Phosphorus in PDB 158d: Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Protein crystallography data
The structure of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna, PDB code: 158d
was solved by
K.Grzeskowiak,
D.S.Goodsell,
M.Kaczor-Grzeskowiak,
D.Cascio,
R.E.Dickerson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.90
|
Space group
|
P 6
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.080,
53.080,
34.320,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Phosphorus atom in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
(pdb code 158d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the
Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna, PDB code: 158d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 1 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:13.2
occ:1.00
|
P
|
A:DC2
|
0.0
|
13.2
|
1.0
|
OP2
|
A:DC2
|
1.5
|
17.5
|
1.0
|
OP1
|
A:DC2
|
1.5
|
17.0
|
1.0
|
O5'
|
A:DC2
|
1.6
|
14.4
|
1.0
|
O3'
|
A:DC1
|
1.6
|
16.2
|
1.0
|
C3'
|
A:DC1
|
2.7
|
11.4
|
1.0
|
C5'
|
A:DC2
|
2.7
|
11.0
|
1.0
|
C2'
|
A:DC1
|
3.5
|
11.2
|
1.0
|
O
|
A:HOH69
|
3.8
|
39.0
|
1.0
|
C4'
|
A:DC2
|
3.9
|
6.8
|
1.0
|
C4'
|
A:DC1
|
3.9
|
13.1
|
1.0
|
C3'
|
A:DC2
|
4.2
|
11.9
|
1.0
|
C2'
|
A:DC2
|
4.3
|
10.3
|
1.0
|
O4'
|
A:DC2
|
4.4
|
12.4
|
1.0
|
C1'
|
A:DC1
|
4.4
|
9.6
|
1.0
|
O4'
|
A:DC1
|
4.7
|
14.0
|
1.0
|
C1'
|
A:DC2
|
5.0
|
10.2
|
1.0
|
C5'
|
A:DC1
|
5.0
|
11.0
|
1.0
|
O5'
|
A:DC1
|
5.0
|
14.1
|
1.0
|
|
Phosphorus binding site 2 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 2 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:13.3
occ:1.00
|
P
|
A:DA3
|
0.0
|
13.3
|
1.0
|
OP2
|
A:DA3
|
1.5
|
15.4
|
1.0
|
OP1
|
A:DA3
|
1.5
|
14.9
|
1.0
|
O3'
|
A:DC2
|
1.6
|
10.4
|
1.0
|
O5'
|
A:DA3
|
1.6
|
14.1
|
1.0
|
C3'
|
A:DC2
|
2.6
|
11.9
|
1.0
|
C5'
|
A:DA3
|
2.7
|
8.7
|
1.0
|
C4'
|
A:DC2
|
3.6
|
6.8
|
1.0
|
C8
|
A:DA3
|
3.7
|
8.2
|
1.0
|
C2'
|
A:DC2
|
3.8
|
10.3
|
1.0
|
C4'
|
A:DA3
|
3.8
|
10.4
|
1.0
|
O4'
|
A:DA3
|
4.1
|
11.9
|
1.0
|
O
|
A:HOH69
|
4.2
|
39.0
|
1.0
|
N9
|
A:DA3
|
4.4
|
9.8
|
1.0
|
C1'
|
A:DC2
|
4.4
|
10.2
|
1.0
|
N7
|
A:DA3
|
4.4
|
6.2
|
1.0
|
C3'
|
A:DA3
|
4.4
|
7.2
|
1.0
|
C2'
