Magnesium in PDB 7m81: Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S

All present enzymatic activity of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S:
2.7.7.7;

The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S, PDB code: 7m81 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)	30.16 / 2.05
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.147, 99.147, 81.761, 90, 90, 120
R / Rfree (%)	17.1 / 22.6

The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 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 100 S (pdb code 7m81). 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 100 S, PDB code: 7m81:
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 100 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 100 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:36.9 occ:0.40 OP1 P:DA9 1.9 34.2 0.6 OD1 A:ASP13 1.9 34.1 0.5 O2A A:DTP506 1.9 34.1 0.5 O A:HOH736 2.0 38.5 1.0 OE2 A:GLU116 2.2 55.5 1.0 OD2 A:ASP13 2.6 43.2 0.6 P P:DA9 2.7 36.0 0.6 OD1 A:ASP13 2.7 30.4 0.6 O3' P:DA8 2.7 23.4 0.6 CG A:ASP13 2.9 30.0 0.5 OD1 A:ASP115 2.9 37.2 1.0 CG A:ASP13 2.9 31.6 0.6 MG A:MG503 3.2 23.5 0.7 CA A:CA502 3.2 23.7 0.3 PA A:DTP506 3.3 37.8 0.5 OD2 A:ASP13 3.4 22.6 0.5 CD A:GLU116 3.4 67.4 1.0 O3' P:DA8 3.4 39.6 0.5 O A:HOH704 3.5 41.2 1.0 OP2 P:DA9 3.5 32.1 0.6 OD2 A:ASP115 3.6 32.3 1.0 CG A:ASP115 3.6 38.4 1.0 C3' P:DA8 3.8 39.3 0.5 O1A A:DTP506 3.8 30.5 0.5 C3' P:DA8 4.0 41.5 0.6 O5' P:DA9 4.1 35.1 0.6 OE1 A:GLU116 4.1 69.7 1.0 CB A:ASP13 4.1 26.5 0.5 O5' A:DTP506 4.2 34.5 0.5 O5 A:DPO507 4.2 24.4 0.6 CB A:GLU116 4.3 28.5 1.0 O3G A:DTP506 4.3 24.5 0.5 CB A:ASP13 4.3 25.9 0.6 NZ A:LYS224 4.3 26.8 0.6 CG A:GLU116 4.3 50.7 1.0 O3A A:DTP506 4.3 26.4 0.5 C5' P:DA8 4.3 40.0 0.5 C4' P:DA8 4.4 37.7 0.5 C4' P:DA8 4.4 37.8 0.6 C5' P:DA9 4.4 30.4 0.6 C5' A:DTP506 4.5 30.1 0.5 OG A:SER113 4.6 41.7 1.0 C5' P:DA8 4.6 40.2 0.6 O1 A:DPO507 4.6 23.9 0.6 O2 A:DPO507 4.7 26.6 0.6 O1B A:DTP506 4.8 23.2 0.5 O A:ASP115 4.9 27.0 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 100 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 100 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.5 occ:0.70 CA A:CA502 0.0 23.7 0.3 O5 A:DPO507 2.1 24.4 0.6 O1 A:DPO507 2.1 23.9 0.6 O3G A:DTP506 2.2 24.5 0.5 O1B A:DTP506 2.2 23.2 0.5 OD1 A:ASP13 2.3 30.4 0.6 OD2 A:ASP13 2.3 22.6 0.5 O A:MET14 2.3 22.9 1.0 OD2 A:ASP115 2.4 32.3 1.0 OP1 P:DA9 2.4 34.2 0.6 O2A A:DTP506 2.5 34.1 0.5 CG A:ASP13 2.9 30.0 0.5 OD1 A:ASP13 3.0 