Magnesium in PDB 7m8d: Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S

All present enzymatic activity of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S:
2.7.7.7;

The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S, PDB code: 7m8d 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)	29.97 / 1.92
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.422, 98.422, 81.618, 90, 90, 120
R / Rfree (%)	16.3 / 21.7

The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S (pdb code 7m8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S, PDB code: 7m8d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 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 300 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:24.3 occ:0.85 O3G A:DTP504 1.9 20.8 0.2 O5 A:DPO505 2.0 18.1 0.4 OD2 A:ASP13 2.0 26.5 0.5 O1B A:DTP504 2.2 18.6 0.2 OD1 A:ASP13 2.2 27.2 0.5 OD2 A:ASP115 2.2 38.2 1.0 O1 A:DPO505 2.2 18.1 0.4 O A:MET14 2.4 18.3 1.0 OP1 P:DA9 2.5 27.7 0.7 O2A A:DTP504 2.6 27.3 0.2 MG A:MG506 3.1 27.3 0.2 CG A:ASP13 3.1 27.7 0.5 PB A:DTP504 3.1 22.8 0.2 PG A:DTP504 3.1 25.5 0.2 P2 A:DPO505 3.2 25.4 0.4 P1 A:DPO505 3.3 22.8 0.4 CG A:ASP13 3.3 28.4 0.5 O3B A:DTP504 3.4 22.8 0.2 CG A:ASP115 3.4 33.1 1.0 O4 A:DPO505 3.5 23.0 0.4 O3A A:DTP504 3.5 26.2 0.2 OD1 A:ASP13 3.5 35.8 0.5 C A:MET14 3.6 13.5 1.0 PA A:DTP504 3.6 24.1 0.2 O2G A:DTP504 3.8 18.5 0.2 O A:HOH682 3.8 36.7 1.0 O A:HOH701 3.8 24.5 1.0 O6 A:DPO505 3.8 18.3 0.4 OD2 A:ASP13 3.9 38.0 0.5 O2 A:DPO505 3.9 26.8 0.4 P P:DA9 3.9 25.4 0.7 C5' A:DTP504 4.1 24.3 0.2 N A:MET14 4.1 13.1 1.0 C5' P:DA9 4.2 24.4 0.7 OD1 A:ASP115 4.2 22.7 1.0 N A:CYS16 4.3 18.8 1.0 O5' A:DTP504 4.3 26.6 0.2 O5' P:DA9 4.3 26.9 0.7 O1G A:DTP504 4.4 22.6 0.2 C A:ASP13 4.4 15.6 1.0 CB A:ASP13 4.4 21.8 0.5 CB A:ASP115 4.4 18.9 1.0 CA A:MET14 4.4 13.9 1.0 O2B A:DTP504 4.5 19.5 0.2 CB A:ASP13 4.5 21.7 0.5 O7 A:DPO505 4.5 22.5 0.4 N A:ASP15 4.5 12.2 1.0 CA A:ASP15 4.5 12.5 1.0 O3 A:DPO505 4.6 19.4 0.4 O A:HOH649 4.6 28.4 0.2 C A:ASP15 4.7 18.7 1.0 O3' P:A8 4.7 30.9 0.7 N A:PHE17 4.7 14.3 1.0 NZ A:LYS231 4.8 44.5 1.0 O A:ASP13 4.8 13.2 1.0 O3' P:A8 4.8 29.4 0.3 CA A:ASP13 4.8 18.3 0.5 CA A:ASP13 4.8 18.3 0.5 O1A A:DTP504 4.9 28.6 0.2 O A:ASP115 4.9 19.8 1.0 CB A:MET14 4.9 17.8 1.0

