Magnesium in PDB 7m84: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S

All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m84 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)	29.91 / 1.47
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.104, 98.104, 82.126, 90, 90, 120
R / Rfree (%)	17.2 / 19.9

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S (pdb code 7m84). 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 Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S


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 Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.3 occ:0.40 CA A:CA501 0.0 7.9 0.6 OD1 A:ASP13 2.1 12.3 0.7 OD2 A:ASP115 2.2 12.4 1.0 O A:MET14 2.3 10.7 1.0 O3G A:DTP506 2.3 11.7 1.0 OD2 A:ASP13 2.4 11.3 0.3 O1B A:DTP506 2.4 9.3 1.0 O2A A:DTP506 2.4 11.3 1.0 OD1 A:ASP13 2.7 16.0 0.3 CG A:ASP13 2.8 13.2 0.3 CG A:ASP13 3.3 14.4 0.7 CG A:ASP115 3.3 11.5 1.0 PB A:DTP506 3.4 9.0 1.0 C A:MET14 3.5 8.6 1.0 MG A:MG507 3.5 13.6 0.6 PG A:DTP506 3.6 9.9 1.0 PA A:DTP506 3.6 11.1 1.0 O3A A:DTP506 3.7 9.8 1.0 OD1 A:ASP115 3.8 12.8 1.0 O3B A:DTP506 3.8 9.3 1.0 OD2 A:ASP13 3.8 21.2 0.7 N A:MET14 3.9 9.4 1.0 NZ A:LYS231 3.9 14.7 1.0 O A:HOH616 4.0 27.3 1.0 C5' A:DTP506 4.1 9.6 1.0 O2G A:DTP506 4.2 11.8 1.0 CA A:MET14 4.2 8.8 1.0 C A:ASP13 4.2 10.5 1.0 CB A:ASP13 4.3 12.3 0.3 O5' A:DTP506 4.3 10.8 1.0 O A:HOH862 4.4 34.9 1.0 CB A:ASP13 4.5 11.6 0.7 N A:ASP15 4.5 8.3 1.0 N A:CYS16 4.6 8.6 1.0 CB A:ASP115 4.6 10.2 1.0 O A:ASP13 4.6 11.9 1.0 CE A:LYS231 4.6 21.2 1.0 CA A:ASP15 4.6 8.6 1.0 CA A:ASP13 4.7 11.8 0.7 CB A:MET14 4.7 11.3 1.0 CA A:ASP13 4.7 11.9 0.3 O3' P:DA8 4.7 13.9 0.3 O1A A:DTP506 4.8 12.8 1.0 O2B A:DTP506 4.8 10.2 1.0 O1G A:DTP506 4.8 12.1 1.0 N A:PHE17 4.8 8.4 1.0 C A:ASP15 4.8 9.2 1.0 CB A:PHE17 4.9 7.5 1.0 O A:ASP115 4.9 11.9 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S


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 Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:13.6 occ:0.55 O3' P:DA8 2.0 13.9 0.3 OD1 A:ASP13 2.2 16.0 0.3 OE2 A:GLU116 2.2 24.1 0.6 OD1 A:ASP115 2.4 12.8 1.0 O A:HOH616 2.5 27.3 1.0 CG A:GLU116 2.6 21.1 0.6 O2A A:DTP506 2.6 11.3 1.0 CG A:GLU116 2.7 21.0 0.5 CD A:GLU116 2.8 20.5 0.6 CD A:GLU116 2.8 20.5 0.5 OE1 A:GLU116 2.9 17.2 0.5 C3' P:DA8 3.0 10.0 0.7 O3' P:DA8 3.1 14.5 0.7 OD1 A:ASP13 3.2 12.3 0.7 C3' P:DA8 3.3 17.1 0.3 CG A:ASP115 3.3 11.5 1.0 CG A:ASP13 3.4 13.2 0.3 C4' P:DA8 3.4 15.8 0.7 OE2 A:GLU116 3.5 18.1 0.5 OD2 A:ASP115 3.5 12.4 1.0 MG A:MG502 3.5 8.3 0.4 OD2 A:ASP13 3.6 21.2 0.7 CA A:CA501 3.6 7.9 0.6 CG A:ASP13 3.6 14.4 0.7 C5' P:DA8 3.6 19.5 0.7 PA A:DTP506 3.8 11.1 1.0 C4' P:DA8 3.9 15.0 0.3 CB A:GLU116 4.0 14.8 1.0 OE1 A:GLU116 4.0 19.9 0.6 OD2 A:ASP13 4.1 11.3 0.3 O5' A:DTP506 4.3 10.8 1.0 O1A A:DTP506 4.3 12.8 1.0 C5' A:DTP506 4.3 9.6 1.0 C2' P:DA8 4.4 16.8 0.7 C2' P:DA8 4.4 16.3 0.3 CB A:ASP13 4.4 12.3 0.3 C5' P:DA8 4.5 22.1 0.3 C A:ASP115 4.5 10.2 1.0 O A:ASP115 4.6 11.9 1.0 N A:GLU116 4.7 9.8 1.0 CB A:ASP115 4.7 10.2 1.0 NZ A:LYS224 4.7 28.7 1.0 CB A:ASP13 4.8 11.6 0.7 CA A:GLU116 4.8 12.2 1.0 CB A:ALA113 4.8 13.9 1.0 O5' P:DA8 4.8 22.4 0.7 O4' P:DA8 4.8 14.4 0.7 OP1 P:DA8 4.9 29.9 0.7 O P:HOH101 5.0 34.3 1.0 O3G A:DTP506 5.0 11.7 1.0 O5' P:DA8 5.0 20.2 0.3

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