Phosphorus in PDB 183d: X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine

Protein crystallography data

The structure of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine, PDB code: 183d was solved by L.A.Lipscomb, M.E.Peek, M.L.Morningstar, S.M.Verghis, E.M.Miller, A.Rich, J.M.Essigmann, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 32.270, 25.560, 34.710, 90.00, 115.77, 90.00
R / Rfree (%) 23.4 / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine (pdb code 183d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 9 binding sites of Phosphorus where determined in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine, PDB code: 183d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Phosphorus binding site 1 out of 9 in 183d

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Phosphorus binding site 1 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:10.4
occ:1.00
 P A:DC2 0.0 10.4 1.0
OP1 A:DC2 1.5 13.2 1.0
OP2 A:DC2 1.5 11.1 1.0
O3' A:DC1 1.6 11.8 1.0
O5' A:DC2 1.6 10.0 1.0
C3' A:DC1 2.6 13.0 1.0
C5' A:DC2 2.7 8.2 1.0
C2' A:DC1 3.4 12.3 1.0
C4' A:DC1 3.9 12.6 1.0
O A:HOH11 3.9 21.6 1.0
O A:HOH49 3.9 31.2 1.0
O A:HOH41 4.0 17.8 1.0
C4' A:DC2 4.0 8.4 1.0
O4' A:DC2 4.4 9.2 1.0
C3' A:DC2 4.4 9.8 1.0
C1' A:DC1 4.5 11.1 1.0
C2' A:DC2 4.6 7.6 1.0
O4' A:DC1 4.8 12.6 1.0
C5' A:DC1 4.9 13.8 1.0

Phosphorus binding site 2 out of 9 in 183d

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Phosphorus binding site 2 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:12.5
occ:1.00
 P A:DA3 0.0 12.5 1.0
OP1 A:DA3 1.4 16.1 1.0
OP2 A:DA3 1.5 14.0 1.0
O3' A:DC2 1.6 10.9 1.0
O5' A:DA3 1.6 12.6 1.0
C3' A:DC2 2.6 9.8 1.0
C5' A:DA3 2.7 10.9 1.0
C4' A:DC2 3.6 8.4 1.0
C2' A:DC2 3.8 7.6 1.0
C8 A:DA3 3.9 5.6 1.0
C4' A:DA3 3.9 9.6 1.0
O4' A:DA3 4.1 8.9 1.0
O A:HOH31 4.2 29.7 1.0
C3' A:DA3 4.4 12.1 1.0
C2' A:DA3 4.4 10.0 1.0
O A:HOH19 4.5 41.3 1.0
N7 A:DA3 4.5 6.5 1.0
C1' A:DC2 4.5 8.1 1.0
N9 A:DA3 4.5 6.0 1.0
C5' A:DC2 4.5 8.2 1.0
C1' A:DA3 4.6 8.7 1.0
O4' A:DC2 4.6 9.2 1.0

Phosphorus binding site 3 out of 9 in 183d

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Phosphorus binding site 3 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:11.0
occ:1.00
 P A:8OG4 0.0 11.0 1.0
OP1 A:8OG4 1.5 14.9 1.0
OP2 A:8OG4 1.5 11.7 1.0
O5' A:8OG4 1.6 15.5 1.0
O3' A:DA3 1.6 13.9 1.0
C5' A:8OG4 2.7 18.1 1.0
C3' A:DA3 2.7 12.1 1.0
C2' A:DA3 3.4 10.0 1.0
C4' A:8OG4 4.0 21.3 1.0
C4' A:DA3 4.0 9.6 1.0
O A:HOH40 4.2 23.6 1.0
C1' A:DA3 4.3 8.7 1.0
C3' A:8OG4 4.3 21.9 1.0
O4' A:8OG4 4.6 20.4 1.0
O4' A:DA3 4.7 8.9 1.0
C2' A:8OG4 4.8 21.2 1.0
C1' A:8OG4 4.9 18.9 1.0

Phosphorus binding site 4 out of 9 in 183d

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Phosphorus binding site 4 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:25.5
occ:1.00
 P A:DC5 0.0 25.5 1.0
OP1 A:DC5 1.5 25.4 1.0
OP2 A:DC5 1.5 26.3 1.0
O3' A:8OG4 1.6 25.6 1.0
O5' A:DC5 1.6 26.1 1.0
C3' A:8OG4 2.6 21.9 1.0
C5' A:DC5 2.8 24.0 1.0
C2' A:8OG4 3.5 21.2 1.0
C4' A:8OG4 3.7 21.3 1.0
C4' A:DC5 3.9 22.4 1.0
O4' A:DC5 4.1 20.3 1.0
C3' A:DC5 4.4 24.0 1.0
C2' A:DC5 4.5 21.1 1.0
C6 A:DC5 4.5 13.5 1.0
C5' A:8OG4 4.6 18.1 1.0
C1' A:8OG4 4.6 18.9 1.0
O4' A:8OG4 4.7 20.4 1.0
C1' A:DC5 4.9 17.8 1.0

