Magnesium in PDB 7m82: Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S

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

The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S, PDB code: 7m82 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)	30.06 / 2.07
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.678, 98.678, 82.163, 90, 90, 120
R / Rfree (%)	16.5 / 22.5

The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 300 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 300 S (pdb code 7m82). 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S, PDB code: 7m82:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Pol Eta with Da-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 with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:14.9 occ:0.35 OP1 P:DA9 1.9 22.1 0.7 OD2 A:ASP13 2.0 27.1 0.7 O2A A:DTP507 2.2 21.7 0.3 O A:HOH653 2.2 23.3 1.0 OE2 A:GLU116 2.3 33.9 1.0 O3' P:DA8 2.4 19.0 0.7 O3' P:DA8 2.5 20.8 0.3 OD1 A:ASP115 2.5 14.6 1.0 P P:DA9 2.6 25.0 0.7 OD1 A:ASP13 2.7 15.7 0.3 OD2 A:ASP13 3.0 18.1 0.3 CG A:ASP13 3.1 17.6 0.3 CG A:ASP13 3.1 17.7 0.7 CD A:GLU116 3.3 31.1 1.0 CG A:ASP115 3.4 15.9 1.0 C3' P:DA8 3.4 24.4 0.3 CA A:CA502 3.5 13.5 0.3 MG A:MG503 3.5 12.0 0.7 PA A:DTP507 3.5 21.2 0.3 OP2 P:DA9 3.5 21.2 0.7 OD2 A:ASP115 3.6 11.2 1.0 C3' P:DA8 3.6 25.0 0.7 OD1 A:ASP13 3.7 16.9 0.7 O A:HOH710 3.9 25.1 1.0 O1A A:DTP507 3.9 20.2 0.3 O5' P:DA9 3.9 19.8 0.7 OE1 A:GLU116 4.0 36.5 1.0 OG A:SER113 4.0 24.4 1.0 CB A:GLU116 4.0 23.0 1.0 C4' P:DA8 4.0 23.4 0.7 C4' P:DA8 4.0 23.4 0.3 CG A:GLU116 4.1 31.4 1.0 O5' A:DTP507 4.2 19.1 0.3 C5' P:DA8 4.3 24.4 0.3 C5' P:DA8 4.3 24.3 0.7 C5' P:DA9 4.3 17.1 0.7 CB A:ASP13 4.3 15.4 0.7 C5' A:DTP507 4.3 17.2 0.3 CB A:ASP13 4.4 15.4 0.3 NZ A:LYS224 4.5 16.9 0.5 O A:ASP115 4.6 15.4 1.0 O3A A:DTP507 4.7 16.6 0.3 C A:ASP115 4.7 16.2 1.0 C2' P:DA8 4.8 21.7 0.3 C2' P:DA8 4.8 21.6 0.7 O3G A:DTP507 4.8 14.9 0.3 CB A:ASP115 4.8 9.6 1.0 O5 A:DPO508 4.8 14.7 0.7 N A:GLU116 4.8 10.9 1.0 O1 A:DPO508 4.9 13.8 0.7 O P:HOH201 4.9 30.7 0.7 O2 A:DPO508 5.0 15.9 0.7 O1B A:DTP507 5.0 13.8 0.3 CA A:GLU116 5.0 7.8 1.0

