Phosphorus in PDB 1a2e: Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct

Protein crystallography data

The structure of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct, PDB code: 1a2e was solved by F.Coste, C.Zelwer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 42.890, 29.980, 46.570, 90.00, 95.98, 90.00
R / Rfree (%) 16.9 / 20.3

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct (pdb code 1a2e). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct, PDB code: 1a2e:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 1a2e

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Phosphorus binding site 1 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:27.2
occ:1.00
P A:DC2 0.0 27.2 1.0
OP1 A:DC2 1.5 30.2 1.0
OP2 A:DC2 1.5 22.3 1.0
O3' A:DC1 1.6 19.9 1.0
O5' A:DC2 1.6 20.5 1.0
C3' A:DC1 2.6 19.4 1.0
C5' A:DC2 2.6 18.3 1.0
C2' A:DC1 3.4 13.3 1.0
O A:HOH117 3.7 25.3 1.0
C4' A:DC2 3.9 12.3 1.0
O A:HOH131 3.9 27.6 1.0
C4' A:DC1 3.9 20.4 1.0
O4' A:DC2 4.3 15.6 1.0
O A:HOH121 4.4 39.5 1.0
C6 A:DC2 4.5 11.7 1.0
C3' A:DC2 4.5 13.0 1.0
C5' A:DC1 4.5 17.6 1.0
O5' A:DC1 4.6 24.1 1.0
O A:HOH127 4.6 25.4 1.0
C1' A:DC1 4.8 10.7 1.0
O4' A:DC1 4.9 16.1 1.0

Phosphorus binding site 2 out of 18 in 1a2e

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Phosphorus binding site 2 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:26.1
occ:1.00
P A:DT3 0.0 26.1 1.0
OP1 A:DT3 1.5 23.4 1.0
OP2 A:DT3 1.5 28.3 1.0
O3' A:DC2 1.6 19.4 1.0
O5' A:DT3 1.6 26.9 1.0
C3' A:DC2 2.6 13.0 1.0
C5' A:DT3 2.7 17.1 1.0
C2' A:DC2 3.3 15.4 1.0
O A:HOH132 3.4 39.6 1.0
O A:HOH127 3.8 25.4 1.0
C4' A:DT3 3.9 18.8 1.0
C4' A:DC2 4.0 12.3 1.0
C3' A:DT3 4.3 28.3 1.0
O4' A:DT3 4.5 24.6 1.0
C6 A:DT3 4.5 16.1 1.0
OP2 A:DC4 4.6 40.1 1.0
C7 A:DT3 4.6 19.4 1.0
C5' A:DC2 4.6 18.3 1.0
O B:HOH51 4.7 22.7 1.0
C1' A:DC2 4.7 23.0 1.0
O3' A:DT3 4.9 28.5 1.0
O5' A:DC2 5.0 20.5 1.0
O4' A:DC2 5.0 15.6 1.0

Phosphorus binding site 3 out of 18 in 1a2e

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Phosphorus binding site 3 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:28.1
occ:1.00
P A:DC4 0.0 28.1 1.0
OP2 A:DC4 1.5 40.1 1.0
OP1 A:DC4 1.5 27.5 1.0
O3' A:DT3 1.6 28.5 1.0
O5' A:DC4 1.6 20.1 1.0
C3' A:DT3 2.6 28.3 1.0
C5' A:DC4 2.7 18.5 1.0
C2' A:DT3 3.5 19.3 1.0
C4' A:DT3 3.8 18.8 1.0
C4' A:DC4 3.9 13.8 1.0
C6 A:DC4 4.1 17.6 1.0
O4' A:DC4 4.2 20.0 1.0
O A:HOH132 4.2 39.6 1.0
C5' A:DT3 4.3 17.1 1.0
O5' A:DT3 4.3 26.9 1.0
O A:HOH123 4.4 51.3 1.0
C3' A:DC4 4.4 18.4 1.0
C2' A:DC4 4.5 13.0 1.0
C1' A:DC4 4.8 19.6 1.0
C5 A:DC4 4.8 20.1 1.0
C1' A:DT3 4.8 28.3 1.0
N1 A:DC4 4.8 13.1 1.0
O4' A:DT3 4.9 24.6 1.0