|
A:DA3
|
4.5
|
8.7
|
1.0
|
O4'
|
A:DC2
|
4.5
|
12.4
|
1.0
|
C5'
|
A:DC2
|
4.6
|
11.0
|
1.0
|
C1'
|
A:DA3
|
4.6
|
9.3
|
1.0
|
O
|
A:HOH40
|
4.7
|
13.6
|
1.0
|
O
|
A:HOH91
|
4.7
|
37.6
|
1.0
|
O5'
|
A:DC2
|
5.0
|
14.4
|
1.0
|
|
Phosphorus binding site 3 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 3 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:13.6
occ:1.00
|
P
|
A:DA4
|
0.0
|
13.6
|
1.0
|
OP2
|
A:DA4
|
1.5
|
14.5
|
1.0
|
OP1
|
A:DA4
|
1.5
|
15.3
|
1.0
|
O3'
|
A:DA3
|
1.6
|
12.0
|
1.0
|
O5'
|
A:DA4
|
1.6
|
7.0
|
1.0
|
C5'
|
A:DA4
|
2.6
|
9.4
|
1.0
|
C3'
|
A:DA3
|
2.6
|
7.2
|
1.0
|
C2'
|
A:DA3
|
3.3
|
8.7
|
1.0
|
O
|
A:HOH32
|
3.7
|
9.4
|
1.0
|
C4'
|
A:DA4
|
3.9
|
8.5
|
1.0
|
C4'
|
A:DA3
|
3.9
|
10.4
|
1.0
|
O
|
A:HOH57
|
4.2
|
29.0
|
1.0
|
O4'
|
A:DA4
|
4.2
|
9.6
|
1.0
|
C1'
|
A:DA3
|
4.2
|
9.3
|
1.0
|
C3'
|
A:DA4
|
4.4
|
8.8
|
1.0
|
C2'
|
A:DA4
|
4.6
|
13.5
|
1.0
|
O4'
|
A:DA3
|
4.6
|
11.9
|
1.0
|
|
Phosphorus binding site 4 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 4 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:8.2
occ:1.00
|
P
|
A:DG5
|
0.0
|
8.2
|
1.0
|
OP1
|
A:DG5
|
1.4
|
8.7
|
1.0
|
OP2
|
A:DG5
|
1.5
|
8.7
|
1.0
|
O3'
|
A:DA4
|
1.6
|
12.8
|
1.0
|
O5'
|
A:DG5
|
1.6
|
8.0
|
1.0
|
C5'
|
A:DG5
|
2.6
|
5.0
|
1.0
|
C3'
|
A:DA4
|
2.7
|
8.8
|
1.0
|
O
|
A:HOH35
|
3.5
|
10.9
|
1.0
|
C4'
|
A:DG5
|
3.7
|
7.4
|
1.0
|
C4'
|
A:DA4
|
3.8
|
8.5
|
1.0
|
C2'
|
A:DA4
|
3.8
|
13.5
|
1.0
|
O
|
A:HOH29
|
3.9
|
11.4
|
1.0
|
O4'
|
A:DG5
|
3.9
|
10.0
|
1.0
|
C3'
|
A:DG5
|
4.3
|
8.0
|
1.0
|
C2'
|
A:DG5
|
4.4
|
5.2
|
1.0
|
C1'
|
A:DA4
|
4.5
|
7.9
|
1.0
|
C8
|
A:DG5
|
4.7
|
7.6
|
1.0
|
O4'
|
A:DA4
|
4.7
|
9.6
|
1.0
|
C1'
|
A:DG5
|
4.8
|
7.8
|
1.0
|
C5'
|
A:DA4
|
4.8
|
9.4
|
1.0
|
|
Phosphorus binding site 5 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 5 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:7.8
occ:1.00
|
P
|
A:DC6
|
0.0
|
7.8
|
1.0
|
OP1
|
A:DC6
|
1.5
|
12.6
|
1.0
|
OP2
|
A:DC6
|
1.5
|
9.0
|
1.0
|
O3'
|
A:DG5
|
1.6
|
4.9
|
1.0
|
O5'
|
A:DC6
|
1.6
|
8.2
|
1.0
|
C5'
|
A:DC6
|
2.6
|
8.6
|
1.0
|
C3'
|
A:DG5
|
2.7
|
8.0
|
1.0
|
C2'
|
A:DG5
|
3.3
|
5.2
|
1.0
|
O
|
A:HOH25
|
3.7
|
