Phosphorus in PDB 111d: Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Protein crystallography data
The structure of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs, PDB code: 111d
was solved by
T.Brown,
G.A.Leonard,
E.D.Booth,
J.Chambers,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.230,
41.160,
65.010,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
22;
Binding sites:
The binding sites of Phosphorus atom in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
(pdb code 111d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the
Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs, PDB code: 111d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 1 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:10.0
occ:1.00
|
P
|
A:DG2
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DG2
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DG2
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DG2
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DC1
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DG2
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DC1
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DC1
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DG2
|
3.8
|
10.0
|
1.0
|
O
|
A:HOH51
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DC1
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DC1
|
4.0
|
10.0
|
1.0
|
C3'
|
A:DG2
|
4.1
|
10.0
|
1.0
|
C2'
|
A:DG2
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DG2
|
4.4
|
10.0
|
1.0
|
C8
|
A:DG2
|
4.6
|
10.0
|
1.0
|
O4'
|
A:DC1
|
4.6
|
10.0
|
1.0
|
C1'
|
A:DG2
|
4.8
|
10.0
|
1.0
|
|
Phosphorus binding site 2 out
of 22 in 111d
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Phosphorus Binding Sites List in 111d
Phosphorus binding site 2 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:10.0
occ:1.00
|
P
|
A:DC3
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DC3
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DC3
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DC3
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DG2
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DC3
|
2.7
|
10.0
|
1.0
|
C3'
|
A:DG2
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DG2
|
3.3
|
10.0
|
1.0
|
O
|
A:HOH28
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DC3
|
3.9
|
10.0
|
1.0
|
O4'
|
A:DC3
|
4.0
|
10.0
|
1.0
|
C4'
|
A:DG2
|
4.0
|
10.0
|
1.0
|
C1'
|
A:DG2
|
4.2
|
10.0
|
1.0
|
C3'
|
A:DC3
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DG2
|
4.7
|
10.0
|
1.0
|
C6
|
A:DC3
|
4.8
|
10.0
|
1.0
|
|
Phosphorus binding site 3 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 3 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:10.0
occ:1.00
|
P
|
A:DA4
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DA4
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DA4
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DC3
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DA4
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DA4
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DC3
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DC3
|
3.2
|
10.0
|
1.0
|
C4'
|
A:DA4
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DC3
|
4.0
|
10.0
|
1.0
|
C8
|
A:DA4
|
4.2
|
10.0
|
1.0
|
O
|
A:HOH44
|
4.2
|
10.0
|
1.0
|
C2'
|
A:DA4
|
4.2
|
10.0
|
1.0
|
O4'
|
A:DA4
|
4.3
|
10.0
|
1.0
|
C3'
|
A:DA4
|
4.4
|
10.0
|
1.0
|
C1'
|
A:DC3
|
4.6
|
10.0
|
1.0
|
C5'
|
A:DC3
|
4.7
|
10.0
|
1.0
|
C1'
|
A:DA4
|
4.7
|
10.0
|
1.0
|
N9
|
A:DA4
|
4.8
|
10.0
|
1.0
|
O4'
|
A:DC3
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 4 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 4 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:10.0
occ:1.00
|
P
|
A:DA5
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DA5
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DA5
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DA5
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DA4
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DA5
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DA4
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DA4
|
3.7
|
10.0
|
1.0
|
C4'
|
A:DA5
|
3.7
|
10.0
|
1.0
|
C4'
|
A:DA4
|
3.8
|
10.0
|
1.0
|
O4'
|
A:DA5
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DA4
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DA4
|
4.5
|
10.0
|
1.0
|
C3'
|
A:DA5
|
4.7
|
10.0
|
1.0
|
C8
|
A:DA5
|
4.9
|
10.0
|
1.0
|
C2'
|
A:DA5
|
4.9
|
10.0
|
1.0
|
C5'
|
A:DA4
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 5 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 5 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:10.0
occ:1.00
|
P
|
A:DA6
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DA6
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DA6
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DA6
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DA5
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DA5
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DA6
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DA5
|
3.5
|
10.0
|
1.0
|
C4'
|
A:DA6
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DA5
|
3.9
|
10.0
|
1.0
|
O4'
|
A:DA6
|
4.1
|
10.0
|
1.0
|
C1'
|
A:DA5
|
4.1
|
10.0
|
1.0
|
C3'
|
A:DA6
|
4.2
|
10.0
|
1.0
|
C2'
|
A:DA6
