4.7
|
0.0
|
0.3
|
|
H1'
|
C:5CM17
|
4.9
|
0.0
|
0.3
|
|
O
|
A:HOH67
|
5.0
|
44.8
|
1.0
|
|
Phosphorus binding site 6 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 6 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P8
b:7.2
occ:0.65
|
P
|
B:DG8
|
0.0
|
7.2
|
0.7
|
|
P
|
D:DG20
|
0.6
|
6.9
|
0.3
|
|
OP1
|
D:DG20
|
1.1
|
7.0
|
0.3
|
|
OP1
|
B:DG8
|
1.5
|
7.2
|
0.7
|
|
OP2
|
B:DG8
|
1.5
|
7.4
|
0.7
|
|
O5'
|
D:DG20
|
1.6
|
6.8
|
0.3
|
|
O3'
|
B:MCY7
|
1.6
|
7.0
|
0.7
|
|
O5'
|
B:DG8
|
1.6
|
7.2
|
0.7
|
|
O3'
|
D:5CM19
|
1.8
|
6.8
|
0.3
|
|
OP2
|
D:DG20
|
2.1
|
7.1
|
0.3
|
|
H3'
|
D:5CM19
|
2.5
|
0.0
|
0.3
|
|
C3'
|
B:MCY7
|
2.6
|
6.8
|
0.7
|
|
C3'
|
D:5CM19
|
2.6
|
6.7
|
0.3
|
|
C5'
|
B:DG8
|
2.7
|
7.1
|
0.7
|
|
H3'
|
B:MCY7
|
2.8
|
0.0
|
0.7
|
|
C5'
|
D:DG20
|
2.8
|
6.6
|
0.3
|
|
H5''
|
B:DG8
|
3.0
|
0.0
|
0.7
|
|
H4'
|
B:MCY7
|
3.0
|
0.0
|
0.7
|
|
H5'
|
B:DG8
|
3.1
|
0.0
|
0.7
|
|
H5''
|
D:DG20
|
3.1
|
0.0
|
0.3
|
|
H2
|
B:HOH50
|
3.1
|
0.0
|
1.0
|
|
H5'
|
D:DG20
|
3.3
|
0.0
|
0.3
|
|
C4'
|
B:MCY7
|
3.3
|
6.9
|
0.7
|
|
H4'
|
D:5CM19
|
3.4
|
0.0
|
0.3
|
|
C4'
|
D:5CM19
|
3.6
|
6.8
|
0.3
|
|
H5''
|
B:MCY7
|
3.8
|
0.0
|
0.7
|
|
C2'
|
B:MCY7
|
3.8
|
6.5
|
0.7
|
|
H1
|
D:HOH69
|
3.8
|
0.0
|
1.0
|
|
C2'
|
D:5CM19
|
3.9
|
6.6
|
0.3
|
|
H2''
|
B:MCY7
|
3.9
|
0.0
|
0.7
|
|
O
|
B:HOH50
|
3.9
|
28.2
|
1.0
|
|
C4'
|
D:DG20
|
4.0
|
6.5
|
0.3
|
|
H1
|
B:HOH42
|
4.0
|
0.0
|
1.0
|
|
C4'
|
B:DG8
|
4.0
|
7.2
|
0.7
|
|
H2''
|
D:5CM19
|
4.0
|
0.0
|
0.3
|
|
H2
|
D:HOH69
|
4.1
|
0.0
|
1.0
|
|
C5'
|
B:MCY7
|
4.1
|
7.4
|
0.7
|
|
H1'
|
B:MCY7
|
4.2
|
0.0
|
0.7
|
|
H5''
|
D:5CM19
|
4.2
|
0.0
|
0.3
|
|
O4'
|
B:DG8
|
4.2
|
7.0
|
0.7
|
|
O4'
|
D:DG20
|
4.2
|
6.2
|
0.3
|
|
H4'
|
D:DG20
|
4.2
|
0.0
|
0.3
|
|
O
|
D:HOH69
|
4.3
|
42.1
|
1.0
|
|
H4'
|
B:DG8
|
4.3
|
0.0
|
0.7
|
|
C1'
|
