Phosphorus in PDB 137d: A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Protein crystallography data
The structure of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form, PDB code: 137d
was solved by
B.Ramakrishnan,
M.Sundaralingam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
24.900,
44.840,
47.970,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Phosphorus atom in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
(pdb code 137d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the
A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form, PDB code: 137d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 1 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:37.4
occ:1.00
|
P
|
A:DC2
|
0.0
|
37.4
|
1.0
|
OP2
|
A:DC2
|
1.5
|
37.6
|
1.0
|
OP1
|
A:DC2
|
1.5
|
37.8
|
1.0
|
O3'
|
A:DG1
|
1.6
|
37.7
|
1.0
|
O5'
|
A:DC2
|
1.6
|
34.1
|
1.0
|
C5'
|
A:DC2
|
2.6
|
29.3
|
1.0
|
C3'
|
A:DG1
|
2.6
|
38.1
|
1.0
|
C2'
|
A:DG1
|
3.6
|
36.5
|
1.0
|
C4'
|
A:DG1
|
3.8
|
38.8
|
1.0
|
C4'
|
A:DC2
|
3.9
|
28.6
|
1.0
|
O
|
A:HOH98
|
4.1
|
62.1
|
1.0
|
O4'
|
A:DC2
|
4.1
|
28.6
|
1.0
|
C5'
|
A:DG1
|
4.2
|
38.3
|
1.0
|
O
|
A:HOH97
|
4.2
|
83.6
|
1.0
|
O
|
A:HOH79
|
4.3
|
60.7
|
1.0
|
C6
|
A:DC2
|
4.4
|
21.9
|
1.0
|
C3'
|
A:DC2
|
4.5
|
27.1
|
1.0
|
O5'
|
A:DG1
|
4.7
|
39.2
|
1.0
|
C1'
|
A:DG1
|
4.8
|
36.1
|
1.0
|
O4'
|
A:DG1
|
4.9
|
38.6
|
1.0
|
|
Phosphorus binding site 2 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 2 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:33.7
occ:1.00
|
P
|
A:DG3
|
0.0
|
33.7
|
1.0
|
OP2
|
A:DG3
|
1.5
|
33.2
|
1.0
|
OP1
|
A:DG3
|
1.5
|
36.3
|
1.0
|
O3'
|
A:DC2
|
1.6
|
30.1
|
1.0
|
O5'
|
A:DG3
|
1.6
|
30.4
|
1.0
|
C5'
|
A:DG3
|
2.6
|
25.1
|
1.0
|
C3'
|
A:DC2
|
2.6
|
27.1
|
1.0
|
C2'
|
A:DC2
|
3.3
|
22.0
|
1.0
|
C4'
|
A:DG3
|
3.8
|
26.2
|
1.0
|
C4'
|
A:DC2
|
3.9
|
28.6
|
1.0
|
O4'
|
A:DG3
|
4.0
|
24.6
|
1.0
|
O
|
A:HOH116
|
4.1
|
98.9
|
1.0
|
O
|
A:HOH79
|
4.4
|
60.7
|
1.0
|
C5'
|
A:DC2
|
4.5
|
29.3
|
1.0
|
C1'
|
