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Platinum in PDB 4q8f: Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G

Enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G

All present enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G, PDB code: 4q8f 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) 29.55 / 2.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.692, 98.692, 81.812, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.3

Other elements in 4q8f:

The structure of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G 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 A Phenanthriplatin Adducted G (pdb code 4q8f). 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 A Phenanthriplatin Adducted G, PDB code: 4q8f:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 4q8f

Go back to Platinum Binding Sites List in 4q8f
Platinum binding site 1 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After 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 Extending Primer Immediately After A Phenanthriplatin Adducted G within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt5

b:54.2
occ:0.80
PT1 T:P9G5 0.0 54.2 0.8
PT1 T:P9G5 0.3 50.3 0.2
N7 T:P9G5 1.9 41.4 0.2
N10 T:P9G5 2.0 42.3 0.2
N10 T:P9G5 2.0 42.6 0.8
N12 T:P9G5 2.0 45.4 0.8
N11 T:P9G5 2.0 50.5 0.8
N7 T:P9G5 2.0 41.9 0.8
N12 T:P9G5 2.1 43.3 0.2
N11 T:P9G5 2.2 49.0 0.2
C5 T:P9G5 2.8 38.5 0.2
C18 T:P9G5 2.9 42.5 0.2
C8 T:P9G5 2.9 40.1 0.2
C18 T:P9G5 2.9 43.9 0.8
C16 T:P9G5 2.9 42.0 0.8
C8 T:P9G5 3.0 40.1 0.8
C16 T:P9G5 3.0 43.3 0.2
C5 T:P9G5 3.1 38.3 0.8
C22 T:P9G5 3.1 42.6 0.8
O6 T:P9G5 3.1 36.9 0.2
C22 T:P9G5 3.3 43.8 0.2
C6 T:P9G5 3.3 36.3 0.2
O6 T:P9G5 3.4 36.6 0.8
C6 T:P9G5 3.6 35.7 0.8
C4 T:P9G5 4.0 37.5 0.2
N9 T:P9G5 4.1 39.2 0.2
C13 T:P9G5 4.2 42.8 0.2
N9 T:P9G5 4.2 39.4 0.8
C13 T:P9G5 4.2 42.6 0.8
C15 T:P9G5 4.3 43.3 0.8
C4 T:P9G5 4.3 37.3 0.8
C15 T:P9G5 4.3 43.2 0.2
C3 A:GOL507 4.3 48.9 1.0
O4 T:DT6 4.5 33.4 1.0
C21 T:P9G5 4.5 44.2 0.8
C21 T:P9G5 4.6 43.9 0.2
O3 A:GOL507 4.7 51.0 1.0
N1 T:P9G5 4.7 34.6 0.2
C14 T:P9G5 4.8 43.0 0.2
C14 T:P9G5 4.8 42.7 0.8
C5 T:DC4 4.8 39.8 0.2
C7 T:DT6 4.9 31.5 1.0
N7 T:DA2 4.9 44.7 0.7
N1 T:P9G5 5.0 34.3 0.8

Platinum binding site 2 out of 2 in 4q8f

Go back to Platinum Binding Sites List in 4q8f
Platinum binding site 2 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After 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 Extending Primer Immediately After A Phenanthriplatin Adducted G within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt5

b:50.3
occ:0.20
PT1 T:P9G5 0.0 50.3 0.2
PT1 T:P9G5 0.3 54.2 0.8
N11 T:P9G5 1.9 50.5 0.8
N10 T:P9G5 2.0 42.6 0.8
N12 T:P9G5 2.0 43.3 0.2
N11 T:P9G5 2.0 49.0 0.2
N10 T:P9G5 2.0 42.3 0.2
N7 T:P9G5 2.0 41.4 0.2
N12 T:P9G5 2.1 45.4 0.8
N7 T:P9G5 2.2 41.9 0.8
C18 T:P9G5 2.8 43.9 0.8
C18 T:P9G5 3.0 42.5 0.2
C16 T:P9G5 3.0 43.3 0.2
C16 T:P9G5 3.0 42.0 0.8
C8 T:P9G5 3.0 40.1 0.2
C5 T:P9G5 3.1 38.5 0.2
C22 T:P9G5 3.1 43.8 0.2
C8 T:P9G5 3.1 40.1 0.8
C22 T:P9G5 3.2 42.6 0.8
C5 T:P9G5 3.3 38.3 0.8
O6 T:P9G5 3.4 36.9 0.2
C6 T:P9G5 3.6 36.3 0.2
O6 T:P9G5 3.7 36.6 0.8
C6 T:P9G5 3.9 35.7 0.8
C13 T:P9G5 4.1 42.6 0.8
C3 A:GOL507 4.2 48.9 1.0
N9 T:P9G5 4.2 39.2 0.2
C15 T:P9G5 4.3 43.3 0.8
C4 T:P9G5 4.3 37.5 0.2
C13 T:P9G5 4.3 42.8 0.2
C15 T:P9G5 4.3 43.2 0.2
N9 T:P9G5 4.4 39.4 0.8
C4 T:P9G5 4.5 37.3 0.8
C21 T:P9G5 4.5 43.9 0.2
O3 A:GOL507 4.5 51.0 1.0
C21 T:P9G5 4.6 44.2 0.8
O4 T:DT6 4.6 33.4 1.0
C14 T:P9G5 4.7 42.7 0.8
C14 T:P9G5 4.8 43.0 0.2
N7 T:DA2 4.8 44.7 0.7
C5 T:DC4 4.9 39.8 0.2
N1 T:P9G5 5.0 34.6 0.2
C7 T:DT6 5.0 31.5 1.0

Reference:

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
Page generated: Wed Dec 16 02:05:00 2020

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