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Platinum in PDB 6brx: Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion

Enzymatic activity of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion

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

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 6brx was solved by V.K.Jha, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.690, 129.060, 168.088, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.9

Other elements in 6brx:

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

Magnesium (Mg) 5 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion (pdb code 6brx). 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 Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion, PDB code: 6brx:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 6brx

Go back to Platinum Binding Sites List in 6brx
Platinum binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Kappa 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 Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt602

b:72.2
occ:1.00
PT1 D:CPT602 0.0 72.2 1.0
N2 D:CPT602 2.0 58.8 1.0
N1 D:CPT602 2.0 61.3 1.0
N7 D:DG5 2.0 79.2 1.0
N7 D:DG6 2.1 60.0 1.0
C8 D:DG5 2.6 71.7 1.0
C5 D:DG6 3.1 55.3 1.0
C5 D:DG5 3.1 85.6 1.0
C8 D:DG6 3.2 57.4 1.0
O6 D:DG6 3.2 51.5 1.0
C6 D:DG6 3.5 53.1 1.0
N9 D:DG5 3.8 71.9 1.0
O D:HOH702 3.8 51.4 1.0
C6 D:DG5 3.9 90.9 1.0
O6 D:DG5 4.0 98.7 1.0
C4 D:DG5 4.0 79.6 1.0
O D:HOH707 4.2 60.1 1.0
O D:HOH706 4.3 58.2 1.0
C4 D:DG6 4.3 55.3 1.0
N9 D:DG6 4.3 55.7 1.0
O C:HOH107 4.5 51.8 1.0
OP2 D:DG5 4.8 65.9 1.0
N1 D:DG6 4.9 52.8 1.0
C2' D:DG5 4.9 70.7 1.0
C1' D:DG5 4.9 70.1 1.0

Platinum binding site 2 out of 2 in 6brx

Go back to Platinum Binding Sites List in 6brx
Platinum binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Kappa 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 Human Dna Polymerase Kappa in Complex with Dna Containing the Major Cisplatin Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt602

b:73.8
occ:1.00
PT1 T:CPT602 0.0 73.8 1.0
N1 T:CPT602 2.0 59.5 1.0
N2 T:CPT602 2.0 57.4 1.0
N7 T:DG5 2.1 82.8 1.0
N7 T:DG6 2.2 66.4 1.0
C8 T:DG5 2.7 77.3 1.0
C8 T:DG6 3.1 61.6 1.0
C5 T:DG5 3.2 87.7 1.0
C5 T:DG6 3.3 67.5 1.0
O T:HOH706 3.6 34.8 1.0
O6 T:DG6 3.6 69.6 1.0
N9 T:DG5 3.8 77.7 1.0
C6 T:DG6 3.8 69.1 1.0
C6 T:DG5 3.9 91.0 1.0
O T:HOH705 4.0 62.8 1.0
O6 T:DG5 4.0 99.3 1.0
O T:HOH703 4.0 58.9 1.0
C4 T:DG5 4.1 83.3 1.0
N9 T:DG6 4.3 61.2 1.0
C4 T:DG6 4.4 67.0 1.0
O T:HOH702 4.5 61.0 1.0
O B:HOH706 4.8 48.3 1.0
OP2 T:DG5 4.9 62.4 1.0
C2' T:DG5 5.0 70.9 1.0
C1' T:DG5 5.0 72.7 1.0

Reference:

V.Jha, H.Ling. Structural Basis For Human Dna Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-Gg) Lesion As An Efficient and Accurate Extender. J. Mol. Biol. V. 430 1577 2018.
ISSN: ESSN 1089-8638
PubMed: 29715472
DOI: 10.1016/J.JMB.2018.04.023
Page generated: Wed Dec 16 02:05:31 2020

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