A:DC2
|
4.7
|
25.5
|
1.0
|
C3'
|
A:DG3
|
4.8
|
27.4
|
1.0
|
O5'
|
A:DC2
|
4.8
|
34.1
|
1.0
|
O
|
A:HOH117
|
4.9
|
90.1
|
1.0
|
C8
|
A:DG3
|
4.9
|
17.9
|
1.0
|
O4'
|
A:DC2
|
4.9
|
28.6
|
1.0
|
|
Phosphorus binding site 3 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 3 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:29.0
occ:1.00
|
P
|
A:DG4
|
0.0
|
29.0
|
1.0
|
OP1
|
A:DG4
|
1.5
|
31.4
|
1.0
|
OP2
|
A:DG4
|
1.5
|
31.6
|
1.0
|
O3'
|
A:DG3
|
1.6
|
26.6
|
1.0
|
O5'
|
A:DG4
|
1.6
|
26.9
|
1.0
|
C3'
|
A:DG3
|
2.6
|
27.4
|
1.0
|
C5'
|
A:DG4
|
2.6
|
24.7
|
1.0
|
C2'
|
A:DG3
|
3.4
|
23.8
|
1.0
|
O
|
A:HOH113
|
3.5
|
95.1
|
1.0
|
O
|
A:HOH92
|
3.7
|
54.9
|
1.0
|
O
|
A:HOH118
|
3.7
|
84.5
|
1.0
|
O
|
A:HOH116
|
3.9
|
98.9
|
1.0
|
C4'
|
A:DG3
|
3.9
|
26.2
|
1.0
|
C4'
|
A:DG4
|
3.9
|
26.9
|
1.0
|
C3'
|
A:DG4
|
4.3
|
28.0
|
1.0
|
C8
|
A:DG4
|
4.4
|
15.9
|
1.0
|
O4'
|
A:DG4
|
4.4
|
25.0
|
1.0
|
C5'
|
A:DG3
|
4.5
|
25.1
|
1.0
|
O
|
A:HOH103
|
4.5
|
59.3
|
1.0
|
O
|
A:HOH57
|
4.5
|
81.3
|
1.0
|
O
|
A:HOH66
|
4.5
|
79.7
|
1.0
|
OP2
|
A:DG5
|
4.6
|
21.3
|
1.0
|
O
|
A:HOH40
|
4.7
|
78.0
|
1.0
|
C1'
|
A:DG3
|
4.8
|
24.0
|
1.0
|
O3'
|
A:DG4
|
4.8
|
29.4
|
1.0
|
O4'
|
A:DG3
|
4.9
|
24.6
|
1.0
|
|
Phosphorus binding site 4 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 4 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:25.5
occ:1.00
|
P
|
A:DG5
|
0.0
|
25.5
|
1.0
|
OP1
|
A:DG5
|
1.5
|
30.6
|
1.0
|
OP2
|
A:DG5
|
1.5
|
21.3
|
1.0
|
O5'
|
A:DG5
|
1.6
|
24.0
|
1.0
|
O3'
|
A:DG4
|
1.6
|
29.4
|
1.0
|
C3'
|
A:DG4
|
2.7
|
28.0
|
1.0
|
C5'
|
A:DG5
|
2.7
|
24.8
|
1.0
|
C2'
|
A:DG4
|
3.6
|
26.8
|
1.0
|
O
|
A:HOH45
|
3.7
|
46.0
|
1.0
|
C4'
|
A:DG5
|
3.9
|
22.6
|
1.0
|
O
|
A:HOH38
|
3.9
|
59.2
|
1.0
|
C4'
|
A:DG4
|
4.0
|
26.9
|
1.0
|
O
|
A:HOH92
|
4.1
|
54.9
|
1.0
|
O4'
|
A:DG5
|
4.1
|
23.2
|
1.0
|
O
|
A:HOH58
|
4.3
|
77.7
|
1.0
|
C5'
|
A:DG4
|
4.4
|
24.7
|
1.0
|
O5'
|
A:DG4
|
4.6
|
26.9
|
1.0
|
O
|
A:HOH40
|
4.8
|
78.0
|
1.0
|
C1'
|
A:DG4
|
4.9
|
23.1
|
1.0
|
|