Phosphorus binding site 4 out of 18 in 1a2e

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Phosphorus binding site 4 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:17.3
occ:1.00
P A:DG5 0.0 17.3 1.0
OP2 A:DG5 1.5 21.1 1.0
OP1 A:DG5 1.5 18.7 1.0
O3' A:DC4 1.6 13.4 1.0
O5' A:DG5 1.6 15.9 1.0
C3' A:DC4 2.6 18.4 1.0
C5' A:DG5 2.6 18.2 1.0
O A:HOH133 3.2 46.2 1.0
C2' A:DC4 3.6 13.0 1.0
O A:HOH108 3.7 22.4 1.0
C4' A:DG5 3.8 14.6 1.0
C4' A:DC4 3.8 13.8 1.0
C2' A:DC6 4.2 12.6 1.0
C5' A:DT7 4.4 13.8 1.0
C3' A:DG5 4.5 18.7 1.0
O A:HOH141 4.6 36.3 1.0
C1' A:DC4 4.6 19.6 1.0
C3' A:DC6 4.7 15.9 1.0
C5' A:DC4 4.7 18.5 1.0
O4' A:DC4 4.7 20.0 1.0
O B:HOH21 4.8 27.0 1.0
O A:HOH128 4.9 29.2 1.0
O4' A:DT7 4.9 12.5 1.0
C4' A:DT7 4.9 10.2 1.0

Phosphorus binding site 5 out of 18 in 1a2e

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Phosphorus binding site 5 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:21.4
occ:1.00
P A:DC6 0.0 21.4 1.0
OP2 A:DC6 1.5 22.5 1.0
OP1 A:DC6 1.5 26.9 1.0
O3' A:DG5 1.6 17.2 1.0
O5' A:DC6 1.6 18.1 1.0
C3' A:DG5 2.7 18.7 1.0
C5' A:DC6 2.8 19.0 1.0
C4' A:DG5 3.6 14.6 1.0
C2' A:DG5 3.9 16.7 1.0
C4' A:DC6 3.9 19.3 1.0
O A:HOH108 4.0 22.4 1.0
C6 A:DC6 4.0 14.2 1.0
O A:HOH140 4.0 38.4 1.0
O4' A:DC6 4.3 15.2 1.0
O5' A:DG5 4.3 15.9 1.0
C3' A:DC6 4.4 15.9 1.0
O4' A:DG5 4.5 14.7 1.0
C2' A:DC6 4.6 12.6 1.0
C5 A:DC6 4.6 13.6 1.0
C1' A:DG5 4.6 14.7 1.0
C5' A:DG5 4.7 18.2 1.0
C1' A:DC6 4.9 11.3 1.0
N1 A:DC6 4.9 12.8 1.0

Phosphorus binding site 6 out of 18 in 1a2e

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Phosphorus binding site 6 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:14.6
occ:1.00
P A:DT7 0.0 14.6 1.0
OP1 A:DT7 1.5 14.6 1.0
OP2 A:DT7 1.5 13.9 1.0
O3' A:DC6 1.6 13.3 1.0
O5' A:DT7 1.6 14.0 1.0
C5' A:DT7 2.7 13.8 1.0
C3' A:DC6 2.7 15.9 1.0
C4' A:DC6 3.4 19.3 1.0
O A:HOH144 3.7 21.7 1.0
O A:HOH110 3.7 26.3 1.0
C4' A:DT7 3.9 10.2 1.0
O A:HOH105 3.9 21.2 1.0
O A:HOH113 4.0 25.1 1.0
C2' A:DC6 4.0 12.6 1.0
O A:HOH137 4.0 22.2 1.0
C3' A:DT7 4.2 14.2 1.0
C6 A:DT7 4.3 11.7 1.0
C5' A:DC6 4.3 19.0 1.0
O4' A:DT7 4.4 12.5 1.0
O4' A:DC6 4.4 15.2 1.0
C2' A:DT7 4.4 17.4 1.0
C1' A:DC6 4.6 11.3 1.0
C7 A:DT7 4.8 18.4 1.0
C1' A:DT7 4.9 13.5 1.0

