Magnesium in PDB 7m7z: Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S

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

The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m7z 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)	30.08 / 1.82
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.779, 98.779, 82.064, 90, 90, 120
R / Rfree (%)	18 / 22.8

The structure of Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S (pdb code 7m7z). 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 Da-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m7z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.3 occ:0.50 OD1 A:ASP13 2.0 17.9 0.5 O A:HOH647 2.1 22.9 1.0 OP1 P:DA9 2.1 16.0 0.2 O2A A:DTP506 2.2 16.8 0.8 OE2 A:GLU116 2.2 36.9 1.0 O3' P:DA8 2.3 17.6 0.2 OD1 A:ASP115 2.4 13.7 1.0 OD1 A:ASP13 2.7 14.7 0.5 P P:DA9 2.7 19.5 0.2 O3' P:DA8 2.9 20.1 0.8 OD2 A:ASP13 2.9 21.8 0.5 CG A:ASP13 3.1 15.2 0.5 CG A:ASP13 3.1 15.3 0.5 CD A:GLU116 3.1 28.8 1.0 CA A:CA502 3.2 10.1 0.5 C3' P:DA8 3.2 21.0 0.8 MG A:MG503 3.2 10.2 0.5 CG A:ASP115 3.3 15.6 1.0 OD2 A:ASP115 3.3 15.1 1.0 PA A:DTP506 3.5 14.4 0.8 C3' P:DA8 3.6 20.1 0.2 OD2 A:ASP13 3.6 15.5 0.5 CG A:GLU116 3.8 26.9 1.0 OP2 P:DA9 3.8 15.6 0.2 C4' P:DA8 3.9 22.7 0.2 O5' P:DA9 3.9 14.9 0.2 OE1 A:GLU116 3.9 26.7 1.0 O1A A:DTP506 4.0 15.3 0.8 C5' P:DA9 4.0 12.9 0.2 C4' P:DA8 4.1 23.3 0.8 O5' A:DTP506 4.1 15.1 0.8 CB A:GLU116 4.1 18.9 1.0 OG A:SER113 4.2 22.6 1.0 C5' A:DTP506 4.2 12.6 0.8 C5' P:DA8 4.3 24.8 0.2 CB A:ASP13 4.3 14.1 0.5 O A:HOH773 4.3 29.3 1.0 C5' P:DA8 4.4 24.9 0.8 C2' P:DA8 4.5 18.9 0.8 CB A:ASP13 4.5 13.9 0.5 O A:ASP115 4.6 12.1 1.0 NZ A:LYS224 4.6 19.8 0.6 O5 A:DPO507 4.6 11.1 0.2 O3G A:DTP506 4.6 10.3 0.8 C A:ASP115 4.6 16.8 1.0 C2' P:DA8 4.6 18.9 0.2 CB A:ASP115 4.7 10.3 1.0 O3A A:DTP506 4.7 13.7 0.8 O1 A:DPO507 4.7 10.9 0.2 O1B A:DTP506 4.8 10.0 0.8 N A:GLU116 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Pol Eta 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:10.2 occ:0.50 CA A:CA502 0.1 10.1 0.5 OP1 P:DA9 2.2 16.0 0.2 OD1 A:ASP13 2.2 14.7 0.5 O A:MET14 2.2 10.3 1.0 O3G A:DTP506 2.2 10.3 0.8 O5 A:DPO507 2.3 11.1 0.2 OD2 A:ASP115 2.3 15.1 1.0 O1B A:DTP506 2.3 10.0 0.8 O1 A:DPO507 2.3 10.9 0.2 OD2 A:ASP13 2.4 15.5 0.5 O2A A:DTP506 2.4 16.8 0.8 OD1 A:ASP13 2.8 17.9 0.5 CG A:ASP13 2.9 15.2 0.5 MG A:MG501 3.2 18.3 0.5 PB A:DTP506 3.3 11.9 0.8 CG A:ASP13 3.3 15.3 0.5 CG A:ASP115 3.4 15.6 1.0 C A:MET14 3.4 7.6 1.0 PG A:DTP506 3.5 14.7 0.8 P1 A:DPO507 3.5 11.7 0.2 P2 A:DPO507 3.5 14.2 0.2 PA A:DTP506 3.5 14.4 0.8 O3A A:DTP506 3.6 13.7 0.8 P P:DA9 3.6 19.5 0.2 O3B A:DTP506 3.7 12.7 0.8 OD1 A:ASP115 3.7 13.7 1.0 O4 A:DPO507 3.8 12.8 0.2 O2 A:DPO507 3.9 13.3 0.2 OD2 A:ASP13 3.9 21.8 0.5 N A:MET14 4.0 8.3 1.0 O A:HOH773 4.1 29.3 1.0 O7 A:DPO507 4.1 12.9 0.2 NZ A:LYS231 4.1 14.7 1.0 C5' P:DA9 4.1 12.9 0.2 O2G A:DTP506 4.1 11.4 0.8 O A:HOH647 4.2 22.9 1.0 C5' A:DTP506 4.2 12.6 0.8 O5' P:DA9 4.2 14.9 0.2 CA A:MET14 4.2 10.2 1.0 C A:ASP13 4.3 7.7 1.0 CB A:ASP13 4.3 14.1 0.5 O5' A:DTP506 4.3 15.1 0.8 CB A:ASP13 4.4 13.9 0.5 N A:ASP15 4.4 5.7 1.0 O3' P:DA8 4.5 17.6 0.2 N A:CYS16 4.5 8.4 1.0 CA A:ASP15 4.6 10.2 1.0 CB A:ASP115 4.6 10.3 1.0 OP2 P:DA9 4.6 15.6 0.2 O2B A:DTP506 4.6 9.6 0.8 O1G A:DTP506 4.7 12.6 0.8 O1A A:DTP506 4.7 15.3 0.8 O A:ASP13 4.7 9.1 1.0 CA A:ASP13 4.7 12.0 0.5 CA A:ASP13 4.7 12.1 0.5 O6 A:DPO507 4.7 13.2 0.2 CB A:MET14 4.7 13.4 1.0 C A:ASP15 4.7 11.2 1.0 O3 A:DPO507 4.8 10.1 0.2 N A:PHE17 4.8 8.6 1.0 CE A:LYS231 4.8 25.1 1.0 O A:ASP115 4.9 12.1 1.0 CB A:PHE17 4.9 7.0 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