Magnesium in PDB 7m7o: Human Dna Pol Eta with Dt-Ended Primer and 0.1 Mm Dampnpp

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

The structure of Human Dna Pol Eta with Dt-Ended Primer and 0.1 Mm Dampnpp, PDB code: 7m7o 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)	30.04 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.589, 98.589, 82.196, 90, 90, 120
R / Rfree (%)	18 / 22.4

The binding sites of Magnesium atom in the Human Dna Pol Eta with Dt-Ended Primer and 0.1 Mm Dampnpp (pdb code 7m7o). 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 Dt-Ended Primer and 0.1 Mm Dampnpp, PDB code: 7m7o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta 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 with Dt-Ended Primer and 0.1 Mm Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.9 occ:1.00 O1G A:DZ4501 2.1 12.7 1.0 OD1 A:ASP13 2.1 13.1 1.0 O A:MET14 2.1 10.2 1.0 O1B A:DZ4501 2.1 10.9 1.0 OD1 A:ASP115 2.2 11.5 1.0 O1A A:DZ4501 2.3 12.7 1.0 PB A:DZ4501 3.0 13.3 1.0 CG A:ASP13 3.1 11.6 1.0 CG A:ASP115 3.2 11.6 1.0 PG A:DZ4501 3.3 16.5 1.0 C A:MET14 3.3 7.8 1.0 PA A:DZ4501 3.4 15.4 1.0 N3A A:DZ4501 3.4 12.8 1.0 O3B A:DZ4501 3.4 13.8 1.0 OD2 A:ASP13 3.5 15.5 1.0 MG A:MG503 3.6 13.6 1.0 NZ A:LYS231 3.7 10.0 1.0 OD2 A:ASP115 3.7 10.9 1.0 O A:HOH708 3.8 18.4 1.0 N A:MET14 3.8 10.1 1.0 O2G A:DZ4501 3.9 11.4 1.0 CA A:MET14 4.1 10.5 1.0 C5' A:DZ4501 4.1 12.6 1.0 C A:ASP13 4.2 9.7 1.0 O5' A:DZ4501 4.3 13.9 1.0 N A:ASP15 4.3 8.3 1.0 O A:HOH736 4.3 12.4 1.0 CB A:ASP13 4.4 11.6 1.0 N A:CYS16 4.4 11.8 1.0 O2B A:DZ4501 4.4 11.5 1.0 CA A:ASP15 4.5 10.9 1.0 CB A:ASP115 4.5 11.1 1.0 O3G A:DZ4501 4.5 12.7 1.0 CE A:LYS231 4.5 17.2 1.0 O A:ASP13 4.5 9.2 1.0 CB A:MET14 4.6 16.3 1.0 O2A A:DZ4501 4.6 14.1 1.0 C A:ASP15 4.6 16.5 1.0 N A:PHE17 4.7 8.8 1.0 CA A:ASP13 4.7 10.8 1.0 CB A:PHE17 4.9 8.6 1.0 O A:ASP115 5.0 13.2 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta 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 with Dt-Ended Primer and 0.1 Mm Dampnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.6 occ:1.00 OD2 A:ASP115 2.0 10.9 1.0 OD2 A:ASP13 2.1 15.5 1.0 OE2 A:GLU116 2.1 15.6 1.0 O A:HOH736 2.1 12.4 1.0 O1A A:DZ4501 2.2 12.7 1.0 O3' P:DT9 2.2 16.0 1.0 CG A:ASP115 3.0 11.6 1.0 CG A:ASP13 3.1 11.6 1.0 CD A:GLU116 3.2 17.8 1.0 C3' P:DT9 3.2 13.1 1.0 OD1 A:ASP115 3.3 11.5 1.0 PA A:DZ4501 3.3 15.4 1.0 OD1 A:ASP13 3.4 13.1 1.0 MG A:MG502 3.6 13.9 1.0 O2A A:DZ4501 3.7 14.1 1.0 OE1 A:GLU116 3.9 19.6 1.0 O5' A:DZ4501 3.9 13.9 1.0 OG A:SER113 3.9 14.9 1.0 C4' P:DT9 4.1 13.3 1.0 C5' A:DZ4501 4.1 12.6 1.0 CB A:GLU116 4.1 15.0 1.0 O A:HOH708 4.1 18.4 1.0 CG A:GLU116 4.1 14.9 1.0 NZ A:LYS224 4.3 14.4 1.0 O P:HOH108 4.4 13.8 1.0 CB A:ASP115 4.4 11.1 1.0 CB A:ASP13 4.4 11.6 1.0 C2' P:DT9 4.5 13.3 1.0 C A:ASP115 4.6 13.9 1.0 O A:ASP115 4.6 13.2 1.0 N3A A:DZ4501 4.7 12.8 1.0 O1G A:DZ4501 4.7 12.7 1.0 C5' P:DT9 4.8 15.7 1.0 N A:GLU116 4.8 11.5 1.0 O A:HOH720 4.8 21.9 1.0 O1B A:DZ4501 4.9 10.9 1.0 CA A:ASP115 4.9 11.3 1.0 CB A:SER113 5.0 15.9 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