Phosphorus in PDB 138d: A-Dna Decamer D(Gcgggcccgc)-Hexagonal Crystal Form

Protein crystallography data

The structure of A-Dna Decamer D(Gcgggcccgc)-Hexagonal Crystal Form, PDB code: 138d 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 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 39.110, 39.110, 79.230, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal Crystal Form (pdb code 138d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 9 binding sites of Phosphorus where determined in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal Crystal Form, PDB code: 138d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Phosphorus binding site 1 out of 9 in 138d

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Phosphorus binding site 1 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:33.8
occ:1.00
 P A:DC2 0.0 33.8 1.0
OP2 A:DC2 1.5 36.5 1.0
OP1 A:DC2 1.5 38.0 1.0
O3' A:DG1 1.6 24.4 1.0
O5' A:DC2 1.6 32.8 1.0
C3' A:DG1 2.6 25.0 1.0
C5' A:DC2 2.6 25.0 1.0
O A:HOH26 3.0 67.1 1.0
C2' A:DG1 3.5 21.4 1.0
C4' A:DG1 3.8 26.1 1.0
O A:HOH24 3.9 58.3 1.0
C4' A:DC2 3.9 23.2 1.0
O4' A:DC2 4.0 24.2 1.0
O A:HOH20 4.1 59.2 1.0
C5' A:DG1 4.2 32.2 1.0
C6 A:DC2 4.3 23.8 1.0
O5' A:DG1 4.3 40.8 1.0
O A:HOH23 4.3 96.1 1.0
C3' A:DC2 4.5 23.7 1.0
C1' A:DG1 4.8 22.3 1.0
O4' A:DG1 4.9 27.7 1.0
C5 A:DC2 5.0 21.8 1.0

Phosphorus binding site 2 out of 9 in 138d

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Phosphorus binding site 2 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:34.2
occ:1.00
 P A:DG3 0.0 34.2 1.0
OP1 A:DG3 1.5 38.2 1.0
OP2 A:DG3 1.5 33.1 1.0
O3' A:DC2 1.6 31.1 1.0
O5' A:DG3 1.6 27.8 1.0
C3' A:DC2 2.6 23.7 1.0
C5' A:DG3 2.6 22.9 1.0
C2' A:DC2 3.4 20.8 1.0
C4' A:DG3 3.9 23.4 1.0
C4' A:DC2 3.9 23.2 1.0
O4' A:DG3 4.0 27.4 1.0
C8 A:DG3 4.3 18.6 1.0
C3' A:DG3 4.3 25.1 1.0
C5' A:DC2 4.3 25.0 1.0
O5' A:DC2 4.6 32.8 1.0
C1' A:DC2 4.7 22.6 1.0
O4' A:DC2 4.8 24.2 1.0

Phosphorus binding site 3 out of 9 in 138d

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Phosphorus binding site 3 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:34.6
occ:1.00
 P A:DG4 0.0 34.6 1.0
OP1 A:DG4 1.5 42.8 1.0
OP2 A:DG4 1.5 37.8 1.0
O3' A:DG3 1.6 29.0 1.0
O5' A:DG4 1.6 33.5 1.0
C3' A:DG3 2.6 25.1 1.0
C5' A:DG4 2.6 27.0 1.0
C2' A:DG3 3.3 26.3 1.0
C4' A:DG4 3.8 30.3 1.0
C4' A:DG3 3.8 23.4 1.0
O A:HOH46 4.0 93.8 1.0
O4' A:DG4 4.0 31.8 1.0
C5' A:DG3 4.3 22.9 1.0
C3' A:DG4 4.4 31.2 1.0
C8 A:DG4 4.5 25.8 1.0
O5' A:DG3 4.5 27.8 1.0
O A:HOH40 4.6 0.9 1.0
C1' A:DG3 4.7 25.8 1.0
O4' A:DG3 4.8 27.4 1.0

Phosphorus binding site 4 out of 9 in 138d

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Phosphorus binding site 4 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:37.5
occ:1.00
 P A:DG5 0.0 37.5 1.0
OP2 A:DG5 1.5 38.6 1.0
OP1 A:DG5 1.5 42.0 1.0
O5' A:DG5 1.6 41.4 1.0
O3' A:DG4 1.6 35.4 1.0
C3' A:DG4 2.6 31.2 1.0
C5' A:DG5 2.6 33.2 1.0
C2' A:DG4 3.4 35.3 1.0
C4' A:DG4 3.9 30.3 1.0
C4' A:DG5 3.9 30.7 1.0
O A:HOH14 4.0 43.5 1.0
O A:HOH29 4.1 89.1 1.0
C8 A:DG5 4.1 21.7 1.0
O4' A:DG5 4.2 31.2 1.0
O A:HOH47 4.3 0.6 1.0
C3' A:DG5 4.4 28.8 1.0
C5' A:DG4 4.4 27.0 1.0
O A:HOH25 4.6 0.4 1.0
O5' A:DG4 4.7 33.5 1.0
C1' A:DG4 4.7 32.4 1.0
O4' A:DG4 4.9 31.8 1.0
N9 A:DG5 5.0 24.2 1.0