Phosphorus binding site 5 out of 9 in 183d

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Phosphorus binding site 5 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:26.1
occ:1.00
 P A:DG6 0.0 26.1 1.0
OP1 A:DG6 1.5 30.8 1.0
OP2 A:DG6 1.5 29.4 1.0
O3' A:DC5 1.6 27.7 1.0
O5' A:DG6 1.6 27.6 1.0
C5' A:DG6 2.7 26.0 1.0
C3' A:DC5 2.7 24.0 1.0
C2' A:DC5 3.4 21.1 1.0
C4' A:DC5 4.0 22.4 1.0
C4' A:DG6 4.1 26.1 1.0
O A:HOH24 4.1 43.9 1.0
C1' A:DC5 4.2 17.8 1.0
C3' A:DG6 4.3 26.3 1.0
C8 A:DG6 4.5 19.2 1.0
C2' A:DG6 4.6 25.3 1.0
O4' A:DG6 4.6 25.7 1.0
O4' A:DC5 4.7 20.3 1.0

Phosphorus binding site 6 out of 9 in 183d

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Phosphorus binding site 6 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:25.7
occ:1.00
 P A:DC7 0.0 25.7 1.0
OP1 A:DC7 1.5 28.3 1.0
OP2 A:DC7 1.5 24.6 1.0
O3' A:DG6 1.6 27.6 1.0
O5' A:DC7 1.6 24.9 1.0
C5' A:DC7 2.7 19.0 1.0
C3' A:DG6 2.7 26.3 1.0
C2' A:DG6 3.3 25.3 1.0
C4' A:DC7 3.9 16.6 1.0
C4' A:DG6 4.1 26.1 1.0
O4' A:DC7 4.1 15.8 1.0
O A:HOH26 4.3 46.3 1.0
C3' A:DC7 4.3 15.9 1.0
C1' A:DG6 4.3 22.9 1.0
O4' A:DG6 4.8 25.7 1.0

Phosphorus binding site 7 out of 9 in 183d

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Phosphorus binding site 7 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:15.9
occ:1.00
 P A:DT8 0.0 15.9 1.0
OP1 A:DT8 1.4 20.4 1.0
OP2 A:DT8 1.5 19.3 1.0
O3' A:DC7 1.6 18.3 1.0
O5' A:DT8 1.6 16.8 1.0
C3' A:DC7 2.7 15.9 1.0
C5' A:DT8 2.7 12.6 1.0
C2' A:DC7 3.3 14.5 1.0
O A:HOH21 3.8 16.9 1.0
C4' A:DC7 3.8 16.6 1.0
C4' A:DT8 4.0 10.5 1.0
C3' A:DT8 4.5 11.0 1.0
C5' A:DC7 4.5 19.0 1.0
O4' A:DT8 4.5 9.7 1.0
C1' A:DC7 4.6 13.2 1.0
C2' A:DT8 4.7 8.7 1.0
O A:HOH38 4.7 34.1 1.0
O4' A:DC7 4.8 15.8 1.0
O5' A:DC7 5.0 24.9 1.0

Phosphorus binding site 8 out of 9 in 183d

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Phosphorus binding site 8 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:10.5
occ:1.00
 P A:DG9 0.0 10.5 1.0
OP2 A:DG9 1.4 12.3 1.0
OP1 A:DG9 1.5 10.2 1.0
O5' A:DG9 1.6 7.7 1.0
O3' A:DT8 1.6 10.3 1.0
C5' A:DG9 2.6 9.3 1.0
C3' A:DT8 2.7 11.0 1.0
C4' A:DT8 3.6 10.5 1.0
C2' A:DT8 3.9 8.7 1.0
C8 A:DG9 3.9 8.4 1.0
C4' A:DG9 3.9 8.5 1.0
O A:HOH37 4.2 30.4 1.0
O4' A:DG9 4.2 9.6 1.0
C3' A:DG9 4.4 10.4 1.0
O A:HOH38 4.4 34.1 1.0
C2' A:DG9 4.5 11.1 1.0
N9 A:DG9 4.5 7.7 1.0
N7 A:DG9 4.5 5.9 1.0
C5' A:DT8 4.5 12.6 1.0
C1' A:DT8 4.6 8.3 1.0
O4' A:DT8 4.6 9.7 1.0
C1' A:DG9 4.7 9.3 1.0

Phosphorus binding site 9 out of 9 in 183d

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Phosphorus binding site 9 out of 9 in the X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of X-Ray Structure of A Dna Decamer Containing 7, 8-Dihydro-8- Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:13.0
occ:1.00
 P A:DG10 0.0 13.0 1.0
OP1 A:DG10 1.5 15.1 1.0
OP2 A:DG10 1.5 13.6 1.0
O3' A:DG9 1.6 12.5 1.0
O5' A:DG10 1.6 12.8 1.0
C5' A:DG10 2.6 11.7 1.0
C3' A:DG9 2.7 10.4 1.0
C2' A:DG9 3.3 11.1 1.0
O A:HOH33 3.7 15.5 1.0
C4' A:DG9 3.9 8.5 1.0
O A:HOH36 3.9 34.0 1.0
C4' A:DG10 4.0 13.2 1.0
C1' A:DG9 4.3 9.3 1.0
O4' A:DG10 4.3 12.2 1.0
C3' A:DG10 4.6 12.7 1.0
O4' A:DG9 4.6 9.6 1.0

Reference:

L.A.Lipscomb, M.E.Peek, M.L.Morningstar, S.M.Verghis, E.M.Miller, A.Rich, J.M.Essigmann, L.D.Williams. X-Ray Structure of A Dna Decamer Containing 7,8-Dihydro-8-Oxoguanine. Proc.Natl.Acad.Sci.Usa V. 92 719 1995.
ISSN: ISSN 0027-8424
PubMed: 7846041
DOI: 10.1073/PNAS.92.3.719
Page generated: Fri Sep 25 11:46:56 2020

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