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Platinum in PDB 2wtf: Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link

Enzymatic activity of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link

All present enzymatic activity of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link, PDB code: 2wtf was solved by T.Reissner, S.Schneider, O.Ziv, S.Schorr, Z.Livneh, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.240, 103.240, 292.740, 90.00, 90.00, 90.00
R / Rfree (%) 22.712 / 26.871

Other elements in 2wtf:

The structure of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link (pdb code 2wtf). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link, PDB code: 2wtf:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 2wtf

Go back to Platinum Binding Sites List in 2wtf
Platinum binding site 1 out of 2 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Pt1014

b:55.1
occ:1.00
PT1 O:CPT1014 0.0 55.1 1.0
N1 O:CPT1014 2.0 45.4 1.0
N2 O:CPT1014 2.1 51.7 1.0
N7 O:DG0 2.1 55.3 1.0
N7 O:DG2 2.2 43.6 1.0
C8 O:DG0 3.1 60.5 1.0
C8 O:DG2 3.2 42.3 1.0
C5 O:DG0 3.2 57.7 1.0
C5 O:DG2 3.3 39.2 1.0
O6 O:DG2 3.5 40.5 1.0
O6 O:DG0 3.6 52.9 1.0
C6 O:DG0 3.7 55.4 1.0
C6 O:DG2 3.7 39.4 1.0
N9 O:DG0 4.3 63.9 1.0
C4 O:DG0 4.4 61.0 1.0
N9 O:DG2 4.4 45.4 1.0
C4 O:DG2 4.4 41.0 1.0
N4 O:DC3 4.9 32.7 1.0

Platinum binding site 2 out of 2 in 2wtf

Go back to Platinum Binding Sites List in 2wtf
Platinum binding site 2 out of 2 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Pt1014

b:68.5
occ:1.00
PT1 S:CPT1014 0.0 68.5 1.0
N2 S:CPT1014 2.1 62.2 1.0
N1 S:CPT1014 2.1 64.0 1.0
N7 S:DG0 2.1 69.5 1.0
N7 S:DG2 2.2 60.8 1.0
C8 S:DG0 2.9 72.4 1.0
C5 S:DG2 3.1 57.8 1.0
C8 S:DG2 3.2 61.4 1.0
O6 S:DG2 3.3 47.2 1.0
C5 S:DG0 3.3 69.9 1.0
O2 S:DT-1 3.5 62.4 1.0
C6 S:DG2 3.5 53.8 1.0
O6 S:DG0 3.8 64.0 1.0
C6 S:DG0 3.9 67.3 1.0
N9 S:DG0 4.2 73.5 1.0
C4 S:DG2 4.3 59.9 1.0
N9 S:DG2 4.3 63.0 1.0
C2 S:DT-1 4.4 63.3 1.0
C4 S:DG0 4.4 71.2 1.0
N3 S:DT-1 4.4 62.3 1.0
N4 S:DC3 4.8 57.2 1.0
O6 T:DG8 4.8 44.4 1.0
N1 S:DG2 4.9 53.6 1.0

Reference:

T.Reissner, S.Schneider, S.Schorr, T.Carell. Crystal Structure of A Cisplatin-(1,3-Gtg) Cross- Link Within Dna Polymerase Eta. Angew.Chem.Int.Ed.Engl. V. 49 3077 2010.
ISSN: ISSN 1433-7851
PubMed: 20333640
DOI: 10.1002/ANIE.201000414
Page generated: Wed Dec 16 02:04:06 2020

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