Magnesium in PDB 7m7s: Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp

All present enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp, PDB code: 7m7s 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)	31.49 / 1.85
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.676, 98.676, 81.832, 90, 90, 120
R / Rfree (%)	18 / 22.8

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm Dampnpp (pdb code 7m7s). 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 0.1 Mm Dampnpp, PDB code: 7m7s:
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 0.1 Mm 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 0.1 Mm Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.4 occ:0.30 OD2 A:ASP13 2.0 17.8 0.3 O A:HOH767 2.1 10.9 0.7 O1B A:DZ4501 2.1 19.0 0.3 O A:MET14 2.1 21.3 1.0 OD1 A:ASP115 2.3 19.4 0.5 O1G A:DZ4501 2.6 26.6 0.3 O1A A:DZ4501 2.7 21.1 0.3 CG A:ASP13 2.9 13.9 0.3 PB A:DZ4501 3.0 16.3 0.3 O3B A:DZ4501 3.1 14.5 0.3 PG A:DZ4501 3.2 36.1 0.3 OD1 A:ASP13 3.2 18.3 0.3 C A:MET14 3.3 14.5 1.0 CG A:ASP115 3.4 20.1 0.5 O2G A:DZ4501 3.4 34.4 0.3 MG A:MG503 3.5 18.2 0.3 N3A A:DZ4501 3.5 20.5 0.3 PA A:DZ4501 3.6 26.1 0.3 O A:HOH615 3.7 18.3 0.9 OD2 A:ASP115 3.8 10.2 0.5 OD2 A:ASP115 3.9 22.0 0.5 N A:CYS16 3.9 17.9 1.0 O A:HOH610 4.0 29.8 1.0 N A:MET14 4.0 12.8 1.0 CA A:ASP15 4.1 15.1 1.0 N A:ASP15 4.2 11.1 1.0 CG A:ASP115 4.2 19.0 0.5 CB A:ASP13 4.2 13.9 0.3 CA A:MET14 4.2 10.1 1.0 CB A:ASP13 4.2 13.6 0.7 C A:ASP15 4.3 20.4 1.0 C A:ASP13 4.3 11.8 1.0 O2B A:DZ4501 4.4 21.2 0.3 CB A:ASP115 4.4 10.5 0.5 CG A:ASP13 4.5 21.9 0.7 CB A:ASP115 4.5 10.6 0.5 N A:PHE17 4.6 15.4 1.0 O3G A:DZ4501 4.7 21.4 0.3 O A:ASP115 4.7 15.9 1.0 O5' A:DZ4501 4.7 28.4 0.3 CA A:CYS16 4.7 16.8 1.0 OD2 A:ASP13 4.7 21.7 0.7 CA A:ASP13 4.7 14.1 0.7 CA A:ASP13 4.8 14.1 0.3 O2A A:DZ4501 4.8 29.9 0.3 O A:ASP13 4.8 12.2 1.0 CB A:MET14 4.8 13.7 1.0 C4' A:DZ4501 4.8 18.9 0.3 OD1 A:ASP115 5.0 8.3 0.5

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and 0.1 Mm 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 0.1 Mm Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:18.2 occ:0.30 OD1 A:ASP13 2.0 18.3 0.3 O A:HOH610 2.1 29.8 1.0 OD2 A:ASP115 2.2 22.0 0.5 O1A A:DZ4501 2.2 21.1 0.3 O3' P:DT9 2.2 21.4 0.3 OD1 A:ASP115 2.8 8.3 0.5 CG A:ASP115 2.8 20.1 0.5 OD1 A:ASP115 2.8 19.4 0.5 C3' P:DT9 2.9 21.9 0.3 CG A:ASP115 3.0 19.0 0.5 OD2 A:ASP13 3.1 21.7 0.7 CG A:ASP13 3.1 13.9 0.3 OD2 A:ASP115 3.2 10.2 0.5 MG A:MG502 3.5 16.4 0.3 PA A:DZ4501 3.5 26.1 0.3 OD2 A:ASP13 3.6 17.8 0.3 OE2 A:GLU116 3.6 28.7 1.0 CG A:ASP13 3.7 21.9 0.7 C2' P:DT9 3.9 25.4 0.3 CB A:GLU116 3.9 17.3 1.0 O2A A:DZ4501 3.9 29.9 0.3 O A:ASP115 3.9 15.9 1.0 CB A:ASP115 4.0 10.5 0.5 C4' P:DT9 4.1 25.8 0.3 OD1 A:ASP13 4.2 20.5 0.7 C A:ASP115 4.2 16.8 1.0 CB A:ASP115 4.3 10.6 0.5 O A:HOH767 4.3 10.9 0.7 C4' P:DT9 4.3 25.6 0.7 CB A:ASP13 4.4 13.9 0.3 O5' A:DZ4501 4.4 28.4 0.3 CD A:GLU116 4.4 33.3 1.0 O1G A:DZ4501 4.4 26.6 0.3 O3' P:DT9 4.5 25.8 0.7 CB A:ASP13 4.5 13.6 0.7 C5' P:DT9 4.6 30.7 0.7 O1B A:DZ4501 4.6 19.0 0.3 N3A A:DZ4501 4.7 20.5 0.3 CA A:ASP115 4.7 11.6 0.5 CG A:GLU116 4.7 24.5 1.0 N A:GLU116 4.7 14.7 1.0 CA A:GLU116 4.7 16.3 1.0 CA A:ASP115 4.8 11.6 0.5 C5' P:DT9 4.9 31.8 0.3 C1' P:DT9 5.0 24.1 0.3 CA A:ASP13 5.0 14.1 0.7 CA A:ASP13 5.0 14.1 0.3 C3' P:DT9 5.0 26.1 0.7

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