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Platinum in PDB 4dl6: Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).

Enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).

All present enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3)., PDB code: 4dl6 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, Y.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 / 2.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.780, 98.780, 81.510, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 22

Other elements in 4dl6:

The structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). 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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). (pdb code 4dl6). 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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3)., PDB code: 4dl6:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 4dl6

Go back to Platinum Binding Sites List in 4dl6
Platinum binding site 1 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).


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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:95.1
occ:0.50
PT1 T:CPT101 0.0 95.1 0.5
N7 T:DG6 1.0 61.0 0.5
C8 T:DG6 1.8 56.3 0.5
PT1 T:CPT101 1.9 99.8 0.5
N2 T:CPT101 2.0 54.2 0.5
N7 T:DG6 2.0 54.0 0.5
N1 T:CPT101 2.1 72.5 0.5
N7 T:DG5 2.1 60.9 0.5
C5 T:DG6 2.3 54.4 0.5
N2 T:CPT101 2.4 66.9 0.5
C5 T:DG5 2.9 56.3 0.5
C8 T:DG5 3.0 56.1 0.5
N9 T:DG6 3.0 52.4 0.5
C8 T:DG6 3.0 51.2 0.5
N7 T:DG5 3.1 58.4 0.5
C5 T:DG6 3.1 52.3 0.5
C4 T:DG6 3.2 52.5 0.5
C6 T:DG6 3.2 53.3 0.5
O6 T:DG5 3.3 56.9 0.5
O6 T:DG6 3.4 54.0 0.5
C6 T:DG5 3.5 54.9 0.5
O6 T:DG6 3.5 54.4 0.5
C8 T:DG5 3.5 55.4 0.5
C6 T:DG6 3.6 51.9 0.5
C5 T:DG5 3.6 54.7 0.5
N1 T:CPT101 3.9 42.8 0.5
C4 T:DG5 4.0 52.5 0.5
N9 T:DG5 4.0 53.0 0.5
C6 T:DG5 4.2 53.1 0.5
N9 T:DG6 4.2 50.6 0.5
C4 T:DG6 4.2 50.6 0.5
O6 T:DG5 4.2 53.6 0.5
O T:HOH202 4.3 56.5 1.0
N9 T:DG5 4.3 52.7 0.5
C4 T:DG5 4.4 51.9 0.5
C1' T:DG6 4.4 51.0 0.5
N1 T:DG6 4.5 50.9 0.5
N3 T:DG6 4.5 49.9 0.5
N4 T:DC7 4.7 48.7 0.5
N1 T:DG5 4.7 51.0 0.5
O4' T:DG6 4.7 55.0 0.5
N4 T:DC7 4.7 48.7 0.5
C2 T:DG6 5.0 50.4 0.5
N1 T:DG6 5.0 50.3 0.5

Platinum binding site 2 out of 2 in 4dl6

Go back to Platinum Binding Sites List in 4dl6
Platinum binding site 2 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).


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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:99.8
occ:0.50
PT1 T:CPT101 0.0 99.8 0.5
N7 T:DG5 1.7 60.9 0.5
N1 T:CPT101 1.9 72.5 0.5
PT1 T:CPT101 1.9 95.1 0.5
N2 T:CPT101 2.0 66.9 0.5
N1 T:CPT101 2.1 42.8 0.5
N7 T:DG5 2.1 58.4 0.5
N7 T:DG6 2.1 61.0 0.5
C5 T:DG5 2.5 56.3 0.5
O6 T:DG5 2.6 56.9 0.5
C6 T:DG5 2.9 54.9 0.5
C8 T:DG5 2.9 56.1 0.5
C8 T:DG6 3.0 56.3 0.5
C5 T:DG5 3.0 54.7 0.5
C8 T:DG5 3.0 55.4 0.5
C5 T:DG6 3.1 54.4 0.5
O6 T:DG5 3.3 53.6 0.5
C6 T:DG5 3.4 53.1 0.5
N7 T:DG6 3.5 54.0 0.5
N2 T:CPT101 3.6 54.2 0.5
O6 T:DG6 3.7 54.4 0.5
C6 T:DG6 3.7 53.3 0.5
C4 T:DG5 3.7 52.5 0.5
O6 T:DG6 3.9 54.0 0.5
N9 T:DG5 3.9 53.0 0.5
C4 T:DG5 4.1 51.9 0.5
N9 T:DG6 4.1 52.4 0.5
N9 T:DG5 4.1 52.7 0.5
C5 T:DG6 4.1 52.3 0.5
C5 T:DC4 4.1 69.0 1.0
C4 T:DG6 4.2 52.5 0.5
N1 T:DG5 4.3 51.0 0.5
C6 T:DG6 4.3 51.9 0.5
C8 T:DG6 4.4 51.2 0.5
O T:HOH203 4.4 63.4 1.0
C6 T:DC4 4.5 74.9 1.0
C4 T:DC4 4.5 58.0 1.0
N1 T:DG5 4.8 50.3 0.5
N4 T:DC4 4.8 57.9 1.0
N3 T:DG5 4.9 49.6 0.5

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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