Magnesium in PDB 7m85: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 80 S

All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 80 S:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 80 S, PDB code: 7m85 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)	25.95 / 1.75
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.362, 98.362, 81.751, 90, 90, 120
R / Rfree (%)	17.4 / 21.2

The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 80 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 80 S (pdb code 7m85). 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 80 S, PDB code: 7m85:
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 80 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 80 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.6 occ:0.50 CA A:CA501 0.1 11.2 0.5 OD1 A:ASP13 2.2 12.9 0.3 O3G A:DTP504 2.2 13.8 1.0 O A:MET14 2.2 13.0 1.0 O1B A:DTP504 2.3 12.6 1.0 OD2 A:ASP115 2.3 17.0 1.0 OD2 A:ASP13 2.3 18.3 0.7 O2A A:DTP504 2.5 14.6 1.0 CG A:ASP13 2.9 15.3 0.7 OD1 A:ASP13 2.9 22.2 0.7 CG A:ASP13 3.3 16.2 0.3 PB A:DTP504 3.3 13.8 1.0 CG A:ASP115 3.4 14.6 1.0 C A:MET14 3.4 12.6 1.0 PG A:DTP504 3.5 13.8 1.0 MG A:MG505 3.6 18.7 0.7 PA A:DTP504 3.6 15.1 1.0 O3A A:DTP504 3.6 12.9 1.0 O3B A:DTP504 3.7 12.4 1.0 OD2 A:ASP13 3.8 18.9 0.3 OD1 A:ASP115 3.8 13.4 1.0 N A:MET14 4.0 12.4 1.0 NZ A:LYS231 4.0 14.9 1.0 O2G A:DTP504 4.1 13.2 1.0 O A:HOH692 4.1 26.5 1.0 C5' A:DTP504 4.1 13.4 1.0 CA A:MET14 4.2 13.4 1.0 C A:ASP13 4.2 13.1 1.0 CB A:ASP13 4.3 14.5 0.7 O5' A:DTP504 4.3 14.2 1.0 O A:HOH887 4.3 32.6 1.0 N A:ASP15 4.4 10.4 1.0 CB A:ASP13 4.5 14.8 0.3 N A:CYS16 4.5 12.5 1.0 CA A:ASP15 4.6 12.3 1.0 O2B A:DTP504 4.6 12.8 1.0 CE A:LYS231 4.6 25.9 1.0 CB A:ASP115 4.6 13.5 1.0 O1G A:DTP504 4.7 14.4 1.0 O A:ASP13 4.7 13.6 1.0 CB A:MET14 4.7 15.4 1.0 C A:ASP15 4.7 15.7 1.0 CA A:ASP13 4.7 14.4 0.3 CA A:ASP13 4.7 14.4 0.7 O1A A:DTP504 4.7 17.2 1.0 N A:PHE17 4.7 10.7 1.0 O3' P:DA8 4.8 17.2 0.4 CB A:PHE17 4.9 10.4 1.0 O A:ASP115 5.0 14.1 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 80 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 80 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:18.7 occ:0.65 O3' P:DA8 2.0 17.2 0.4 OD1 A:ASP13 2.1 22.2 0.7 OD1 A:ASP115 2.4 13.4 1.0 O A:HOH692 2.4 26.5 1.0 OE2 A:GLU116 2.4 27.2 0.7 O2A A:DTP504 2.5 14.6 1.0 CG A:GLU116 2.6 21.6 0.3 CG A:GLU116 2.7 22.0 0.7 CD A:GLU116 2.7 23.3 0.3 CD A:GLU116 2.9 23.6 0.7 OE2 A:GLU116 3.0 24.3 0.3 C3' P:DA8 3.1 14.9 0.6 OD1 A:ASP13 3.1 12.9 0.3 O3' P:DA8 3.2 17.7 0.6 CG A:ASP115 3.2 14.6 1.0 C3' P:DA8 3.3 20.2 0.4 CG A:ASP13 3.3 15.3 0.7 OD2 A:ASP13 3.4 18.9 0.3 OE1 A:GLU116 3.4 22.7 0.3 CA A:CA501 3.4 11.2 0.5 OD2 A:ASP115 3.4 17.0 1.0 CG A:ASP13 3.5 16.2 0.3 MG A:MG502 3.6 11.6 0.5 C4' P:DA8 3.6 22.1 0.6 PA A:DTP504 3.7 15.1 1.0 C5' P:DA8 3.8 22.6 0.6 C4' P:DA8 4.0 22.3 0.4 OD2 A:ASP13 4.0 18.3 0.7 CB A:GLU116 4.1 17.7 1.0 OE1 A:GLU116 4.1 24.1 0.7 O5' A:DTP504 4.2 14.2 1.0 O1A A:DTP504 4.2 17.2 1.0 C5' A:DTP504 4.3 13.4 1.0 C2' P:DA8 4.4 20.1 0.4 CB A:ASP13 4.5 14.5 0.7 C A:ASP115 4.5 15.3 1.0 C2' P:DA8 4.5 20.8 0.6 O A:ASP115 4.5 14.1 1.0 C5' P:DA8 4.5 25.2 0.4 N A:GLU116 4.6 14.0 1.0 CB A:ASP115 4.6 13.5 1.0 CB A:ASP13 4.7 14.8 0.3 CA A:GLU116 4.8 13.6 1.0 O A:HOH887 4.9 32.6 1.0 CB A:ALA113 4.9 16.9 1.0 O3G A:DTP504 4.9 13.8 1.0 O5' P:DA8 4.9 26.6 0.6 CA A:ASP115 5.0 13.4 1.0 O3A A:DTP504 5.0 12.9 1.0 O4' P:DA8 5.0 19.8 0.6

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