Magnesium in PDB 7m8a: Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S

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

The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m8a 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)	29.98 / 1.91
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.393, 98.393, 82.025, 90, 90, 120
R / Rfree (%)	16.6 / 21.5

The structure of Human Dna Pol Eta S113A with Ra-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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S (pdb code 7m8a). 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m8a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta S113A with Ra-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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.4 occ:0.55 CA A:CA501 0.1 24.3 0.3 O5 A:DPO507 2.0 21.1 0.4 O1B A:DTP506 2.1 18.6 0.4 O1 A:DPO507 2.2 18.7 0.4 O3G A:DTP506 2.2 22.6 0.4 OD1 A:ASP13 2.2 22.6 0.7 OD2 A:ASP115 2.2 32.3 1.0 O A:MET14 2.4 20.9 1.0 OD2 A:ASP13 2.4 23.3 0.3 OP1 P:DA9 2.5 23.0 0.5 O2A A:DTP506 2.5 23.0 0.4 OD1 A:ASP13 2.8 28.2 0.3 CG A:ASP13 2.9 23.8 0.3 MG A:MG508 3.0 26.5 0.3 PB A:DTP506 3.1 25.3 0.4 P2 A:DPO507 3.2 26.0 0.4 P1 A:DPO507 3.3 24.8 0.4 PG A:DTP506 3.3 27.8 0.4 CG A:ASP13 3.3 26.5 0.7 CG A:ASP115 3.4 31.3 1.0 O4 A:DPO507 3.5 22.2 0.4 O3B A:DTP506 3.5 21.8 0.4 O3A A:DTP506 3.5 24.5 0.4 PA A:DTP506 3.6 25.7 0.4 C A:MET14 3.6 16.0 1.0 O2G A:DTP506 3.8 18.8 0.4 P P:DA9 3.9 24.6 0.5 O A:HOH604 3.9 23.8 1.0 O6 A:DPO507 3.9 20.4 0.4 OD2 A:ASP13 3.9 37.4 0.7 O2 A:DPO507 3.9 27.0 0.4 C5' A:DTP506 4.0 24.8 0.4 OD1 A:ASP115 4.1 26.1 1.0 O A:HOH733 4.1 38.4 1.0 N A:MET14 4.2 15.8 1.0 C5' P:DA9 4.2 24.5 0.5 O5' A:DTP506 4.3 25.0 0.4 O5' P:DA9 4.3 25.1 0.5 CB A:ASP13 4.3 20.1 0.3 N A:CYS16 4.3 15.7 1.0 C A:ASP13 4.4 16.8 0.7 C A:ASP13 4.4 16.9 0.3 CA A:MET14 4.4 13.1 1.0 O2B A:DTP506 4.4 19.0 0.4 O7 A:DPO507 4.5 25.1 0.4 CB A:ASP115 4.5 16.2 1.0 CB A:ASP13 4.5 19.5 0.7 N A:ASP15 4.5 14.1 1.0 NZ A:LYS231 4.5 41.8 1.0 O3 A:DPO507 4.5 20.4 0.4 CA A:ASP15 4.6 13.8 1.0 O1G A:DTP506 4.6 24.7 0.4 O3' P:A8 4.6 29.9 0.5 C A:ASP15 4.7 18.8 1.0 O3' P:A8 4.7 29.9 0.6 N A:PHE17 4.7 12.7 1.0 O A:ASP13 4.8 15.6 0.7 CA A:ASP13 4.8 19.8 0.7 O1A A:DTP506 4.8 27.2 0.4 CA A:ASP13 4.8 19.6 0.3 O A:ASP13 4.8 15.7 0.3 O A:ASP115 4.9 18.2 1.0 CB A:MET14 4.9 18.4 1.0 OP2 P:DA9 5.0 27.3 0.5 CA A:CYS16 5.0 20.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta S113A with Ra-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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:26.5 occ:0.30 OD1 A:ASP13 2.1 28.2 0.3 O2A A:DTP506 2.1 23.0 0.4 OP1 P:DA9 2.1 23.0 0.5 O3' P:A8 2.3 29.9 0.6 O A:HOH733 2.3 38.4 1.0 OD1 A:ASP115 2.5 26.1 1.0 O3' P:A8 2.5 29.9 0.5 OD2 A:ASP115 2.7 32.3 1.0 OE2 A:GLU116 2.7 39.3 0.5 OE2 A:GLU116 2.7 39.3 0.5 OD1 A:ASP13 2.8 22.6 0.7 P P:DA9 2.9 24.6 0.5 CG A:ASP115 2.9 31.3 1.0 CA A:CA501 3.0 24.3 0.3 MG A:MG502 3.0 24.4 0.6 OD2 A:ASP13 3.1 37.4 0.7 CG A:ASP13 3.2 23.8 0.3 CG A:ASP13 3.3 26.5 0.7 PA A:DTP506 3.4 25.7 0.4 CD A:GLU116 3.6 34.7 0.5 CD A:GLU116 3.6 34.6 0.5 C3' P:A8 3.7 32.2 0.6 C3' P:A8 3.8 32.2 0.5 CG A:GLU116 3.8 30.9 0.5 CG A:GLU116 3.8 30.9 0.5 OD2 A:ASP13 3.8 23.3 0.3 O5' P:DA9 3.9 25.1 0.5 C5' P:DA9 4.0 24.5 0.5 C5' A:DTP506 4.0 24.8 0.4 O5' A:DTP506 4.0 25.0 0.4 OP2 P:DA9 4.0 27.3 0.5 O1A A:DTP506 4.0 27.2 0.4 C4' P:A8 4.1 33.4 0.5 O5 A:DPO507 4.1 21.1 0.4 O3G A:DTP506 4.2 22.6 0.4 C4' P:A8 4.2 33.7 0.6 CB A:GLU116 4.2 29.1 1.0 O1 A:DPO507 4.3 18.7 0.4 C5' P:A8 4.4 33.1 0.5 CB A:ASP115 4.4 16.2 1.0 CB A:ASP13 4.4 20.1 0.3 O1B A:DTP506 4.4 18.6 0.4 O3A A:DTP506 4.5 24.5 0.4 O A:ASP115 4.5 18.2 1.0 C5' P:A8 4.5 32.9 0.6 O2' P:A8 4.6 35.1 0.6 O2' P:A8 4.6 34.9 0.5 C A:ASP115 4.6 22.1 1.0 CB A:ASP13 4.7 19.5 0.7 C2' P:A8 4.7 32.3 0.6 C2' P:A8 4.8 32.0 0.5 OE1 A:GLU116 4.8 34.9 0.5 OE1 A:GLU116 4.8 34.9 0.5 O A:HOH605 4.8 40.4 1.0 N A:GLU116 4.9 18.9 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