Phosphorus binding site 5 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 5 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:30.6
occ:1.00
|
P
|
A:DC6
|
0.0
|
30.6
|
1.0
|
OP1
|
A:DC6
|
1.5
|
37.1
|
1.0
|
OP2
|
A:DC6
|
1.5
|
32.7
|
1.0
|
O5'
|
A:DC6
|
1.6
|
31.0
|
1.0
|
O3'
|
A:DG5
|
1.6
|
30.9
|
1.0
|
C3'
|
A:DG5
|
2.6
|
25.1
|
1.0
|
C5'
|
A:DC6
|
2.6
|
32.7
|
1.0
|
O
|
A:HOH61
|
3.6
|
45.6
|
1.0
|
C2'
|
A:DG5
|
3.6
|
22.4
|
1.0
|
O
|
A:HOH65
|
3.7
|
74.5
|
1.0
|
C4'
|
A:DG5
|
3.7
|
22.6
|
1.0
|
C4'
|
A:DC6
|
3.9
|
32.2
|
1.0
|
C5'
|
A:DG5
|
3.9
|
24.8
|
1.0
|
O
|
A:HOH109
|
4.1
|
94.9
|
1.0
|
O4'
|
A:DC6
|
4.2
|
31.1
|
1.0
|
C6
|
A:DC6
|
4.2
|
18.2
|
1.0
|
C3'
|
A:DC6
|
4.4
|
32.6
|
1.0
|
OP2
|
A:DC7
|
4.7
|
37.2
|
1.0
|
O
|
A:HOH47
|
4.7
|
70.5
|
1.0
|
C1'
|
A:DG5
|
4.8
|
18.8
|
1.0
|
O4'
|
A:DG5
|
4.8
|
23.2
|
1.0
|
C5
|
A:DC6
|
4.9
|
18.1
|
1.0
|
O
|
A:HOH38
|
5.0
|
59.2
|
1.0
|
|
Phosphorus binding site 6 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 6 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:38.2
occ:1.00
|
P
|
A:DC7
|
0.0
|
38.2
|
1.0
|
OP1
|
A:DC7
|
1.5
|
37.7
|
1.0
|
OP2
|
A:DC7
|
1.5
|
37.2
|
1.0
|
O3'
|
A:DC6
|
1.6
|
31.3
|
1.0
|
O5'
|
A:DC7
|
1.6
|
33.8
|
1.0
|
C3'
|
A:DC6
|
2.5
|
32.6
|
1.0
|
C5'
|
A:DC7
|
2.6
|
28.5
|
1.0
|
C2'
|
A:DC6
|
3.5
|
27.8
|
1.0
|
C4'
|
A:DC6
|
3.8
|
32.2
|
1.0
|
C4'
|
A:DC7
|
3.8
|
26.1
|
1.0
|
O4'
|
A:DC7
|
4.0
|
24.0
|
1.0
|
C5'
|
A:DC6
|
4.1
|
32.7
|
1.0
|
O5'
|
A:DC6
|
4.3
|
31.0
|
1.0
|
O
|
A:HOH47
|
4.4
|
70.5
|
1.0
|
C3'
|
A:DC7
|
4.5
|
26.3
|
1.0
|
O
|
A:HOH53
|
4.5
|
93.3
|
1.0
|
C1'
|
A:DC6
|
4.7
|
27.1
|
1.0
|
C6
|
A:DC7
|
4.8
|
18.9
|
1.0
|
O4'
|
A:DC6
|
4.9
|
31.1
|
1.0
|
|
Phosphorus binding site 7 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 7 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:27.8
occ:1.00
|
P
|
A:DC8
|
0.0
|
27.8
|
1.0
|
OP2
|
A:DC8
|
1.5
|
27.8
|
1.0
|
OP1
|
A:DC8
|
1.5
|
29.3
|
1.0
|
O3'
|
A:DC7
|
1.6
|
27.2
|
1.0
|
O5'
|
A:DC8
|
1.6
|
21.2
|
1.0