B:MCY7
|
4.4
|
6.4
|
0.7
|
|
O4'
|
B:MCY7
|
4.5
|
6.7
|
0.7
|
|
H1'
|
D:5CM19
|
4.5
|
0.0
|
0.3
|
|
C5'
|
D:5CM19
|
4.5
|
6.9
|
0.3
|
|
H1
|
B:HOH50
|
4.6
|
0.0
|
1.0
|
|
H2'
|
D:5CM19
|
4.6
|
0.0
|
0.3
|
|
H2'
|
B:MCY7
|
4.6
|
0.0
|
0.7
|
|
O4'
|
D:5CM19
|
4.7
|
6.7
|
0.3
|
|
C1'
|
D:5CM19
|
4.7
|
6.5
|
0.3
|
|
H2
|
B:HOH34
|
4.7
|
0.0
|
1.0
|
|
O
|
B:HOH42
|
4.8
|
19.2
|
1.0
|
|
H1
|
B:HOH38
|
4.8
|
0.0
|
1.0
|
|
H5'
|
B:MCY7
|
5.0
|
0.0
|
0.7
|
|
O5'
|
B:MCY7
|
5.0
|
8.0
|
0.7
|
|
Phosphorus binding site 7 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 7 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P9
b:7.9
occ:0.65
|
P
|
B:DC9
|
0.0
|
7.9
|
0.7
|
|
P
|
D:DG21
|
0.9
|
7.4
|
0.3
|
|
O3'
|
D:DG20
|
1.2
|
6.8
|
0.3
|
|
OP2
|
B:DC9
|
1.5
|
8.2
|
0.7
|
|
OP1
|
B:DC9
|
1.5
|
7.9
|
0.7
|
|
O3'
|
B:DG8
|
1.6
|
7.7
|
0.7
|
|
O5'
|
B:DC9
|
1.6
|
8.0
|
0.7
|
|
OP1
|
D:DG21
|
1.6
|
7.3
|
0.3
|
|
O5'
|
D:DG21
|
1.7
|
7.0
|
0.3
|
|
OP2
|
D:DG21
|
2.3
|
7.5
|
0.3
|
|
C3'
|
D:DG20
|
2.4
|
6.5
|
0.3
|
|
C3'
|
B:DG8
|
2.7
|
7.3
|
0.7
|
|
C5'
|
B:DC9
|
2.7
|
7.6
|
0.7
|
|
H5''
|
B:DC9
|
2.8
|
0.0
|
0.7
|
|
H3'
|
D:DG20
|
2.8
|
0.0
|
0.3
|
|
H3'
|
B:DG8
|
2.8
|
0.0
|
0.7
|
|
C5'
|
D:DG21
|
2.9
|
6.6
|
0.3
|
|
H2''
|
D:DG20
|
3.1
|
0.0
|
0.3
|
|
H5''
|
D:DG21
|
3.2
|
0.0
|
0.3
|
|
H5'
|
B:DC9
|
3.2
|
0.0
|
0.7
|
|
H5'
|
D:DG21
|
3.3
|
0.0
|
0.3
|
|
C2'
|
D:DG20
|
3.3
|
6.3
|
0.3
|
|
H4'
|
D:DG20
|
3.4
|
0.0
|
0.3
|
|
C4'
|
D:DG20
|
3.5
|
6.5
|
0.3
|
|
H2'
|
B:DC9
|
3.5
|
0.0
|
0.7
|
|
H5'
|
D:DG20
|
3.6
|
0.0
|
0.3
|
|
H2
|
B:HOH55
|
3.6
|
0.0
|
1.0
|
|
H4'
|
B:DG8
|
3.6
|
0.0
|
0.7
|
|
H2''
|
B:DG8
|
3.6
|
0.0
|
0.7
|
|
H5'
|
B:DG8
|
3.7
|
0.0
|
0.7
|
|
C4'
|
B:DG8
|
3.7
|
7.2
|
0.7
|
|
H2'
|
D:DG20
|
3.7
|
0.0
|
0.3
|
|
H3'
|
B:DC9
|
3.7
|
0.0
|
0.7
|
|
C2'
|
B:DG8
|
