Magnesium in PDB 6m7p: Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position

All present enzymatic activity of Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position:
2.7.7.7;

The structure of Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position, PDB code: 6m7p 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)	29.99 / 1.75
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.495, 98.495, 81.708, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.8

The binding sites of Magnesium atom in the Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position (pdb code 6m7p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position, PDB code: 6m7p:
Jump to Magnesium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.6 occ:1.00 OD1 A:ASP115 2.1 15.6 1.0 OD1 A:ASP13 2.1 17.7 1.0 O1B A:DZ4501 2.1 14.0 1.0 O A:MET14 2.1 15.2 1.0 O1G A:DZ4501 2.2 16.6 1.0 O1A A:DZ4501 2.2 16.8 1.0 CG A:ASP13 3.1 15.1 1.0 PB A:DZ4501 3.2 15.8 1.0 CG A:ASP115 3.2 19.7 1.0 C A:MET14 3.3 16.0 1.0 PA A:DZ4501 3.3 18.9 1.0 PG A:DZ4501 3.4 17.3 1.0 OD2 A:ASP13 3.5 19.3 1.0 MG A:MG503 3.5 18.2 1.0 N3A A:DZ4501 3.5 18.2 1.0 O3B A:DZ4501 3.6 16.4 1.0 OD2 A:ASP115 3.6 16.2 1.0 N A:MET14 3.8 14.4 1.0 NZ A:LYS231 3.9 13.1 1.0 O A:HOH771 3.9 21.0 1.0 C5' A:DZ4501 4.0 16.9 1.0 CA A:MET14 4.0 14.6 1.0 O2G A:DZ4501 4.1 18.4 1.0 O5' A:DZ4501 4.2 17.8 1.0 C A:ASP13 4.2 14.4 1.0 N A:ASP15 4.3 14.0 1.0 CB A:ASP13 4.3 15.6 1.0 O A:HOH761 4.4 18.9 1.0 CB A:ASP115 4.5 16.7 1.0 O2B A:DZ4501 4.5 16.3 1.0 CB A:MET14 4.5 18.1 1.0 CE A:LYS231 4.5 19.4 1.0 N A:CYS16 4.6 15.4 1.0 O3G A:DZ4501 4.6 18.2 1.0 O2A A:DZ4501 4.6 19.1 1.0 CA A:ASP15 4.6 14.3 1.0 O A:ASP13 4.6 15.3 1.0 N A:PHE17 4.7 12.9 1.0 CA A:ASP13 4.7 14.5 1.0 C A:ASP15 4.8 17.0 1.0 CB A:PHE17 4.8 15.2 1.0 O A:ASP115 4.9 17.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta Extension Complex with Cda at the -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:18.2 occ:1.00 OD2 A:ASP13 2.0 19.3 1.0 O A:HOH761 2.1 18.9 1.0 OD2 A:ASP115 2.2 16.2 1.0 OE2 A:GLU116 2.2 20.5 1.0 O1A A:DZ4501 2.2 16.8 1.0 O3' P:DG9 2.3 21.2 1.0 CG A:ASP13 3.1 15.1 1.0 CG A:ASP115 3.1 19.7 1.0 CD A:GLU116 3.2 23.0 1.0 C3' P:DG9 3.2 20.6 1.0 PA A:DZ4501 3.3 18.9 1.0 OD1 A:ASP115 3.4 15.6 1.0 OD1 A:ASP13 3.4 17.7 1.0 MG A:MG502 3.5 15.6 1.0 O2A A:DZ4501 3.7 19.1 1.0 O5' A:DZ4501 3.7 17.8 1.0 OE1 A:GLU116 3.9 25.9 1.0 OG A:SER113 3.9 18.6 1.0 C5' A:DZ4501 4.1 16.9 1.0 O A:HOH771 4.1 21.0 1.0 CG A:GLU116 4.1 16.7 1.0 C4' P:DG9 4.1 22.1 1.0 CB A:GLU116 4.1 16.2 1.0 O P:HOH103 4.2 25.2 1.0 NZ A:LYS224 4.2 23.1 1.0 CB A:ASP13 4.4 15.6 1.0 C2' P:DG9 4.4 26.6 1.0 CB A:ASP115 4.6 16.7 1.0 C A:ASP115 4.6 18.2 1.0 O A:ASP115 4.6 17.4 1.0 N3A A:DZ4501 4.7 18.2 1.0 O1G A:DZ4501 4.7 16.6 1.0 C5' P:DG9 4.7 24.2 1.0 N A:GLU116 4.9 14.7 1.0 O1B A:DZ4501 4.9 14.0 1.0 O A:HOH690 4.9 25.4 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