Magnesium binding site 2 out of 3 in the Human Dna Pol Eta with Da-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 with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:12.0 occ:0.70 CA A:CA502 0.0 13.5 0.3 O1 A:DPO508 2.1 13.8 0.7 O1B A:DTP507 2.2 13.8 0.3 O3G A:DTP507 2.2 14.9 0.3 O5 A:DPO508 2.2 14.7 0.7 O A:MET14 2.3 15.2 1.0 OP1 P:DA9 2.3 22.1 0.7 OD1 A:ASP13 2.3 16.9 0.7 OD2 A:ASP115 2.3 11.2 1.0 O2A A:DTP507 2.4 21.7 0.3 OD1 A:ASP13 2.5 15.7 0.3 PB A:DTP507 3.0 17.0 0.3 CG A:ASP13 3.1 17.7 0.7 P1 A:DPO508 3.2 17.0 0.7 OD2 A:ASP13 3.2 27.1 0.7 CG A:ASP13 3.2 17.6 0.3 O3A A:DTP507 3.3 16.6 0.3 PG A:DTP507 3.4 19.9 0.3 PA A:DTP507 3.4 21.2 0.3 P2 A:DPO508 3.4 20.1 0.7 CG A:ASP115 3.4 15.9 1.0 O2 A:DPO508 3.4 15.9 0.7 OD2 A:ASP13 3.5 18.1 0.3 O3B A:DTP507 3.5 17.6 0.3 MG A:MG501 3.5 14.9 0.3 C A:MET14 3.5 8.8 1.0 O4 A:DPO508 3.5 17.6 0.7 O A:HOH710 3.6 25.1 1.0 P P:DA9 3.6 25.0 0.7 OD1 A:ASP115 3.7 14.6 1.0 C5' A:DTP507 4.1 17.2 0.3 O2G A:DTP507 4.1 17.3 0.3 N A:MET14 4.1 12.2 1.0 NZ A:LYS231 4.2 13.1 1.0 O A:HOH653 4.2 23.3 1.0 O7 A:DPO508 4.2 17.4 0.7 O5' P:DA9 4.2 19.8 0.7 O5' A:DTP507 4.2 19.1 0.3 C5' P:DA9 4.2 17.1 0.7 OP2 P:DA9 4.3 21.2 0.7 C A:ASP13 4.4 12.3 1.0 CA A:MET14 4.4 13.3 1.0 O2B A:DTP507 4.4 13.9 0.3 N A:CYS16 4.4 10.5 1.0 CB A:ASP13 4.5 15.4 0.7 N A:ASP15 4.5 9.1 1.0 O6 A:DPO508 4.5 18.1 0.7 CB A:ASP13 4.5 15.4 0.3 O3 A:DPO508 4.5 13.7 0.7 O1G A:DTP507 4.5 18.2 0.3 O1A A:DTP507 4.6 20.2 0.3 CA A:ASP15 4.6 10.2 1.0 C A:ASP15 4.7 14.6 1.0 N A:PHE17 4.7 12.0 1.0 O A:ASP13 4.7 12.4 1.0 CB A:ASP115 4.7 9.6 1.0 O3' P:DA8 4.8 19.0 0.7 MG P:MG101 4.8 26.9 0.7 CB A:MET14 4.8 12.6 1.0 CA A:ASP13 4.8 12.2 0.3 CA A:ASP13 4.9 13.1 0.7 CB A:PHE17 4.9 9.8 1.0

Magnesium binding site 3 out of 3 in the Human Dna Pol Eta with Da-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 with Da-Ended Primer and Datp: in Crystallo Reaction For 300 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:26.9 occ:0.65 O P:HOH201 1.9 30.7 0.7 O2 A:DPO508 2.2 15.9 0.7 O1A A:DTP507 2.2 20.2 0.3 O3A A:DTP507 2.3 16.6 0.3 O A:HOH760 2.3 21.6 0.7 O A:HOH649 2.3 21.1 1.0 OP2 P:DA9 2.4 21.2 0.7 O A:HOH710 2.5 25.1 1.0 NH1 A:ARG61 2.7 22.9 0.3 PA A:DTP507 2.8 21.2 0.3 O A:HOH992 3.2 44.1 1.0 O6 A:DPO508 3.5 18.1 0.7 PB A:DTP507 3.6 17.0 0.3 P1 A:DPO508 3.6 17.0 0.7 CZ A:ARG61 3.6 21.6 0.3 NH2 A:ARG61 3.6 20.2 0.3 P P:DA9 3.6 25.0 0.7 O1G A:DTP507 3.6 18.2 0.3 O3B A:DTP507 3.7 17.6 0.3 O2A A:DTP507 3.7 21.7 0.3 O4 A:DPO508 3.8 17.6 0.7 O A:HOH888 3.8 21.4 0.7 O5 A:DPO508 3.9 14.7 0.7 PG A:DTP507 4.0 19.9 0.3 O3G A:DTP507 4.0 14.9 0.3 P2 A:DPO508 4.0 20.1 0.7 OP1 P:DA9 4.1 22.1 0.7 O5' A:DTP507 4.1 19.1 0.3 O A:HOH947 4.1 19.3 1.0 O5' P:DA9 4.2 19.8 0.7 O A:HOH653 4.3 23.3 1.0 O2B A:DTP507 4.4 13.9 0.3 O3 A:DPO508 4.4 13.7 0.7 O1 A:DPO508 4.5 13.8 0.7 NH1 A:ARG61 4.6 28.4 0.7 O A:HOH801 4.6 27.6 1.0 O A:HOH652 4.6 34.0 1.0 O1B A:DTP507 4.7 13.8 0.3 MG A:MG503 4.8 12.0 0.7 CA A:CA502 4.8 13.5 0.3 NE A:ARG61 4.9 20.3 0.3 O3' P:DA8 4.9 19.0 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