3.7
|
7.2
|
0.7
|
|
H3'
|
D:DG21
|
3.9
|
0.0
|
0.3
|
|
O
|
B:HOH55
|
3.9
|
42.7
|
1.0
|
|
C4'
|
B:DC9
|
3.9
|
7.7
|
0.7
|
|
H2'
|
D:DG21
|
3.9
|
0.0
|
0.3
|
|
C4'
|
D:DG21
|
4.1
|
6.3
|
0.3
|
|
C5'
|
D:DG20
|
4.1
|
6.6
|
0.3
|
|
H2'
|
B:DG8
|
4.1
|
0.0
|
0.7
|
|
H8
|
D:DG21
|
4.1
|
0.0
|
0.3
|
|
H6
|
B:DC9
|
4.1
|
0.0
|
0.7
|
|
H1
|
B:HOH55
|
4.2
|
0.0
|
1.0
|
|
C3'
|
B:DC9
|
4.2
|
7.9
|
0.7
|
|
C5'
|
B:DG8
|
4.2
|
7.1
|
0.7
|
|
C2'
|
B:DC9
|
4.3
|
7.5
|
0.7
|
|
C3'
|
D:DG21
|
4.4
|
6.2
|
0.3
|
|
O4'
|
D:DG21
|
4.4
|
6.2
|
0.3
|
|
H5''
|
B:DG8
|
4.5
|
0.0
|
0.7
|
|
H5''
|
D:DG20
|
4.5
|
0.0
|
0.3
|
|
O4'
|
B:DC9
|
4.5
|
7.5
|
0.7
|
|
O
|
D:HOH57
|
4.6
|
16.9
|
1.0
|
|
C1'
|
D:DG20
|
4.6
|
6.2
|
0.3
|
|
O4'
|
D:DG20
|
4.6
|
6.2
|
0.3
|
|
C2'
|
D:DG21
|
4.7
|
6.1
|
0.3
|
|
H2
|
D:HOH57
|
4.7
|
0.0
|
1.0
|
|
H4'
|
B:DC9
|
4.7
|
0.0
|
0.7
|
|
H1
|
D:HOH57
|
4.8
|
0.0
|
1.0
|
|
O4'
|
B:DG8
|
4.9
|
7.0
|
0.7
|
|
H1
|
B:HOH42
|
4.9
|
0.0
|
1.0
|
|
C1'
|
B:DG8
|
4.9
|
7.0
|
0.7
|
|
H4'
|
D:DG21
|
5.0
|
0.0
|
0.3
|
|
C6
|
B:DC9
|
5.0
|
6.9
|
0.7
|
|
Phosphorus binding site 8 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 8 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P10
b:8.9
occ:0.65
|
P
|
B:DC10
|
0.0
|
8.9
|
0.7
|
|
P
|
D:DG22
|
0.6
|
6.1
|
0.3
|
|
O3'
|
D:DG21
|
1.2
|
6.1
|
0.3
|
|
OP1
|
B:DC10
|
1.5
|
9.0
|
0.7
|
|
OP2
|
B:DC10
|
1.5
|
9.0
|
0.7
|
|
O5'
|
D:DG22
|
1.6
|
6.0
|
0.3
|
|
OP2
|
D:DG22
|
1.6
|
6.1
|
0.3
|
|
O3'
|
B:DC9
|
1.6
|
8.5
|
0.7
|
|
O5'
|
B:DC10
|
1.6
|
9.1
|
0.7
|
|
OP1
|
D:DG22
|
2.0
|
6.1
|
0.3
|
|
C5'
|
D:DG22
|
2.4
|
6.0
|
0.3
|
|
H5''
|
D:DG22
|
2.4
|
0.0
|
0.3
|
|
C3'
|
D:DG21
|
2.4
|
6.2
|
0.3
|
|
C5'
|
B:DC10
|
2.6
|
9.6
|
0.7
|
|
C3'
|
B:DC9
|
2.6
|
7.9
|
0.7
|
|
H4'
|
D:DG21
|
2.7
|
0.0
|
0.3
|
|
H5'
|
D:DG22
|
2.7
|
0.0
|
