Platinum in PDB 4q8e: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G:
2.7.7.7;

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G, PDB code: 4q8e was solved by M.T.Gregory, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.94 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.766, 98.766, 82.197, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.5

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Platinum atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G (pdb code 4q8e). 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 A Phenanthriplatin Adducted G, PDB code: 4q8e:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G


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 A Phenanthriplatin Adducted G within 5.0Å range: probe atom residue distance (Å) B Occ T:Pt4 b:18.2 occ:0.66 PT1 T:P9G4 0.0 18.2 0.7 N10 T:P9G4 0.9 15.0 0.3 PT1 T:P9G4 1.2 27.4 0.3 N12 T:P9G4 2.0 20.8 0.7 N10 T:P9G4 2.0 20.1 0.7 N11 T:P9G4 2.0 14.3 0.7 N7 T:P9G4 2.1 14.3 0.7 N11 T:P9G4 2.3 17.9 0.3 N7 T:P9G4 2.4 14.4 0.3 C18 T:P9G4 2.9 24.6 0.7 C16 T:P9G4 3.0 22.3 0.7 C8 T:P9G4 3.0 16.8 0.7 C5 T:P9G4 3.1 15.6 0.7 C22 T:P9G4 3.1 20.4 0.7 N12 T:P9G4 3.2 20.6 0.3 C5 T:P9G4 3.3 15.2 0.3 C8 T:P9G4 3.3 16.9 0.3 O6 T:P9G4 3.4 15.1 0.7 O6 T:P9G4 3.5 13.0 0.3 C6 T:P9G4 3.6 14.4 0.7 C6 T:P9G4 3.7 14.2 0.3 N9 T:P9G4 4.2 16.3 0.7 C13 T:P9G4 4.3 28.8 0.7 C15 T:P9G4 4.3 27.1 0.7 C4 T:P9G4 4.3 14.0 0.7 O T:HOH119 4.3 23.1 0.7 C4 T:P9G4 4.4 14.2 0.3 N9 T:P9G4 4.4 16.6 0.3 C21 T:P9G4 4.5 19.3 0.7 C14 T:P9G4 4.8 26.5 0.7 O T:HOH111 4.9 32.5 1.0 N4 T:DC5 5.0 16.7 1.0

Platinum binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G


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 A Phenanthriplatin Adducted G within 5.0Å range: probe atom residue distance (Å) B Occ T:Pt4 b:27.4 occ:0.34 PT1 T:P9G4 0.0 27.4 0.3 PT1 T:P9G4 1.2 18.2 0.7 N12 T:P9G4 1.3 20.8 0.7 N7 T:P9G4 2.0 14.4 0.3 N11 T:P9G4 2.0 17.9 0.3 N10 T:P9G4 2.0 15.0 0.3 N12 T:P9G4 2.0 20.6 0.3 N7 T:P9G4 2.1 14.3 0.7 N11 T:P9G4 2.7 14.3 0.7 C8 T:P9G4 2.9 16.8 0.7 C8 T:P9G4 3.0 16.9 0.3 O T:HOH119 3.1 23.1 0.7 C5 T:P9G4 3.1 15.2 0.3 C5 T:P9G4 3.1 15.6 0.7 N10 T:P9G4 3.1 20.1 0.7 O6 T:P9G4 3.4 13.0 0.3 C6 T:P9G4 3.6 14.2 0.3 O6 T:P9G4 3.6 15.1 0.7 C6 T:P9G4 3.7 14.4 0.7 C18 T:P9G4 3.9 24.6 0.7 O T:HOH111 4.0 32.5 1.0 N4 T:DC5 4.0 16.7 1.0 N9 T:P9G4 4.0 16.3 0.7 C16 T:P9G4 4.0 22.3 0.7 C22 T:P9G4 4.1 20.4 0.7 C4 T:P9G4 4.1 14.0 0.7 N9 T:P9G4 4.2 16.6 0.3 C4 T:P9G4 4.2 14.2 0.3 O T:HOH105 4.4 38.9 1.0 O P:HOH115 4.6 29.9 1.0 C4 T:DC5 4.8 18.5 1.0 OP1 T:P9G4 4.8 35.5 0.3 OP1 T:P9G4 4.9 35.6 0.7 N1 T:P9G4 5.0 12.1 0.3 N1 T:P9G4 5.0 11.7 0.7

M.T.Gregory, G.Y.Park, T.C.Johnstone, Y.S.Lee, W.Yang, S.J.Lippard. Structural and Mechanistic Studies of Polymerase Eta Bypass of Phenanthriplatin Dna Damage. Proc.Natl.Acad.Sci.Usa V. 111 9133 2014.
ISSN: ISSN 0027-8424
PubMed: 24927576
DOI: 10.1073/PNAS.1405739111