Magnesium in PDB 7m7u: Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S

All present enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S, PDB code: 7m7u 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)	29.47 / 1.94
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.215, 98.215, 81.728, 90, 90, 120
R / Rfree (%)	17.9 / 22.2

The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S (pdb code 7m7u). 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 Datp: in Crystallo Reaction For 480S, PDB code: 7m7u:
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 Datp: in Crystallo Reaction For 480S


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 Datp: in Crystallo Reaction For 480S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.8 occ:0.50 CA A:CA501 0.0 23.0 0.2 O1B A:DTP507 2.1 21.9 0.5 O A:MET14 2.1 20.3 1.0 OD2 A:ASP115 2.2 21.9 0.7 O A:HOH865 2.2 18.4 0.5 OD1 A:ASP13 2.2 23.3 0.7 O3G A:DTP507 2.3 21.0 0.5 O2A A:DTP507 2.7 22.1 0.5 OD1 A:ASP13 2.8 22.2 0.3 MG A:MG503 3.1 22.2 0.3 OD2 A:ASP13 3.1 26.7 0.3 PB A:DTP507 3.1 20.4 0.5 CG A:ASP13 3.2 22.4 0.3 PG A:DTP507 3.3 22.6 0.5 C A:MET14 3.3 17.5 1.0 CG A:ASP13 3.3 23.9 0.7 CG A:ASP115 3.4 21.2 0.7 O3B A:DTP507 3.5 21.3 0.5 O3A A:DTP507 3.6 21.4 0.5 O2G A:DTP507 3.6 21.9 0.5 PA A:DTP507 3.6 27.0 0.5 OD2 A:ASP115 3.7 18.5 0.3 O A:HOH617 3.7 21.8 1.0 N A:MET14 3.9 13.9 1.0 OD1 A:ASP115 4.0 23.0 0.7 C5' A:DTP507 4.0 23.1 0.5 OD2 A:ASP13 4.1 33.9 0.7 CG A:ASP115 4.1 22.3 0.3 C A:ASP13 4.2 19.4 0.3 CA A:MET14 4.2 16.4 1.0 O A:ASP115 4.2 18.9 0.3 C A:ASP13 4.2 19.0 0.7 N A:CYS16 4.2 19.8 1.0 CB A:ASP115 4.3 19.2 0.3 N A:ASP15 4.3 15.2 1.0 O5' A:DTP507 4.3 23.4 0.5 CA A:ASP15 4.3 17.4 1.0 CB A:ASP13 4.3 21.1 0.7 O A:HOH688 4.3 27.0 0.3 CB A:ASP13 4.4 21.1 0.3 C A:ASP15 4.4 18.8 1.0 O2B A:DTP507 4.5 19.1 0.5 CB A:ASP115 4.5 19.9 0.7 O A:ASP13 4.6 18.7 0.3 CA A:ASP13 4.6 19.9 0.7 CA A:ASP13 4.6 19.9 0.3 O1G A:DTP507 4.6 25.0 0.5 O A:ASP13 4.6 17.9 0.7 N A:PHE17 4.6 14.9 1.0 CB A:MET14 4.7 19.1 1.0 O A:ASP115 4.8 19.2 0.7 OD1 A:ASP115 4.9 18.6 0.3 O1A A:DTP507 4.9 25.2 0.5 CA A:CYS16 4.9 17.7 1.0 CB A:PHE17 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S


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 Datp: in Crystallo Reaction For 480S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:22.2 occ:0.30 OD2 A:ASP13 2.0 26.7 0.3 O2A A:DTP507 2.2 22.1 0.5 O A:HOH688 2.3 27.0 0.3 OD1 A:ASP115 2.3 23.0 0.7 OD1 A:ASP13 2.4 23.3 0.7 OD2 A:ASP115 2.8 21.9 0.7 O3' P:DT8 2.8 24.7 0.5 CG A:ASP115 2.9 21.2 0.7 OD1 A:ASP115 2.9 18.6 0.3 CG A:ASP13 3.0 23.9 0.7 OE2 A:GLU116 3.0 38.1 1.0 CG A:ASP115 3.0 22.3 0.3 OD2 A:ASP13 3.1 33.9 0.7 CA A:CA501 3.1 23.0 0.2 MG A:MG502 3.1 22.8 0.5 CG A:ASP13 3.2 22.4 0.3 O A:ASP115 3.2 18.9 0.3 OD2 A:ASP115 3.2 18.5 0.3 PA A:DTP507 3.6 27.0 0.5 C3' P:DT8 3.6 26.1 0.5 OD1 A:ASP13 3.8 22.2 0.3 CB A:GLU116 3.8 22.0 1.0 C A:ASP115 3.9 19.8 0.3 CB A:ASP115 3.9 19.2 0.3 CD A:GLU116 4.0 28.6 1.0 O5' A:DTP507 4.0 23.4 0.5 C5' A:DTP507 4.1 23.1 0.5 CG A:GLU116 4.2 25.3 1.0 O A:ASP115 4.2 19.2 0.7 O3G A:DTP507 4.2 21.0 0.5 O A:HOH865 4.3 18.4 0.5 CB A:ASP115 4.3 19.9 0.7 C A:ASP115 4.3 22.0 0.7 CB A:ASP13 4.3 21.1 0.3 O1A A:DTP507 4.3 25.2 0.5 CB A:ASP13 4.4 21.1 0.7 O1B A:DTP507 4.5 21.9 0.5 CA A:ASP115 4.5 18.7 0.3 C4' P:DT8 4.6 27.3 0.5 N A:GLU116 4.6 18.4 1.0 CA A:GLU116 4.6 19.1 1.0 O3A A:DTP507 4.6 21.4 0.5 CA A:ASP13 4.7 19.9 0.3 CA A:ASP13 4.7 19.9 0.7 CA A:ASP115 4.8 18.5 0.7 C2' P:DT8 4.8 26.7 0.5 O A:MET14 4.9 20.3 1.0 NZ A:LYS224 4.9 26.6 0.7 C4' P:DT8 5.0 27.4 0.5 O3' P:DT8 5.0 25.8 0.5

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