0.3
|
|
H3'
|
B:DC9
|
2.8
|
0.0
|
0.7
|
|
H3'
|
D:DG21
|
2.8
|
0.0
|
0.3
|
|
H5''
|
B:DC10
|
2.8
|
0.0
|
0.7
|
|
H5'
|
B:DC10
|
2.9
|
0.0
|
0.7
|
|
C4'
|
D:DG21
|
3.1
|
6.3
|
0.3
|
|
H1
|
B:HOH52
|
3.1
|
0.0
|
1.0
|
|
H4'
|
B:DC9
|
3.2
|
0.0
|
0.7
|
|
H2
|
D:HOH57
|
3.3
|
0.0
|
1.0
|
|
C4'
|
B:DC9
|
3.5
|
7.7
|
0.7
|
|
H2
|
B:HOH52
|
3.6
|
0.0
|
1.0
|
|
H1
|
D:HOH33
|
3.6
|
0.0
|
1.0
|
|
C2'
|
D:DG21
|
3.6
|
6.1
|
0.3
|
|
H1
|
B:HOH40
|
3.7
|
0.0
|
1.0
|
|
C4'
|
D:DG22
|
3.7
|
5.9
|
0.3
|
|
H2''
|
D:DG21
|
3.7
|
0.0
|
0.3
|
|
H5''
|
D:DG21
|
3.7
|
0.0
|
0.3
|
|
O
|
B:HOH52
|
3.8
|
54.4
|
1.0
|
|
C2'
|
B:DC9
|
3.8
|
7.5
|
0.7
|
|
H2''
|
B:DC9
|
3.9
|
0.0
|
0.7
|
|
C4'
|
B:DC10
|
3.9
|
10.0
|
0.7
|
|
H1'
|
D:DG21
|
4.0
|
0.0
|
0.3
|
|
C5'
|
D:DG21
|
4.0
|
6.6
|
0.3
|
|
O4'
|
D:DG22
|
4.1
|
5.9
|
0.3
|
|
H1'
|
B:DC9
|
4.1
|
0.0
|
0.7
|
|
O4'
|
D:DG21
|
4.2
|
6.2
|
0.3
|
|
O
|
D:HOH57
|
4.2
|
16.9
|
1.0
|
|
C1'
|
D:DG21
|
4.2
|
6.0
|
0.3
|
|
O4'
|
B:DC10
|
4.2
|
9.9
|
0.7
|
|
H4'
|
D:DG22
|
4.2
|
0.0
|
0.3
|
|
H1
|
C:HOH54
|
4.3
|
0.0
|
1.0
|
|
O
|
D:HOH33
|
4.3
|
26.8
|
1.0
|
|
H4'
|
B:DC10
|
4.3
|
0.0
|
0.7
|
|
H5''
|
B:DC9
|
4.3
|
0.0
|
0.7
|
|
C1'
|
B:DC9
|
4.4
|
7.3
|
0.7
|
|
H2'
|
D:DG21
|
4.4
|
0.0
|
0.3
|
|
O4'
|
B:DC9
|
4.5
|
7.5
|
0.7
|
|
H3'
|
D:DG22
|
4.6
|
0.0
|
0.3
|
|
C5'
|
B:DC9
|
4.6
|
7.6
|
0.7
|
|
O
|
B:HOH40
|
4.6
|
30.8
|
1.0
|
|
H2'
|
B:DC9
|
4.7
|
0.0
|
0.7
|
|
H1
|
D:HOH57
|
4.7
|
0.0
|
1.0
|
|
C3'
|
D:DG22
|
4.8
|
6.0
|
0.3
|
|
H2
|
B:HOH42
|
4.8
|
0.0
|
1.0
|
|
H5'
|
D:DG21
|
4.8
|
0.0
|
0.3
|
|
H21
|
D:DG22
|
4.9
|
15.0
|
0.3
|
|
N3
|
D:DG22
|
4.9
|
5.7
|
0.3
|
|
O5'
|
D:DG21
|
4.9
|
7.0
|
0.3
|
|
Phosphorus binding site 9 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 9 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P11
b:12.0
