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Platinum in PDB 3m9n: Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion

Enzymatic activity of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion

All present enzymatic activity of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9n was solved by J.H.Y.Wong, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 1.93
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.227, 103.233, 52.259, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 26.1

Other elements in 3m9n:

The structure of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion (pdb code 3m9n). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 3m9n:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 3m9n

Go back to Platinum Binding Sites List in 3m9n
Platinum binding site 1 out of 2 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt1005

b:47.9
occ:0.50
PT1 T:CPT1005 0.0 47.9 0.5
N7 T:DG5 0.6 33.5 0.5
C8 T:DG5 0.8 34.4 0.5
C5 T:DG5 1.7 33.9 0.5
N1 T:CPT1005 2.0 36.0 0.5
N2 T:CPT1005 2.0 36.7 0.5
N7 T:DG5 2.0 38.7 0.5
N9 T:DG5 2.0 32.0 0.5
N7 T:DG4 2.1 34.8 0.5
C4 T:DG5 2.3 33.0 0.5
PT1 T:CPT1005 2.4 33.2 0.5
C8 T:DG4 2.7 36.3 0.5
N7 T:DG4 2.9 32.9 0.5
C6 T:DG5 3.0 32.7 0.5
C5 T:DG5 3.0 35.8 0.5
C5 T:DG4 3.1 35.1 0.5
C8 T:DG5 3.2 36.3 0.5
C8 T:DG4 3.2 30.4 0.5
N1 T:CPT1005 3.4 31.7 0.5
O6 T:DG5 3.4 29.0 0.5
C5 T:DG4 3.5 30.4 0.5
C6 T:DG5 3.5 31.3 0.5
C1' T:DG5 3.5 31.6 0.5
N3 T:DG5 3.6 33.5 0.5
O6 T:DG5 3.6 33.8 0.5
N9 T:DG4 3.9 33.0 0.5
C6 T:DG4 3.9 32.4 0.5
N9 T:DG4 4.0 31.1 0.5
O6 T:DG4 4.0 32.1 0.5
N1 T:DG5 4.0 31.8 0.5
C4 T:DG4 4.1 31.0 0.5
C4 T:DG4 4.1 32.9 0.5
C6 T:DG4 4.1 30.9 0.5
O4' T:DG5 4.2 31.9 0.5
C4 T:DG5 4.2 32.0 0.5
C2 T:DG5 4.3 32.5 0.5
N9 T:DG5 4.3 31.1 0.5
N2 T:CPT1005 4.3 31.9 0.5
O6 T:DG4 4.4 30.5 0.5
C2' T:DG5 4.5 31.7 0.5
OP1 T:DG4 4.7 33.0 0.5
OP1 T:DG4 4.7 33.1 0.5
N1 T:DG5 4.9 28.9 0.5
C2' T:DG4 4.9 31.4 0.5
C1' T:DG4 5.0 30.5 0.5

Platinum binding site 2 out of 2 in 3m9n

Go back to Platinum Binding Sites List in 3m9n
Platinum binding site 2 out of 2 in the Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of DPO4 in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt1005

b:33.2
occ:0.50
PT1 T:CPT1005 0.0 33.2 0.5
N2 T:CPT1005 1.5 36.7 0.5
N2 T:CPT1005 2.0 31.9 0.5
N7 T:DG4 2.0 32.9 0.5
N1 T:CPT1005 2.0 31.7 0.5
N7 T:DG5 2.0 33.5 0.5
N7 T:DG4 2.1 34.8 0.5
PT1 T:CPT1005 2.4 47.9 0.5
C5 T:DG5 3.0 33.9 0.5
C8 T:DG4 3.0 30.4 0.5
C8 T:DG5 3.0 34.4 0.5
C5 T:DG4 3.0 30.4 0.5
C5 T:DG4 3.1 35.1 0.5
C8 T:DG4 3.1 36.3 0.5
O6 T:DG4 3.4 32.1 0.5
O6 T:DG4 3.5 30.5 0.5
O6 T:DG5 3.6 33.8 0.5
C6 T:DG4 3.6 32.4 0.5
C6 T:DG5 3.6 32.7 0.5
C6 T:DG4 3.6 30.9 0.5
N1 T:CPT1005 3.9 36.0 0.5
C4 T:DG5 4.1 33.0 0.5
N9 T:DG4 4.2 31.1 0.5
N9 T:DG5 4.2 32.0 0.5
C4 T:DG4 4.2 31.0 0.5
N7 T:DG5 4.2 38.7 0.5
C4 T:DG4 4.3 32.9 0.5
N9 T:DG4 4.3 33.0 0.5
O B:GLY58 4.3 30.9 1.0
OP1 T:DG4 4.4 33.0 0.5
O6 T:DG5 4.4 29.0 0.5
CA B:GLY58 4.5 29.5 1.0
OP1 T:DG4 4.5 33.1 0.5
C5 T:DG5 4.8 35.8 0.5
O T:HOH283 4.8 50.0 1.0
C6 T:DG5 4.8 31.3 0.5
N1 T:DG5 4.9 31.8 0.5
C B:GLY58 4.9 30.0 1.0
N1 T:DG4 5.0 30.8 0.5
N1 T:DG4 5.0 29.8 0.5

Reference:

J.H.Wong, J.A.Brown, Z.Suo, P.Blum, T.Nohmi, H.Ling. Structural Insight Into Dynamic Bypass of the Major Cisplatin-Dna Adduct By Y-Family Polymerase DPO4. Embo J. V. 29 2059 2010.
ISSN: ISSN 0261-4189
PubMed: 20512114
DOI: 10.1038/EMBOJ.2010.101
Page generated: Wed Dec 16 02:04:20 2020

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