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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Go back to Phosphorus Binding Sites List in 183d
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

Last articles

Na in 5ZNQ
Na in 5ZO8
Na in 5ZMV
Na in 5ZMW
Na in 5ZCQ
Na in 5ZCP
Na in 5ZCO
Na in 5ZK0
Na in 5ZMI
Na in 5ZC7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy