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Platinum in PDB 4dl4: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).

Enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1)., PDB code: 4dl4 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, Y.-J.Hua, F.Hanaoka, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 99.210, 99.210, 82.150, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 21.7

Other elements in 4dl4:

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). (pdb code 4dl4). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1)., PDB code: 4dl4:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 4dl4

Go back to Platinum Binding Sites List in 4dl4
Platinum binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:26.2
occ:0.60
PT1 T:CPT101 0.0 26.2 0.6
PT1 T:CPT101 0.6 27.9 0.4
N7 T:DG3 1.6 25.6 0.4
N2 T:CPT101 2.0 21.1 0.6
N7 T:DG3 2.0 26.6 0.6
N1 T:CPT101 2.1 26.5 0.6
N7 T:DG4 2.1 22.7 0.6
N7 T:DG4 2.1 22.7 0.4
N1 T:CPT101 2.3 27.0 0.4
N2 T:CPT101 2.6 22.7 0.4
C5 T:DG3 2.6 26.2 0.4
C8 T:DG3 2.7 28.2 0.4
C8 T:DG4 3.0 21.9 0.4
C5 T:DG3 3.0 24.9 0.6
C8 T:DG4 3.0 21.8 0.6
C8 T:DG3 3.0 29.5 0.6
O6 T:DG3 3.1 29.0 0.4
C5 T:DG4 3.1 23.6 0.6
O6 T:DG3 3.1 32.3 0.6
C5 T:DG4 3.1 23.5 0.4
C6 T:DG3 3.2 28.6 0.4
O6 T:DG4 3.4 19.7 0.6
C6 T:DG3 3.4 28.6 0.6
O6 T:DG4 3.5 19.8 0.4
C6 T:DG4 3.6 21.0 0.6
C6 T:DG4 3.7 21.1 0.4
C4 T:DG3 3.7 26.8 0.4
N9 T:DG3 3.8 26.8 0.4
C4 T:DG3 4.2 24.9 0.6
N9 T:DG4 4.2 23.1 0.4
N9 T:DG3 4.2 25.4 0.6
N9 T:DG4 4.2 23.1 0.6
C4 T:DG4 4.2 21.1 0.4
C4 T:DG4 4.2 21.1 0.6
O T:HOH201 4.4 25.9 1.0
O T:HOH212 4.5 32.9 1.0
N1 T:DG3 4.6 23.1 0.4
N4 T:DC5 4.6 24.3 1.0
N1 T:DG3 4.8 29.1 0.6
N1 T:DG4 5.0 18.8 0.6
N3 T:DG3 5.0 26.8 0.4

Platinum binding site 2 out of 2 in 4dl4

Go back to Platinum Binding Sites List in 4dl4
Platinum binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:27.9
occ:0.40
PT1 T:CPT101 0.0 27.9 0.4
PT1 T:CPT101 0.6 26.2 0.6
N2 T:CPT101 1.5 21.1 0.6
N2 T:CPT101 2.0 22.7 0.4
N1 T:CPT101 2.1 27.0 0.4
N7 T:DG3 2.1 25.6 0.4
N7 T:DG4 2.1 22.7 0.4
N7 T:DG4 2.1 22.7 0.6
N1 T:CPT101 2.2 26.5 0.6
N7 T:DG3 2.6 26.6 0.6
C8 T:DG4 3.0 21.9 0.4
C5 T:DG4 3.1 23.6 0.6
C5 T:DG3 3.1 26.2 0.4
C8 T:DG3 3.1 28.2 0.4
C5 T:DG4 3.1 23.5 0.4
C8 T:DG4 3.1 21.8 0.6
O6 T:DG4 3.3 19.7 0.6
O6 T:DG3 3.4 29.0 0.4
O6 T:DG4 3.4 19.8 0.4
O6 T:DG3 3.5 32.3 0.6
C6 T:DG4 3.6 21.0 0.6
C8 T:DG3 3.6 29.5 0.6
C5 T:DG3 3.6 24.9 0.6
C6 T:DG3 3.6 28.6 0.4
C6 T:DG4 3.6 21.1 0.4
O T:HOH212 3.9 32.9 1.0
C6 T:DG3 4.0 28.6 0.6
N4 T:DC5 4.2 24.3 1.0
N9 T:DG4 4.2 23.1 0.4
C4 T:DG4 4.3 21.1 0.4
N9 T:DG4 4.3 23.1 0.6
C4 T:DG3 4.3 26.8 0.4
C4 T:DG4 4.3 21.1 0.6
N9 T:DG3 4.3 26.8 0.4
O T:HOH201 4.4 25.9 1.0
N9 T:DG3 4.8 25.4 0.6
C4 T:DG3 4.8 24.9 0.6
N1 T:DG4 4.9 18.8 0.6

Reference:

Y.Zhao, C.Biertumpfel, M.T.Gregory, Y.J.Hua, F.Hanaoka, W.Yang. Structural Basis For Chemoresistance to Cisplatin Mediated By Dna Polymerase Eta Proc.Natl.Acad.Sci.Usa V. 109 7269 2012.
ISSN: ISSN 0027-8424
PubMed: 22529383
DOI: 10.1073/PNAS.1202681109
Page generated: Wed Dec 16 02:04:42 2020

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