34.1 0.5 PB A:DTP506 3.0 28.6 0.5 P1 A:DPO507 3.2 28.3 0.6 CG A:ASP13 3.2 31.6 0.6 MG A:MG501 3.2 36.9 0.4 O3A A:DTP506 3.3 26.4 0.5 P2 A:DPO507 3.3 30.8 0.6 PG A:DTP506 3.3 30.6 0.5 PA A:DTP506 3.4 37.8 0.5 CG A:ASP115 3.4 38.4 1.0 O3B A:DTP506 3.4 28.2 0.5 O2 A:DPO507 3.4 26.6 0.6 O4 A:DPO507 3.4 28.0 0.6 OD2 A:ASP13 3.5 43.2 0.6 C A:MET14 3.5 21.3 1.0 O A:HOH704 3.7 41.2 1.0 P P:DA9 3.8 36.0 0.6 OD1 A:ASP115 3.8 37.2 1.0 O2G A:DTP506 4.0 26.2 0.5 O7 A:DPO507 4.0 26.1 0.6 C5' A:DTP506 4.1 30.1 0.5 N A:MET14 4.2 14.7 1.0 NZ A:LYS231 4.2 35.7 1.0 C5' P:DA9 4.2 30.4 0.6 O5' A:DTP506 4.3 34.5 0.5 CB A:ASP13 4.4 26.5 0.5 O A:HOH736 4.4 38.5 1.0 N A:CYS16 4.4 22.2 1.0 O6 A:DPO507 4.4 28.8 0.6 O5' P:DA9 4.4 35.1 0.6 O2B A:DTP506 4.4 27.8 0.5 CA A:MET14 4.4 22.6 1.0 C A:ASP13 4.4 21.3 0.6 C A:ASP13 4.5 21.4 0.5 N A:ASP15 4.5 21.7 1.0 CB A:ASP13 4.5 25.9 0.6 O3 A:DPO507 4.5 27.9 0.6 CA A:ASP15 4.5 28.6 1.0 OP2 P:DA9 4.5 32.1 0.6 O1G A:DTP506 4.6 29.1 0.5 O1A A:DTP506 4.6 30.5 0.5 C A:ASP15 4.7 30.0 1.0 CB A:ASP115 4.7 22.7 1.0 N A:PHE17 4.8 19.6 1.0 O A:ASP13 4.9 24.2 0.6 CA A:ASP13 4.9 21.1 0.6 O3' P:DA8 4.9 23.4 0.6 CA A:ASP13 4.9 21.1 0.5 CB A:MET14 4.9 27.7 1.0 O A:ASP13 4.9 24.2 0.5 CE A:LYS231 5.0 49.8 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 100 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 100 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:39.2 occ:0.55 NH1 A:ARG61 2.2 23.4 0.5 O2 A:DPO507 2.2 26.6 0.6 O A:HOH649 2.2 36.5 1.0 O A:HOH696 2.3 40.9 1.0 O3A A:DTP506 2.4 26.4 0.5 O1A A:DTP506 2.4 30.5 0.5 OP2 P:DA9 2.6 32.1 0.6 O A:HOH704 2.9 41.2 1.0 PA A:DTP506 3.0 37.8 0.5 CZ A:ARG61 3.2 26.5 0.5 NH2 A:ARG61 3.4 17.0 0.5 P1 A:DPO507 3.6 28.3 0.6 PB A:DTP506 3.6 28.6 0.5 O A:HOH833 3.7 40.1 1.0 O A:HOH881 3.7 43.2 1.0 P P:DA9 3.8 36.0 0.6 O3B A:DTP506 3.8 28.2 0.5 O6 A:DPO507 3.8 28.8 0.6 NH1 A:ARG61 3.9 26.7 0.6 NE A:ARG61 3.9 40.3 0.6 O4 A:DPO507 3.9 28.0 0.6 O2A A:DTP506 4.0 34.1 0.5 O1G A:DTP506 4.0 29.1 0.5 O5' A:DTP506 4.1 34.5 0.5 O2B A:DTP506 4.2 27.8 0.5 OP1 P:DA9 4.2 34.2 0.6 CZ A:ARG61 4.2 36.0 0.6 O3 A:DPO507 4.3 27.9 0.6 O5' P:DA9 4.3 35.1 0.6 PG A:DTP506 4.3 30.6 0.5 O3G A:DTP506 4.3 24.5 0.5 O P:HOH207 4.3 43.6 1.0 P2 A:DPO507 4.4 30.8 0.6 O5 A:DPO507 4.4 24.4 0.6 NE A:ARG61 4.4 32.4 0.5 O1 A:DPO507 4.6 23.9 0.6 O A:HOH630 4.7 24.9 1.0 O A:HOH736 4.7 38.5 1.0 O1B A:DTP506 4.8 23.2 0.5 CD A:ARG61 4.9 39.0 0.6 C8 A:DTP506 5.0 32.6 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