Magnesium in PDB 7m7m: Human Dna Pol Eta with Ra-Ended Primer and Dampnpp

All present enzymatic activity of Human Dna Pol Eta with Ra-Ended Primer and Dampnpp:
2.7.7.7;

The structure of Human Dna Pol Eta with Ra-Ended Primer and Dampnpp, PDB code: 7m7m was solved by M.T.Gregory, Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.31 / 1.46
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.444, 98.444, 82.105, 90, 90, 120
R / Rfree (%)	18.1 / 21.1

The binding sites of Magnesium atom in the Human Dna Pol Eta with Ra-Ended Primer and Dampnpp (pdb code 7m7m). 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 Pol Eta with Ra-Ended Primer and Dampnpp, PDB code: 7m7m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta with Ra-Ended Primer and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Pol Eta with Ra-Ended Primer and Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.6 occ:1.00 OD1 A:ASP13 2.0 10.1 1.0 OD1 A:ASP115 2.0 9.2 1.0 O A:MET14 2.1 9.3 1.0 O1G A:DZ4501 2.2 10.8 1.0 O1B A:DZ4501 2.2 8.9 1.0 O1A A:DZ4501 2.3 11.6 1.0 CG A:ASP13 3.0 10.9 1.0 CG A:ASP115 3.1 9.1 1.0 PB A:DZ4501 3.2 9.2 1.0 C A:MET14 3.3 9.6 1.0 PG A:DZ4501 3.4 9.8 1.0 PA A:DZ4501 3.4 10.0 1.0 OD2 A:ASP13 3.4 10.7 1.0 MG A:MG503 3.5 9.6 1.0 N3A A:DZ4501 3.5 9.6 1.0 O3B A:DZ4501 3.6 8.7 1.0 OD2 A:ASP115 3.6 9.8 1.0 NZ A:LYS231 3.7 9.6 1.0 O A:HOH743 3.8 13.7 1.0 N A:MET14 3.8 8.9 1.0 O2G A:DZ4501 3.9 10.1 1.0 CA A:MET14 4.0 8.8 1.0 C5' A:DZ4501 4.1 9.6 1.0 C A:ASP13 4.2 8.0 1.0 O5' A:DZ4501 4.2 9.5 1.0 CB A:ASP13 4.3 9.3 1.0 N A:ASP15 4.4 7.9 1.0 CB A:ASP115 4.4 9.7 1.0 O A:HOH779 4.4 12.2 1.0 N A:CYS16 4.5 9.7 1.0 CB A:MET14 4.5 11.4 1.0 CE A:LYS231 4.5 14.2 1.0 CA A:ASP15 4.5 9.3 1.0 O A:ASP13 4.6 10.2 1.0 O2B A:DZ4501 4.6 9.6 1.0 O2A A:DZ4501 4.6 11.8 1.0 O3G A:DZ4501 4.6 10.8 1.0 N A:PHE17 4.7 8.8 1.0 C A:ASP15 4.7 10.5 1.0 CA A:ASP13 4.7 9.7 1.0 CB A:PHE17 4.8 9.4 1.0 O A:ASP115 4.9 10.9 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta with Ra-Ended Primer and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Pol Eta with Ra-Ended Primer and Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:9.6 occ:1.00 OD2 A:ASP13 2.0 10.7 1.0 O A:HOH779 2.1 12.2 1.0 OD2 A:ASP115 2.1 9.8 1.0 O3' P:A9 2.1 12.7 1.0 OE2 A:GLU116 2.2 14.5 1.0 O1A A:DZ4501 2.2 11.6 1.0 CG A:ASP13 3.0 10.9 1.0 CG A:ASP115 3.1 9.1 1.0 CD A:GLU116 3.3 18.9 1.0 C3' P:A9 3.3 10.8 1.0 PA A:DZ4501 3.3 10.0 1.0 OD1 A:ASP115 3.4 9.2 1.0 OD1 A:ASP13 3.4 10.1 1.0 MG A:MG502 3.5 8.6 1.0 O2A A:DZ4501 3.7 11.8 1.0 OG A:SER113 3.8 12.6 1.0 O5' A:DZ4501 3.9 9.5 1.0 O A:HOH743 3.9 13.7 1.0 OE1 A:GLU116 4.0 19.1 1.0 C4' P:A9 4.0 12.9 1.0 C5' A:DZ4501 4.1 9.6 1.0 CG A:GLU116 4.1 12.8 1.0 CB A:GLU116 4.2 12.1 1.0 C5' P:A9 4.2 14.8 1.0 CB A:ASP13 4.3 9.3 1.0 NZ A:LYS224 4.3 16.7 1.0 CB A:ASP115 4.5 9.7 1.0 C2' P:A9 4.5 13.0 1.0 O2' P:A9 4.6 16.6 1.0 C A:ASP115 4.6 10.5 1.0 O A:ASP115 4.6 10.9 1.0 O1G A:DZ4501 4.6 10.8 1.0 N3A A:DZ4501 4.7 9.6 1.0 O5' P:A9 4.8 15.3 1.0 N A:GLU116 4.8 10.6 1.0 CB A:SER113 4.9 13.5 1.0 O A:HOH733 4.9 20.4 1.0 O1B A:DZ4501 4.9 8.9 1.0 CA A:ASP115 5.0 9.4 1.0

M.T.Gregory, Y.Gao, Q.Cui, W.Yang. Multiple Deprotonation Paths of the Nucleophile 3'-Oh in the Dna Synthesis Reaction Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490