Manganese in PDB 6m7v: 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;

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

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

Nickel

(Ni)

1 atom

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position, PDB code: 6m7v:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn503 b:15.6 occ:1.00 OD1 A:ASP115 2.0 15.1 1.0 O1B A:DZ4502 2.0 27.1 1.0 O1A A:DZ4502 2.1 26.8 1.0 O A:MET14 2.2 31.6 1.0 OD1 A:ASP13 2.2 27.9 1.0 O1G A:DZ4502 2.6 24.3 1.0 PB A:DZ4502 2.9 34.8 1.0 CG A:ASP13 3.1 26.9 1.0 CG A:ASP115 3.2 20.2 1.0 O3B A:DZ4502 3.2 20.5 1.0 PA A:DZ4502 3.2 20.1 1.0 PG A:DZ4502 3.3 17.4 1.0 OD2 A:ASP13 3.3 24.9 1.0 MN A:MN504 3.4 20.3 1.0 C A:MET14 3.4 32.5 1.0 N3A A:DZ4502 3.4 32.6 1.0 O3G A:DZ4502 3.6 21.4 1.0 OD2 A:ASP115 3.7 22.6 1.0 C5' A:DZ4502 3.8 31.9 1.0 O5' A:DZ4502 4.0 20.6 1.0 N A:MET14 4.1 28.9 1.0 CA A:MET14 4.2 28.8 1.0 O2B A:DZ4502 4.3 28.9 1.0 CB A:ASP115 4.4 21.6 1.0 O A:HOH606 4.4 14.4 1.0 N A:CYS16 4.4 56.8 1.0 N A:ASP15 4.4 30.2 1.0 O2A A:DZ4502 4.4 25.4 1.0 C A:ASP13 4.5 27.8 1.0 CB A:ASP13 4.5 26.2 1.0 CA A:ASP15 4.5 37.2 1.0 CB A:MET14 4.6 36.1 1.0 C A:ASP15 4.6 49.3 1.0 N A:PHE17 4.6 29.3 1.0 O2G A:DZ4502 4.7 27.3 1.0 OP1 P:DT9 4.9 25.9 1.0 O A:ASP13 4.9 28.2 1.0 CB A:PHE17 4.9 22.4 1.0 O A:ASP115 5.0 27.1 1.0 CA A:ASP13 5.0 22.3 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta Extension Complex with Cda at the -1 Position


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 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:Mn504 b:20.3 occ:1.00 OD2 A:ASP13 1.9 24.9 1.0 OP1 P:DT9 2.0 25.9 1.0 OD2 A:ASP115 2.1 22.6 1.0 O1A A:DZ4502 2.2 26.8 1.0 OE2 A:GLU116 2.3 22.0 1.0 O A:HOH606 2.4 14.4 1.0 CG A:ASP115 2.9 20.2 1.0 OD1 A:ASP115 3.0 15.1 1.0 CG A:ASP13 3.0 26.9 1.0 PA A:DZ4502 3.2 20.1 1.0 MN A:MN503 3.4 15.6 1.0 P P:DT9 3.4 34.0 1.0 OD1 A:ASP13 3.4 27.9 1.0 O2A A:DZ4502 3.5 25.4 1.0 CD A:GLU116 3.5 27.0 1.0 O5' A:DZ4502 3.7 20.6 1.0 OG A:SER113 4.0 17.6 1.0 O3' P:DG8 4.0 16.9 1.0 C5' A:DZ4502 4.1 31.9 1.0 OP2 P:DT9 4.1 25.4 1.0 CB A:ASP13 4.3 26.2 1.0 CG A:GLU116 4.3 21.4 1.0 CB A:GLU116 4.3 21.6 1.0 CB A:ASP115 4.3 21.6 1.0 OE1 A:GLU116 4.4 30.4 1.0 O5' P:DT9 4.6 39.2 1.0 O1B A:DZ4502 4.6 27.1 1.0 C A:ASP115 4.6 23.4 1.0 O A:ASP115 4.6 27.1 1.0 N3A A:DZ4502 4.6 32.6 1.0 C5' P:DT9 4.7 32.2 1.0 N A:GLU116 4.9 21.6 1.0 CA A:ASP115 4.9 16.5 1.0

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