|
C3'
|
A:DC7
|
2.5
|
26.3
|
1.0
|
C5'
|
A:DC8
|
2.6
|
17.9
|
1.0
|
C2'
|
A:DC7
|
3.3
|
24.3
|
1.0
|
O
|
A:HOH55
|
3.6
|
67.1
|
1.0
|
C4'
|
A:DC7
|
3.8
|
26.1
|
1.0
|
C4'
|
A:DC8
|
3.9
|
16.0
|
1.0
|
O4'
|
A:DC8
|
4.1
|
14.0
|
1.0
|
O
|
A:HOH104
|
4.2
|
64.2
|
1.0
|
O
|
A:HOH42
|
4.3
|
82.6
|
1.0
|
C5'
|
A:DC7
|
4.3
|
28.5
|
1.0
|
O
|
A:HOH24
|
4.4
|
43.1
|
1.0
|
C3'
|
A:DC8
|
4.4
|
15.7
|
1.0
|
C6
|
A:DC8
|
4.5
|
15.0
|
1.0
|
O5'
|
A:DC7
|
4.6
|
33.8
|
1.0
|
C1'
|
A:DC7
|
4.7
|
22.2
|
1.0
|
O
|
A:HOH89
|
4.7
|
64.8
|
1.0
|
O4'
|
A:DC7
|
4.8
|
24.0
|
1.0
|
|
Phosphorus binding site 8 out
of 18 in 137d
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Phosphorus Binding Sites List in 137d
Phosphorus binding site 8 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P9
b:23.1
occ:1.00
|
P
|
A:DG9
|
0.0
|
23.1
|
1.0
|
OP1
|
A:DG9
|
1.5
|
27.2
|
1.0
|
OP2
|
A:DG9
|
1.5
|
26.1
|
1.0
|
O3'
|
A:DC8
|
1.6
|
17.3
|
1.0
|
O5'
|
A:DG9
|
1.6
|
19.6
|
1.0
|
C5'
|
A:DG9
|
2.6
|
17.7
|
1.0
|
C3'
|
A:DC8
|
2.6
|
15.7
|
1.0
|
C2'
|
A:DC8
|
3.4
|
15.5
|
1.0
|
C4'
|
A:DG9
|
3.9
|
16.0
|
1.0
|
C4'
|
A:DC8
|
3.9
|
16.0
|
1.0
|
O
|
A:HOH89
|
4.0
|
64.8
|
1.0
|
O4'
|
A:DG9
|
4.2
|
16.4
|
1.0
|
O
|
A:HOH50
|
4.3
|
60.5
|
1.0
|
C3'
|
A:DG9
|
4.3
|
17.8
|
1.0
|
O
|
A:HOH91
|
4.4
|
87.5
|
1.0
|
C8
|
A:DG9
|
4.4
|
9.2
|
1.0
|
C5'
|
A:DC8
|
4.4
|
17.9
|
1.0
|
O
|
A:HOH63
|
4.5
|
90.0
|
1.0
|
O
|
A:HOH42
|
4.6
|
82.6
|
1.0
|
O
|
A:HOH108
|
4.6
|
58.8
|
1.0
|
C1'
|
A:DC8
|
4.8
|
12.4
|
1.0
|
O5'
|
A:DC8
|
4.8
|
21.2
|
1.0
|
OP2
|
A:DC10
|
4.9
|
23.8
|
1.0
|
O4'
|
A:DC8
|
5.0
|
14.0
|
1.0
|
O3'
|
A:DG9
|
5.0
|
14.3
|
1.0
|
|
Phosphorus binding site 9 out
of 18 in 137d
Go back to
Phosphorus Binding Sites List in 137d
Phosphorus binding site 9 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P10
b:21.5
occ:1.00
|
P
|
A:DC10
|
0.0
|
21.5
|
1.0
|
OP1
|
A:DC10
|
1.5
|
24.2
|
1.0
|
OP2
|
A:DC10
|
1.5
|
23.8
|
1.0
|
O5'
|
A:DC10
|
1.6
|
19.9
|
1.0
|
O3'
|
A:DG9
|
1.6
|
14.3
|
1.0
|
C3'
|