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DA5
|
4.6
|
10.0
|
1.0
|
C5'
|
A:DA5
|
4.9
|
10.0
|
1.0
|
C1'
|
A:DA6
|
5.0
|
10.0
|
1.0
|
C8
|
A:DA6
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 6 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 6 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:10.0
occ:1.00
|
P
|
A:DT7
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DT7
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DT7
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DT7
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DA6
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DA6
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DT7
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DA6
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DT7
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DA6
|
3.9
|
10.0
|
1.0
|
O4'
|
A:DT7
|
4.0
|
10.0
|
1.0
|
C1'
|
A:DA6
|
4.2
|
10.0
|
1.0
|
C3'
|
A:DT7
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DA6
|
4.7
|
10.0
|
1.0
|
C5'
|
A:DA6
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 7 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 7 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:10.0
occ:1.00
|
P
|
A:DT8
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DT8
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DT8
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DT7
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DT8
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DT8
|
2.5
|
10.0
|
1.0
|
C3'
|
A:DT7
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DT7
|
3.2
|
10.0
|
1.0
|
C4'
|
A:DT8
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DT7
|
3.9
|
10.0
|
1.0
|
C3'
|
A:DT8
|
4.2
|
10.0
|
1.0
|
O
|
A:HOH67
|
4.3
|
10.0
|
1.0
|
C1'
|
A:DT7
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DT8
|
4.4
|
10.0
|
1.0
|
C5'
|
A:DT7
|
4.7
|
10.0
|
1.0
|
O
|
A:HOH32
|
4.8
|
10.0
|
1.0
|
O4'
|
A:DT7
|
4.8
|
10.0
|
1.0
|
C2'
|
A:DT8
|
4.9
|
10.0
|
1.0
|
C6
|
A:DT8
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 8 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 8 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P9
b:10.0
occ:1.00
|
P
|
A:DG9
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DG9
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DG9
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DT8
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DG9
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DG9
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DT8
|
2.8
|
10.0
|
1.0
|
C2'
|
A:DT8
|
3.5
|
10.0
|
1.0
|
C4'
|
A:DG9
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DT8
|
3.9
|
10.0
|
1.0
|
C3'
|
A:DG9
|
4.2
|
10.0
|
1.0
|
C1'
|
A:DT8
|
4.4
|
10.0
|
1.0
|
O
|
A:HOH32
|
4.7
|
10.0
|
1.0
|
C2'
|
A:DG9
|
4.7
|
10.0
|
1.0
|
O4'
|
A:DT8
|
4.8
|
10.0
|
1.0
|
O4'
|
A:DG9
|
4.8
|
10.0
|
1.0
|
O
|
A:HOH68
|
5.0
|
10.0
|
1.0
|
C5'
|
A:DT8
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 9 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 9 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P10
b:10.0
occ:1.00
|
P
|
A:DG10
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DG10
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DG10
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DG10
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DG9
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DG10
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DG9
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DG9
|
3.6
|
10.0
|
1.0
|
C4'
|
A:DG10
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DG9
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DG9
|
4.1
|
10.0
|
1.0
|
O4'
|
A:DG10
|
4.3
|
10.0
|
1.0
|
C2'
|
A:DG10
|
4.4
|
10.0
|
1.0
|
C3'
|
A:DG10
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DG9
|
4.5
|
10.0
|
1.0
|
O
|
A:HOH81
|
4.6
|
10.0
|
1.0
|
O5'
|
A:DG9
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 10 out
of 22 in 111d
Go back to
Phosphorus Binding Sites List in 111d
Phosphorus binding site 10 out
of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P11
b:10.0
occ:1.00
|
P
|
A:DC11
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DC11
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DC11
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DC11
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DG10
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DC11
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DG10
|
2.6
|
10.0
|
1.0
|
O
|
A:HOH31
|
3.4
|
10.0
|
1.0
|
C4'
|
A:DC11
|
3.6
|
10.0
|
1.0
|
C4'
|
A:DG10
|
3.7
|
10.0
|
1.0
|
O4'
|
A:DC11
|
3.7
|
10.0
|
1.0
|
C2'
|
A:DG10
|
3.8
|
10.0
|
1.0
|
C6
|
A:DC11
|
3.9
|
10.0
|
1.0
|
C3'
|
A:DC11
|
4.2
|
10.0
|
1.0
|
C2'
|
A:DC11
|
4.2
|
10.0
|
1.0
|
C1'
|
A:DG10
|
4.3
|
10.0
|
1.0
|
C1'
|
A:DC11
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DG10
|
4.5
|
10.0
|
1.0
|
O
|
A:HOH79
|
4.6
|
10.0
|
1.0
|
N1
|
A:DC11
|
4.6
|
10.0
|
1.0
|
C5
|
A:DC11
|
4.7
|
10.0
|
1.0
|
C5'
|
A:DG10
|
4.8
|
10.0
|
1.0
|
|
Reference:
T.Brown,
G.A.Leonard,
E.D.Booth,
J.Chambers.
Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs. J.Mol.Biol. V. 207 455 1989.
ISSN: ISSN 0022-2836
PubMed: 2754734
DOI: 10.1016/0022-2836(89)90268-4
Page generated: Fri Sep 25 11:07:52 2020
|