Magnesium binding site 2 out of 3 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 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 300 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:27.3 occ:0.20 O A:HOH649 2.1 28.4 0.2 OP1 P:DA9 2.2 27.7 0.7 OD1 A:ASP13 2.2 35.8 0.5 O2A A:DTP504 2.2 27.3 0.2 O3' P:A8 2.6 29.4 0.3 OD2 A:ASP115 2.7 38.2 1.0 OD1 A:ASP13 2.7 27.2 0.5 O3' P:A8 2.7 30.9 0.7 OE2 A:GLU116 2.8 40.8 1.0 OD1 A:ASP115 2.8 22.7 1.0 OD2 A:ASP13 2.9 38.0 0.5 CG A:ASP13 3.0 27.7 0.5 P P:DA9 3.0 25.4 0.7 MG A:MG501 3.1 24.3 0.8 CG A:ASP115 3.1 33.1 1.0 CG A:ASP13 3.1 28.4 0.5 OD2 A:ASP13 3.1 26.5 0.5 PA A:DTP504 3.6 24.1 0.2 O A:HOH682 3.7 36.7 1.0 CD A:GLU116 3.7 32.3 1.0 C3' P:A8 3.9 32.5 0.3 CG A:GLU116 3.9 36.2 1.0 C3' P:A8 3.9 32.7 0.7 O3G A:DTP504 4.0 20.8 0.2 OP2 P:DA9 4.1 28.8 0.7 O5 A:DPO505 4.1 18.1 0.4 O5' P:DA9 4.1 26.9 0.7 CB A:GLU116 4.2 29.3 1.0 O1A A:DTP504 4.2 28.6 0.2 C4' P:A8 4.2 32.7 0.7 C5' P:DA9 4.2 24.4 0.7 C5' A:DTP504 4.3 24.3 0.2 O5' A:DTP504 4.3 26.6 0.2 C5' P:A8 4.3 33.5 0.7 CB A:ASP13 4.4 21.8 0.5 C4' P:A8 4.4 32.5 0.3 NZ A:LYS224 4.5 25.0 0.5 CB A:ASP13 4.5 21.7 0.5 O1 A:DPO505 4.5 18.1 0.4 O1B A:DTP504 4.5 18.6 0.2 CB A:ASP115 4.5 18.9 1.0 C5' P:A8 4.6 33.2 0.3 O3A A:DTP504 4.6 26.2 0.2 O A:ASP115 4.7 19.8 1.0 C A:ASP115 4.8 26.9 1.0 O A:HOH621 4.8 39.3 1.0 OE1 A:GLU116 4.9 40.2 1.0 O2' P:A8 4.9 35.5 0.7 O2' P:A8 4.9 35.2 0.3 CA A:ASP13 5.0 18.3 0.5 CA A:ASP13 5.0 18.3 0.5 N A:GLU116 5.0 17.6 1.0

Magnesium binding site 3 out of 3 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 300 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:24.9 occ:0.30 O2 A:DPO505 2.0 26.8 0.4 O A:HOH747 2.1 32.6 1.0 O3A A:DTP504 2.2 26.2 0.2 O1A A:DTP504 2.2 28.6 0.2 NH1 A:ARG61 2.4 25.9 0.4 OP2 P:DA9 2.6 28.8 0.7 PA A:DTP504 2.7 24.1 0.2 O A:HOH682 3.0 36.7 1.0 CZ A:ARG61 3.2 28.1 0.4 NH2 A:ARG61 3.3 17.8 0.4 P P:DA9 3.4 25.4 0.7 P1 A:DPO505 3.4 22.8 0.4 O A:HOH861 3.4 38.5 1.0 PB A:DTP504 3.5 22.8 0.2 O2A A:DTP504 3.6 27.3 0.2 OP1 P:DA9 3.6 27.7 0.7 O3B A:DTP504 3.7 22.8 0.2 NH2 A:ARG61 3.8 38.6 0.6 O4 A:DPO505 3.8 23.0 0.4 O5' A:DTP504 3.9 26.6 0.2 O1G A:DTP504 3.9 22.6 0.2 O5' P:DA9 3.9 26.9 0.7 O7 A:DPO505 4.0 22.5 0.4 NE A:ARG61 4.1 40.7 0.6 O2B A:DTP504 4.2 19.5 0.2 O A:HOH807 4.2 37.2 1.0 O3 A:DPO505 4.2 19.4 0.4 O5 A:DPO505 4.2 18.1 0.4 P2 A:DPO505 4.3 25.4 0.4 PG A:DTP504 4.3 25.5 0.2 CZ A:ARG61 4.4 31.5 0.6 O3G A:DTP504 4.4 20.8 0.2 O1 A:DPO505 4.5 18.1 0.4 NE A:ARG61 4.5 27.2 0.4 O A:HOH640 4.6 21.4 1.0 O1B A:DTP504 4.7 18.6 0.2 NH2 A:ARG55 4.7 25.1 1.0 O3' P:A8 4.9 30.9 0.7

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