Phosphorus binding site 5 out of 9 in 138d

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Phosphorus binding site 5 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:26.7
occ:1.00
 P A:DC6 0.0 26.7 1.0
OP2 A:DC6 1.5 27.7 1.0
OP1 A:DC6 1.5 32.2 1.0
O3' A:DG5 1.6 24.9 1.0
O5' A:DC6 1.6 26.4 1.0
C3' A:DG5 2.6 28.8 1.0
C5' A:DC6 2.6 20.8 1.0
C2' A:DG5 3.4 27.4 1.0
O A:HOH14 3.7 43.5 1.0
O A:HOH36 3.8 65.7 1.0
C4' A:DC6 3.9 18.1 1.0
C4' A:DG5 3.9 30.7 1.0
O4' A:DC6 4.1 20.6 1.0
C6 A:DC6 4.1 18.9 1.0
O A:HOH30 4.3 66.5 1.0
O A:HOH44 4.4 0.2 1.0
C3' A:DC6 4.4 18.4 1.0
C5' A:DG5 4.4 33.2 1.0
O A:HOH17 4.5 63.9 1.0
O A:HOH42 4.5 0.9 1.0
O A:HOH29 4.6 89.1 1.0
O5' A:DG5 4.7 41.4 1.0
C1' A:DG5 4.7 27.8 1.0
C5 A:DC6 4.7 17.3 1.0
OP2 A:DC7 4.9 31.9 1.0
O4' A:DG5 4.9 31.2 1.0
O3' A:DC6 5.0 20.9 1.0

Phosphorus binding site 6 out of 9 in 138d

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Phosphorus binding site 6 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:30.2
occ:1.00
 P A:DC7 0.0 30.2 1.0
OP1 A:DC7 1.5 30.0 1.0
OP2 A:DC7 1.5 31.9 1.0
O3' A:DC6 1.6 20.9 1.0
O5' A:DC7 1.6 28.0 1.0
C3' A:DC6 2.6 18.4 1.0
C5' A:DC7 2.6 29.9 1.0
C2' A:DC6 3.5 15.3 1.0
C4' A:DC6 3.8 18.1 1.0
O A:HOH19 3.9 62.5 1.0
C4' A:DC7 3.9 24.6 1.0
O4' A:DC7 4.2 21.1 1.0
O A:HOH36 4.3 65.7 1.0
C5' A:DC6 4.3 20.8 1.0
O A:HOH30 4.3 66.5 1.0
C6 A:DC7 4.4 16.2 1.0
O5' A:DC6 4.5 26.4 1.0
C3' A:DC7 4.5 25.6 1.0
C1' A:DC6 4.7 19.9 1.0
O4' A:DC6 4.9 20.6 1.0

Phosphorus binding site 7 out of 9 in 138d

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Phosphorus binding site 7 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:31.6
occ:1.00
 P A:DC8 0.0 31.6 1.0
OP1 A:DC8 1.5 32.6 1.0
OP2 A:DC8 1.5 32.2 1.0
O5' A:DC8 1.6 22.9 1.0
O3' A:DC7 1.6 30.0 1.0
C5' A:DC8 2.6 20.9 1.0
C3' A:DC7 2.6 25.6 1.0
C2' A:DC7 3.5 23.0 1.0
C4' A:DC8 3.8 21.4 1.0
C4' A:DC7 3.9 24.6 1.0
O4' A:DC8 4.0 22.8 1.0
C5' A:DC7 4.2 29.9 1.0
O A:HOH35 4.4 88.6 1.0
O A:HOH19 4.4 62.5 1.0
O A:HOH38 4.5 87.2 1.0
O5' A:DC7 4.5 28.0 1.0
O A:HOH45 4.6 81.1 1.0
C1' A:DC7 4.8 20.4 1.0
O4' A:DC7 5.0 21.1 1.0

Phosphorus binding site 8 out of 9 in 138d

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Phosphorus binding site 8 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:28.7
occ:1.00
 P A:DG9 0.0 28.7 1.0
OP1 A:DG9 1.5 34.6 1.0
OP2 A:DG9 1.5 31.7 1.0
O3' A:DC8 1.6 27.7 1.0
O5' A:DG9 1.6 26.7 1.0
C3' A:DC8 2.6 25.0 1.0
C5' A:DG9 2.6 27.9 1.0
O A:HOH37 3.1 0.2 1.0
C2' A:DC8 3.5 20.5 1.0
C4' A:DC8 3.8 21.4 1.0
C4' A:DG9 3.9 30.7 1.0
O A:HOH34 4.1 85.4 1.0
C5' A:DC8 4.2 20.9 1.0
O A:HOH16 4.3 67.8 1.0
O4' A:DG9 4.3 30.4 1.0
C3' A:DG9 4.5 29.9 1.0
C8 A:DG9 4.6 15.0 1.0
C1' A:DC8 4.8 20.1 1.0
O4' A:DC8 4.9 22.8 1.0

Phosphorus binding site 9 out of 9 in 138d

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Phosphorus binding site 9 out of 9 in the A-Dna Decamer D(Gcgggcccgc)-Hexagonal 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)-Hexagonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:36.6
occ:1.00
 P A:DC10 0.0 36.6 1.0
OP1 A:DC10 1.5 40.1 1.0
OP2 A:DC10 1.5 39.6 1.0
O3' A:DG9 1.6 33.1 1.0
O5' A:DC10 1.6 31.3 1.0
C3' A:DG9 2.6 29.9 1.0
C5' A:DC10 2.6 25.1 1.0
C2' A:DG9 3.5 28.4 1.0
C4' A:DG9 3.8 30.7 1.0
C4' A:DC10 3.9 25.3 1.0
O4' A:DC10 4.1 27.0 1.0
O A:HOH16 4.1 67.8 1.0
C3' A:DC10 4.3 24.4 1.0
C5' A:DG9 4.3 27.9 1.0
C6 A:DC10 4.3 22.1 1.0
O5' A:DG9 4.7 26.7 1.0
C1' A:DG9 4.8 27.1 1.0
O4' A:DG9 4.9 30.4 1.0
O3' A:DC10 4.9 30.7 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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