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Nickel in PDB 6m7v: Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position

Enzymatic activity of Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position

All present enzymatic activity of Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position, PDB code: 6m7v was solved by P.Weng, Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.18 / 3.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.075, 81.387, 145.006, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 26.8

Other elements in 6m7v:

The structure of Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position (pdb code 6m7v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position, PDB code: 6m7v:

Nickel binding site 1 out of 1 in 6m7v

Go back to Nickel Binding Sites List in 6m7v
Nickel binding site 1 out of 1 in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:9.3
occ:1.00
NE2 A:HIS393 2.0 9.6 1.0
NE2 A:HIS397 2.0 13.2 1.0
CE1 A:HIS397 2.9 14.9 1.0
CE1 A:HIS393 2.9 9.0 1.0
CD2 A:HIS393 3.1 10.5 1.0
CD2 A:HIS397 3.1 18.5 1.0
ND1 A:HIS393 4.0 7.6 1.0
ND1 A:HIS397 4.0 19.7 1.0
CG A:HIS393 4.1 9.4 1.0
CG A:HIS397 4.2 18.1 1.0
O A:HOH608 4.2 17.8 1.0

Reference:

P.J.Weng, Y.Gao, M.T.Gregory, P.Wang, Y.Wang, W.Yang. Bypassing A 8,5'-Cyclo-2'-Deoxyadenosine Lesion By Human Dna Polymerase Eta at Atomic Resolution. Proc. Natl. Acad. Sci. V. 115 10660 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30275308
DOI: 10.1073/PNAS.1812856115
Page generated: Wed Dec 16 01:52:43 2020

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