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 site 1 out of 18 in the A-Dna Decamer D(Gcgggcccgc)-Orthorhombic Crystal Form


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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 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 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 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 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 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 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 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

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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

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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

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