occ:0.65
|
P
|
B:5CM11
|
0.0
|
12.0
|
0.7
|
|
P
|
D:5CM23
|
0.9
|
6.2
|
0.3
|
|
O3'
|
D:DG22
|
1.3
|
6.0
|
0.3
|
|
OP1
|
B:5CM11
|
1.5
|
12.1
|
0.7
|
|
OP1
|
D:5CM23
|
1.5
|
6.2
|
0.3
|
|
OP2
|
B:5CM11
|
1.5
|
12.1
|
0.7
|
|
O3'
|
B:DC10
|
1.6
|
11.2
|
0.7
|
|
O5'
|
B:5CM11
|
1.6
|
11.9
|
0.7
|
|
O5'
|
D:5CM23
|
1.7
|
6.2
|
0.3
|
|
OP2
|
D:5CM23
|
2.4
|
6.4
|
0.3
|
|
C3'
|
D:DG22
|
2.5
|
6.0
|
0.3
|
|
C3'
|
B:DC10
|
2.7
|
10.4
|
0.7
|
|
C5'
|
B:5CM11
|
2.7
|
11.5
|
0.7
|
|
H5''
|
B:5CM11
|
2.8
|
0.0
|
0.7
|
|
C5'
|
D:5CM23
|
2.8
|
5.8
|
0.3
|
|
H3'
|
B:DC10
|
2.9
|
0.0
|
0.7
|
|
H3'
|
D:DG22
|
3.0
|
0.0
|
0.3
|
|
H5''
|
D:5CM23
|
3.0
|
0.0
|
0.3
|
|
H2''
|
D:DG22
|
3.2
|
0.0
|
0.3
|
|
H5'
|
D:5CM23
|
3.2
|
0.0
|
0.3
|
|
H3'
|
B:5CM11
|
3.2
|
0.0
|
0.7
|
|
C2'
|
D:DG22
|
3.3
|
5.8
|
0.3
|
|
H5'
|
B:5CM11
|
3.4
|
0.0
|
0.7
|
|
H4'
|
D:DG22
|
3.6
|
0.0
|
0.3
|
|
H1
|
B:HOH47
|
3.6
|
0.0
|
1.0
|
|
H5'
|
B:DC10
|
3.6
|
0.0
|
0.7
|
|
C4'
|
D:DG22
|
3.6
|
5.9
|
0.3
|
|
H2'
|
D:DG22
|
3.6
|
0.0
|
0.3
|
|
C4'
|
B:DC10
|
3.7
|
10.0
|
0.7
|
|
H4'
|
B:DC10
|
3.7
|
0.0
|
0.7
|
|
C2'
|
B:DC10
|
3.8
|
10.1
|
0.7
|
|
H2''
|
B:DC10
|
3.8
|
0.0
|
0.7
|
|
C4'
|
B:5CM11
|
3.8
|
11.5
|
0.7
|
|
H5'
|
D:DG22
|
3.8
|
0.0
|
0.3
|
|
H2'
|
B:5CM11
|
3.8
|
0.0
|
0.7
|
|
H2'
|
D:5CM23
|
3.9
|
0.0
|
0.3
|
|
C3'
|
B:5CM11
|
3.9
|
11.5
|
0.7
|
|
H3'
|
D:5CM23
|
4.0
|
0.0
|
0.3
|
|
H2'
|
B:DC10
|
4.1
|
0.0
|
0.7
|
|
H2
|
B:HOH47
|
4.1
|
0.0
|
1.0
|
|
C4'
|
D:5CM23
|
4.1
|
5.7
|
0.3
|
|
C5'
|
B:DC10
|
4.1
|
9.6
|
0.7
|
|
O
|
B:HOH47
|
4.2
|
43.3
|
1.0
|
|
C5'
|
D:DG22
|
4.2
|
6.0
|
0.3
|
|
H6
|
D:5CM23
|
4.3
|
0.0
|
0.3
|
|
H6
|
B:5CM11
|
4.4
|
0.0
|
0.7
|
|
O4'
|
B:5CM11
|
4.4
|
11.2
|
0.7
|
|
C2'
|
B:5CM11
|
4.5
|
11.2
|
0.7
|
|
C3'
|
D:5CM23
|
4.5
|
5.7
|
0.3
|
|
H5''
|
B:DC10
|
4.5
|
0.0
|
0.7