A:DG9
|
2.6
|
17.8
|
1.0
|
C5'
|
A:DC10
|
2.7
|
18.1
|
1.0
|
C2'
|
A:DG9
|
3.4
|
15.1
|
1.0
|
O
|
A:HOH107
|
3.5
|
83.0
|
1.0
|
O
|
A:HOH120
|
3.6
|
0.0
|
1.0
|
C4'
|
A:DC10
|
3.9
|
18.2
|
1.0
|
C4'
|
A:DG9
|
3.9
|
16.0
|
1.0
|
O
|
A:HOH50
|
4.2
|
60.5
|
1.0
|
O
|
A:HOH72
|
4.2
|
77.6
|
1.0
|
O
|
A:HOH22
|
4.2
|
29.3
|
1.0
|
O4'
|
A:DC10
|
4.3
|
15.8
|
1.0
|
O
|
A:HOH108
|
4.3
|
58.8
|
1.0
|
O
|
A:HOH63
|
4.3
|
90.0
|
1.0
|
C3'
|
A:DC10
|
4.4
|
18.2
|
1.0
|
C5'
|
A:DG9
|
4.5
|
17.7
|
1.0
|
O5'
|
A:DG9
|
4.5
|
19.6
|
1.0
|
C6
|
A:DC10
|
4.6
|
17.3
|
1.0
|
C1'
|
A:DG9
|
4.7
|
17.4
|
1.0
|
O4'
|
A:DG9
|
4.9
|
16.4
|
1.0
|
|
Phosphorus binding site 10 out
of 18 in 137d
Go back to
Phosphorus Binding Sites List in 137d
Phosphorus binding site 10 out
of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P12
b:31.6
occ:1.00
|
P
|
B:DC12
|
0.0
|
31.6
|
1.0
|
OP1
|
B:DC12
|
1.5
|
34.0
|
1.0
|
OP2
|
B:DC12
|
1.5
|
30.0
|
1.0
|
O3'
|
B:DG11
|
1.6
|
31.1
|
1.0
|
O5'
|
B:DC12
|
1.6
|
30.6
|
1.0
|
C3'
|
B:DG11
|
2.6
|
34.4
|
1.0
|
C5'
|
B:DC12
|
2.6
|
27.5
|
1.0
|
O
|
B:HOH80
|
3.4
|
0.8
|
1.0
|
C2'
|
B:DG11
|
3.4
|
33.0
|
1.0
|
O
|
B:HOH36
|
3.8
|
47.6
|
1.0
|
C4'
|
B:DG11
|
3.9
|
36.2
|
1.0
|
C4'
|
B:DC12
|
3.9
|
26.6
|
1.0
|
O4'
|
B:DC12
|
4.2
|
25.6
|
1.0
|
O
|
B:HOH27
|
4.2
|
67.3
|
1.0
|
C6
|
B:DC12
|
4.2
|
19.6
|
1.0
|
C3'
|
B:DC12
|
4.3
|
25.7
|
1.0
|
C5'
|
B:DG11
|
4.4
|
39.2
|
1.0
|
C1'
|
B:DG11
|
4.7
|
33.0
|
1.0
|
OP2
|
B:DG13
|
4.9
|
25.2
|
1.0
|
O5'
|
B:DG11
|
4.9
|
45.2
|
1.0
|
C5
|
B:DC12
|
4.9
|
15.5
|
1.0
|
O4'
|
B:DG11
|
4.9
|
35.9
|
1.0
|
|
Reference:
B.Ramakrishnan,
M.Sundaralingam.
Evidence For Crystal Environment Dominating Base Sequence Effects on Dna Conformation: Crystal Structures of the Orthorhombic and Hexagonal Polymorphs of the A-Dna Decamer D(Gcgggcccgc) and Comparison with Their Isomorphous Crystal Structures. Biochemistry V. 32 11458 1993.
ISSN: ISSN 0006-2960
PubMed: 8218212
DOI: 10.1021/BI00093A025
Page generated: Fri Sep 25 11:22:28 2020
|