Magnesium in PDB 7m7q: Human Dna Pol Eta S113A with Dt-Ended Primer and Dampnpp

All present enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and Dampnpp:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and Dampnpp, PDB code: 7m7q 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)	32.38 / 2.27
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.927, 98.927, 81.807, 90, 90, 120
R / Rfree (%)	16.9 / 22.4

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Dt-Ended Primer and Dampnpp (pdb code 7m7q). 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 S113A with Dt-Ended Primer and Dampnpp, PDB code: 7m7q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta S113A with Dt-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 S113A with Dt-Ended Primer and Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.9 occ:1.00 O1G A:DZ4501 2.0 15.4 1.0 O1B A:DZ4501 2.1 12.7 1.0 OD1 A:ASP13 2.2 18.9 1.0 O A:MET14 2.2 14.4 1.0 OD2 A:ASP115 2.3 15.8 1.0 O1A A:DZ4501 2.3 15.1 1.0 PB A:DZ4501 3.1 15.2 1.0 PG A:DZ4501 3.1 18.7 1.0 CG A:ASP13 3.2 14.5 1.0 PA A:DZ4501 3.3 18.4 1.0 O3B A:DZ4501 3.4 16.3 1.0 N3A A:DZ4501 3.4 15.8 1.0 C A:MET14 3.4 13.7 1.0 CG A:ASP115 3.4 18.0 1.0 MG A:MG503 3.6 13.1 1.0 OD2 A:ASP13 3.6 19.6 1.0 O A:HOH650 3.7 18.2 1.0 NZ A:LYS231 3.7 14.2 1.0 O2G A:DZ4501 3.8 13.9 1.0 OD1 A:ASP115 3.9 15.8 1.0 N A:MET14 4.0 12.9 1.0 C5' A:DZ4501 4.1 14.2 1.0 O5' A:DZ4501 4.2 17.9 1.0 O A:HOH687 4.2 15.6 1.0 CA A:MET14 4.2 13.5 1.0 C A:ASP13 4.3 13.6 1.0 O3G A:DZ4501 4.4 20.2 1.0 N A:ASP15 4.4 11.3 1.0 CE A:LYS231 4.4 22.6 1.0 N A:CYS16 4.4 15.7 1.0 CB A:ASP13 4.4 18.9 1.0 O2B A:DZ4501 4.5 14.0 1.0 O2A A:DZ4501 4.5 18.5 1.0 CA A:ASP15 4.5 12.9 1.0 C A:ASP15 4.7 17.2 1.0 CB A:MET14 4.7 20.5 1.0 O A:ASP13 4.7 13.1 1.0 CB A:ASP115 4.7 11.3 1.0 N A:PHE17 4.7 10.2 1.0 CA A:ASP13 4.9 16.1 1.0 CB A:PHE17 5.0 12.7 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Dt-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 S113A with Dt-Ended Primer and Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.1 occ:1.00 OD2 A:ASP13 2.1 19.6 1.0 O A:HOH687 2.1 15.6 1.0 O1A A:DZ4501 2.2 15.1 1.0 OD1 A:ASP115 2.2 15.8 1.0 OE2 A:GLU116 2.2 20.1 1.0 O3' P:DT9 2.3 19.8 1.0 CG A:ASP13 3.1 14.5 1.0 CG A:ASP115 3.1 18.0 1.0 C3' P:DT9 3.2 17.4 1.0 OD2 A:ASP115 3.3 15.8 1.0 CD A:GLU116 3.3 25.6 1.0 PA A:DZ4501 3.4 18.4 1.0 OD1 A:ASP13 3.4 18.9 1.0 MG A:MG502 3.6 17.9 1.0 O2A A:DZ4501 3.8 18.5 1.0 O5' A:DZ4501 3.8 17.9 1.0 C5' A:DZ4501 4.0 14.2 1.0 C4' P:DT9 4.1 22.3 1.0 O A:HOH650 4.1 18.2 1.0 OE1 A:GLU116 4.1 30.7 1.0 CG A:GLU116 4.2 18.6 1.0 CB A:GLU116 4.2 17.1 1.0 C2' P:DT9 4.4 20.5 1.0 O P:HOH111 4.4 17.3 1.0 NZ A:LYS224 4.4 22.4 1.0 CB A:ASP13 4.4 18.9 1.0 CB A:ASP115 4.6 11.3 1.0 O A:ASP115 4.6 18.3 1.0 O1G A:DZ4501 4.6 15.4 1.0 C A:ASP115 4.7 15.9 1.0 N3A A:DZ4501 4.8 15.8 1.0 C5' P:DT9 4.8 22.1 1.0 N A:GLU116 4.9 18.7 1.0 O1B A:DZ4501 4.9 12.7 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