|
|
H5''
|
D:DG22
|
4.6
|
0.0
|
0.3
|
|
O4'
|
D:5CM23
|
4.6
|
5.6
|
0.3
|
|
H1
|
D:HOH33
|
4.6
|
0.0
|
1.0
|
|
C2'
|
D:5CM23
|
4.7
|
5.4
|
0.3
|
|
C1'
|
D:DG22
|
4.7
|
5.9
|
0.3
|
|
H4'
|
B:5CM11
|
4.7
|
0.0
|
0.7
|
|
O4'
|
D:DG22
|
4.8
|
5.9
|
0.3
|
|
H2
|
D:HOH33
|
4.8
|
0.0
|
1.0
|
|
H4'
|
D:5CM23
|
4.9
|
0.0
|
0.3
|
|
O4'
|
B:DC10
|
5.0
|
9.9
|
0.7
|
|
Phosphorus binding site 10 out
of 20 in 145d
Go back to
Phosphorus Binding Sites List in 145d
Phosphorus binding site 10 out
of 20 in the Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg)
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Structure and Thermodynamics of Nonalternating C/G Base Pairs in Z-Dna: the 1.3 Angstroms Crystal Structure of the Asymmetric Hexanucleotide D(M(5)Cgggm(5) Cg)/D(M(5) Cgccm(5)Cg) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P12
b:12.4
occ:0.65
|
P
|
B:DG12
|
0.0
|
12.4
|
0.7
|
|
OP1
|
D:DG24
|
0.9
|
5.9
|
0.3
|
|
P
|
D:DG24
|
0.9
|
6.1
|
0.3
|
|
OP1
|
B:DG12
|
1.5
|
12.5
|
0.7
|
|
OP2
|
B:DG12
|
1.5
|
12.5
|
0.7
|
|
O5'
|
B:DG12
|
1.6
|
12.2
|
0.7
|
|
O3'
|
B:5CM11
|
1.6
|
11.9
|
0.7
|
|
O3'
|
D:5CM23
|
1.8
|
5.8
|
0.3
|
|
O5'
|
D:DG24
|
1.9
|
6.1
|
0.3
|
|
H3'
|
D:5CM23
|
2.1
|
0.0
|
0.3
|
|
OP2
|
D:DG24
|
2.3
|
6.1
|
0.3
|
|
C3'
|
D:5CM23
|
2.3
|
5.7
|
0.3
|
|
C5'
|
B:DG12
|
2.6
|
11.9
|
0.7
|
|
C3'
|
B:5CM11
|
2.7
|
11.5
|
0.7
|
|
H3'
|
B:5CM11
|
2.9
|
0.0
|
0.7
|
|
H5'
|
B:DG12
|
2.9
|
0.0
|
0.7
|
|
H5''
|
B:DG12
|
2.9
|
0.0
|
0.7
|
|
H1
|
D:HOH68
|
3.0
|
0.0
|
1.0
|
|
H2
|
B:HOH47
|
3.0
|
0.0
|
1.0
|
|
H4'
|
B:5CM11
|
3.2
|
0.0
|
0.7
|
|
C5'
|
D:DG24
|
3.2
|
5.9
|
0.3
|
|
H4'
|
D:5CM23
|
3.3
|
0.0
|
0.3
|
|
C4'
|
D:5CM23
|
3.4
|
5.7
|
0.3
|
|
C4'
|
B:5CM11
|
3.5
|
11.5
|
0.7
|
|
H5''
|
D:DG24
|
3.6
|
0.0
|
0.3
|
|
H5'
|
D:DG24
|
3.6
|
0.0
|
0.3
|
|
H5''
|
D:5CM23