Phosphorus binding site 7 out of 18 in 1a2e

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Phosphorus binding site 7 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:19.9
occ:1.00
P A:DC8 0.0 19.9 1.0
OP1 A:DC8 1.5 24.4 1.0
OP2 A:DC8 1.5 22.7 1.0
O3' A:DT7 1.6 17.4 1.0
O5' A:DC8 1.6 16.3 1.0
C5' A:DC8 2.6 15.3 1.0
C3' A:DT7 2.6 14.2 1.0
C2' A:DT7 3.2 17.4 1.0
O A:HOH124 3.6 29.6 1.0
O A:HOH142 3.6 24.2 1.0
O A:HOH120 3.6 23.0 1.0
O A:HOH118 3.8 28.3 1.0
C4' A:DC8 3.9 22.7 1.0
C4' A:DT7 3.9 10.2 1.0
C1' A:DT7 4.1 13.5 1.0
O4' A:DC8 4.4 17.8 1.0
C3' A:DC8 4.4 24.8 1.0
O4' A:DT7 4.5 12.5 1.0
O A:HOH113 4.8 25.1 1.0
C6 A:DC8 4.8 14.1 1.0
O A:HOH143 4.9 44.9 1.0
O A:HOH136 4.9 38.0 1.0
C2' A:DC8 4.9 17.6 1.0

Phosphorus binding site 8 out of 18 in 1a2e

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Phosphorus binding site 8 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:24.4
occ:1.00
P A:DT9 0.0 24.4 1.0
OP2 A:DT9 1.5 23.4 1.0
OP1 A:DT9 1.5 23.3 1.0
O3' A:DC8 1.6 18.0 1.0
O5' A:DT9 1.6 20.1 1.0
C3' A:DC8 2.6 24.8 1.0
C5' A:DT9 2.7 21.1 1.0
C2' A:DC8 3.3 17.6 1.0
C4' A:DT9 3.9 19.0 1.0
C4' A:DC8 3.9 22.7 1.0
C1' A:DC8 4.2 15.0 1.0
O A:HOH148 4.3 26.8 1.0
O4' A:DT9 4.3 20.2 1.0
C3' A:DT9 4.5 28.3 1.0
O4' A:DC8 4.7 17.8 1.0

Phosphorus binding site 9 out of 18 in 1a2e

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Phosphorus binding site 9 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:22.2
occ:1.00
P A:DC10 0.0 22.2 1.0
OP2 A:DC10 1.5 29.0 1.0
OP1 A:DC10 1.5 21.2 1.0
O3' A:DT9 1.6 23.6 1.0
O5' A:DC10 1.6 24.2 1.0
C3' A:DT9 2.6 28.3 1.0
C5' A:DC10 2.6 19.5 1.0
C2' A:DT9 3.2 22.4 1.0
C4' A:DC10 3.9 31.0 1.0
C4' A:DT9 3.9 19.0 1.0
O4' A:DC10 4.2 25.1 1.0
C3' A:DC10 4.5 17.6 1.0
C1' A:DT9 4.5 18.5 1.0
C5' A:DT9 4.7 21.1 1.0
O4' A:DT9 4.9 20.2 1.0
O A:HOH125 4.9 29.3 1.0

Phosphorus binding site 10 out of 18 in 1a2e

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Phosphorus binding site 10 out of 18 in the Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure of A Double-Stranded Dna Decamer Containing A Cisplatin Interstrand Cross-Link Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:24.7
occ:1.00
P B:DA12 0.0 24.7 1.0
OP2 B:DA12 1.5 34.6 1.0
OP1 B:DA12 1.5 25.4 1.0
O3' B:DG11 1.6 20.9 1.0
O5' B:DA12 1.6 22.6 1.0
C5' B:DA12 2.6 19.9 1.0
C3' B:DG11 2.6 17.1 1.0
C2' B:DG11 3.2 21.0 1.0
O B:HOH37 3.6 30.2 1.0
C4' B:DA12 3.8 34.0 1.0
C4' B:DG11 3.9 21.4 1.0
C1' B:DG11 4.1 22.8 1.0
C3' B:DA12 4.2 27.4 1.0
O4' B:DA12 4.3 33.0 1.0
O4' B:DG11 4.4 18.4 1.0
C2' B:DA12 4.4 35.1 1.0
C1' B:DA12 5.0 28.6 1.0

Reference:

F.Coste, J.M.Malinge, L.Serre, W.Shepard, M.Roth, M.Leng, C.Zelwer. Crystal Structure of A Double-Stranded Dna Containing A Cisplatin Interstrand Cross-Link at 1.63 A Resolution: Hydration at the Platinated Site. Nucleic Acids Res. V. 27 1837 1999.
ISSN: ISSN 0305-1048
PubMed: 10101191
DOI: 10.1093/NAR/27.8.1837
Page generated: Fri Sep 25 12:03:21 2020

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