11.1
|
1.0
|
C4'
|
A:DC6
|
3.9
|
9.8
|
1.0
|
C4'
|
A:DG5
|
3.9
|
7.4
|
1.0
|
C1'
|
A:DG5
|
4.0
|
7.8
|
1.0
|
C3'
|
A:DC6
|
4.3
|
8.8
|
1.0
|
O4'
|
A:DC6
|
4.5
|
10.5
|
1.0
|
O4'
|
A:DG5
|
4.6
|
10.0
|
1.0
|
C2'
|
A:DC6
|
4.6
|
11.6
|
1.0
|
C6
|
A:DC6
|
4.9
|
5.9
|
1.0
|
|
Phosphorus binding site 6 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 6 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:12.5
occ:1.00
|
P
|
A:DT7
|
0.0
|
12.5
|
1.0
|
OP1
|
A:DT7
|
1.5
|
17.5
|
1.0
|
OP2
|
A:DT7
|
1.5
|
10.4
|
1.0
|
O3'
|
A:DC6
|
1.6
|
13.2
|
1.0
|
O5'
|
A:DT7
|
1.6
|
15.2
|
1.0
|
C3'
|
A:DC6
|
2.7
|
8.8
|
1.0
|
C5'
|
A:DT7
|
2.8
|
12.2
|
1.0
|
C2'
|
A:DC6
|
3.3
|
11.6
|
1.0
|
O
|
A:HOH81
|
3.8
|
31.7
|
1.0
|
C4'
|
A:DC6
|
3.9
|
9.8
|
1.0
|
C4'
|
A:DT7
|
4.0
|
11.1
|
1.0
|
C1'
|
A:DC6
|
4.1
|
8.5
|
1.0
|
C3'
|
A:DT7
|
4.4
|
11.2
|
1.0
|
O4'
|
A:DT7
|
4.5
|
11.8
|
1.0
|
O4'
|
A:DC6
|
4.6
|
10.5
|
1.0
|
C2'
|
A:DT7
|
4.9
|
10.1
|
1.0
|
|
Phosphorus binding site 7 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 7 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:17.2
occ:1.00
|
P
|
A:DT8
|
0.0
|
17.2
|
1.0
|
OP2
|
A:DT8
|
1.5
|
15.6
|
1.0
|
OP1
|
A:DT8
|
1.5
|
16.7
|
1.0
|
O5'
|
A:DT8
|
1.6
|
17.0
|
1.0
|
O3'
|
A:DT7
|
1.6
|
15.0
|
1.0
|
C5'
|
A:DT8
|
2.6
|
10.7
|
1.0
|
C3'
|
A:DT7
|
2.7
|
11.2
|
1.0
|
C2'
|
A:DT7
|
3.4
|
10.1
|
1.0
|
C4'
|
A:DT8
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DT7
|
3.9
|
11.1
|
1.0
|
C3'
|
A:DT8
|
4.2
|
12.1
|
1.0
|
O4'
|
A:DT8
|
4.2
|
10.6
|
1.0
|
C1'
|
A:DT7
|
4.3
|
8.2
|
1.0
|
C2'
|
A:DT8
|
4.5
|
12.8
|
1.0
|
O4'
|
A:DT7
|
4.8
|
11.8
|
1.0
|
C5'
|
A:DT7
|
4.9
|
12.2
|
1.0
|
|
Phosphorus binding site 8 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 8 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P9
b:12.7
occ:1.00
|
P
|
A:DG9
|
0.0
|
12.7
|
1.0
|
OP1
|
A:DG9
|
1.5
|
15.4
|
1.0
|
OP2
|
A:DG9
|
1.5
|
17.0
|
1.0
|
O3'
|
A:DT8
|
1.6
|
12.2
|
1.0
|
O5'
|
A:DG9
|
1.6
|
10.2
|
1.0
|
C5'
|
A:DG9
|
2.5
|
9.3
|
1.0
|
C3'
|
A:DT8
|
2.7
|
12.1
|
1.0
|
C4'
|
A:DT8
|
3.6
|
10.0
|
1.0
|
O
|
A:HOH52
|
3.7
|
9.0
|
1.0
|
C4'
|
A:DG9
|
3.8
|
10.2
|
1.0
|
C2'
|
A:DT8
|
3.9
|