|
3.6
|
0.0
|
0.3
|
|
C2'
|
D:5CM23
|
3.6
|
5.4
|
0.3
|
|
H1
|
D:HOH30
|
3.7
|
0.0
|
1.0
|
|
O
|
D:HOH68
|
3.8
|
40.9
|
1.0
|
|
H2''
|
D:5CM23
|
3.8
|
0.0
|
0.3
|
|
O
|
B:HOH47
|
3.9
|
43.3
|
1.0
|
|
H2
|
D:HOH68
|
3.9
|
0.0
|
1.0
|
|
C4'
|
B:DG12
|
3.9
|
11.8
|
0.7
|
|
H2
|
D:HOH33
|
3.9
|
0.0
|
1.0
|
|
H1
|
D:HOH49
|
3.9
|
0.0
|
1.0
|
|
C2'
|
B:5CM11
|
3.9
|
11.2
|
0.7
|
|
H5''
|
B:5CM11
|
4.0
|
0.0
|
0.7
|
|
H2''
|
B:5CM11
|
4.0
|
0.0
|
0.7
|
|
H4'
|
B:DG12
|
4.1
|
0.0
|
0.7
|
|
C5'
|
D:5CM23
|
4.1
|
5.8
|
0.3
|
|
O
|
D:HOH65
|
4.1
|
45.5
|
1.0
|
|
H2'
|
D:5CM23
|
4.2
|
0.0
|
0.3
|
|
O4'
|
B:DG12
|
4.3
|
11.5
|
0.7
|
|
C4'
|
D:DG24
|
4.3
|
5.7
|
0.3
|
|
H1
|
B:HOH47
|
4.3
|
0.0
|
1.0
|
|
H2
|
D:HOH30
|
4.3
|
0.0
|
1.0
|
|
H4'
|
D:DG24
|
4.4
|
0.0
|
0.3
|
|
C5'
|
B:5CM11
|
4.4
|
11.5
|
0.7
|
|
H1'
|
B:5CM11
|
4.4
|
0.0
|
0.7
|
|
H1'
|
D:5CM23
|
4.5
|
0.0
|
0.3
|
|
H2
|
D:HOH65
|
4.5
|
0.0
|
1.0
|
|
O4'
|
D:DG24
|
4.5
|
5.6
|
0.3
|
|
O4'
|
D:5CM23
|
4.5
|
5.6
|
0.3
|
|
O
|
D:HOH30
|
4.5
|
22.1
|
1.0
|
|
C1'
|
D:5CM23
|
4.5
|
5.4
|
0.3
|
|
OP2
|
D:5CM23
|
4.5
|
6.4
|
0.3
|
|
H1
|
D:HOH65
|
4.5
|
0.0
|
1.0
|
|
O
|
D:HOH49
|
4.5
|
56.4
|
1.0
|
|
C1'
|
B:5CM11
|
4.6
|
11.1
|
0.7
|
|
O4'
|
B:5CM11
|
4.6
|
11.2
|
0.7
|
|
H2'
|
B:5CM11
|
4.7
|
0.0
|
0.7
|
|
O5'
|
D:5CM23
|
4.8
|
6.2
|
0.3
|
|
O
|
D:HOH33
|
4.8
|
26.8
|
1.0
|
|
O
|
C:HOH27
|
4.9
|
30.9
|
1.0
|
|
H1
|
C:HOH27
|
4.9
|
0.0
|
1.0
|
|
H5'
|
D:5CM23
|
5.0
|
0.0
|
0.3
|
|
Reference:
G.P.Schroth,
T.F.Kagawa,
P.S.Ho.
Structure and Thermodynamics of Nonalternating C.G Base Pairs in Z-Dna: the 1.3-A Crystal Structure of the Asymmetric Hexanucleotide D(M5CGGGM5CG).D(M5CGCCM5CG). Biochemistry V. 32 13381 1993.
ISSN: ISSN 0006-2960
PubMed: 8257675
DOI: 10.1021/BI00212A002
Page generated: Fri Sep 25 11:28:16 2020
|