12.8
|
1.0
|
O4'
|
A:DG9
|
4.1
|
12.6
|
1.0
|
C8
|
A:DG9
|
4.2
|
8.0
|
1.0
|
C3'
|
A:DG9
|
4.3
|
12.3
|
1.0
|
C2'
|
A:DG9
|
4.4
|
10.6
|
1.0
|
C1'
|
A:DT8
|
4.6
|
10.3
|
1.0
|
C5'
|
A:DT8
|
4.6
|
10.7
|
1.0
|
O4'
|
A:DT8
|
4.7
|
10.6
|
1.0
|
N9
|
A:DG9
|
4.7
|
7.6
|
1.0
|
C1'
|
A:DG9
|
4.7
|
8.2
|
1.0
|
N7
|
A:DG9
|
4.9
|
8.9
|
1.0
|
|
Phosphorus binding site 9 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 9 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P10
b:16.1
occ:1.00
|
P
|
A:DG10
|
0.0
|
16.1
|
1.0
|
OP1
|
A:DG10
|
1.5
|
23.5
|
1.0
|
OP2
|
A:DG10
|
1.5
|
17.2
|
1.0
|
O5'
|
A:DG10
|
1.6
|
16.8
|
1.0
|
O3'
|
A:DG9
|
1.6
|
12.8
|
1.0
|
C5'
|
A:DG10
|
2.6
|
12.1
|
1.0
|
C3'
|
A:DG9
|
2.7
|
12.3
|
1.0
|
C2'
|
A:DG9
|
3.3
|
10.6
|
1.0
|
C4'
|
A:DG10
|
3.9
|
12.8
|
1.0
|
O
|
A:HOH76
|
3.9
|
34.1
|
0.5
|
C4'
|
A:DG9
|
4.0
|
10.2
|
1.0
|
C1'
|
A:DG9
|
4.1
|
8.2
|
1.0
|
C3'
|
A:DG10
|
4.3
|
10.2
|
1.0
|
O4'
|
A:DG10
|
4.3
|
17.4
|
1.0
|
O
|
A:HOH75
|
4.5
|
38.6
|
1.0
|
O4'
|
A:DG9
|
4.5
|
12.6
|
1.0
|
C2'
|
A:DG10
|
4.6
|
15.1
|
1.0
|
|
Phosphorus binding site 10 out
of 18 in 158d
Go back to
Phosphorus Binding Sites List in 158d
Phosphorus binding site 10 out
of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P12
b:15.1
occ:1.00
|
P
|
B:DC12
|
0.0
|
15.1
|
1.0
|
OP2
|
B:DC12
|
1.5
|
10.4
|
1.0
|
OP1
|
B:DC12
|
1.5
|
17.6
|
1.0
|
O3'
|
B:DC11
|
1.6
|
13.8
|
1.0
|
O5'
|
B:DC12
|
1.6
|
13.4
|
1.0
|
C3'
|
B:DC11
|
2.6
|
17.6
|
1.0
|
C5'
|
B:DC12
|
2.7
|
14.3
|
1.0
|
C2'
|
B:DC11
|
3.4
|
13.1
|
1.0
|
O
|
B:HOH62
|
3.8
|
18.9
|
1.0
|
C4'
|
B:DC11
|
3.9
|
19.2
|
1.0
|
C4'
|
B:DC12
|
3.9
|
11.5
|
1.0
|
C3'
|
B:DC12
|
4.3
|
8.6
|
1.0
|
C1'
|
B:DC11
|
4.4
|
13.7
|
1.0
|
O4'
|
B:DC12
|
4.5
|
10.8
|
1.0
|
C2'
|
B:DC12
|
4.5
|
10.3
|
1.0
|
O4'
|
B:DC11
|
4.7
|
17.2
|
1.0
|
O5'
|
B:DC11
|
4.7
|
23.1
|
1.0
|
C5'
|
B:DC11
|
4.9
|
21.4
|
1.0
|
|
Reference:
K.Grzeskowiak,
D.S.Goodsell,
M.Kaczor-Grzeskowiak,
D.Cascio,
R.E.Dickerson.
Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna. Biochemistry V. 32 8923 1993.
ISSN: ISSN 0006-2960
PubMed: 8364037
DOI: 10.1021/BI00085A025
Page generated: Fri Sep 25 11:34:36 2020
|