Magnesium in PDB 7m80: 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: 7m80 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)	30.10 / 1.98
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.844, 98.844, 82.037, 90, 90, 120
R / Rfree (%)	15.7 / 21.4

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 7m80). 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: 7m80:
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:26.3 occ:0.50 OP1 P:DA9 1.9 24.8 0.4 OD1 A:ASP13 2.0 26.3 0.5 O2A A:DTP507 2.1 24.7 0.6 O A:HOH808 2.1 28.0 1.0 OE2 A:GLU116 2.3 41.3 1.0 O3' P:DA8 2.4 22.3 0.4 OD1 A:ASP115 2.6 23.3 1.0 P P:DA9 2.6 29.0 0.4 OD1 A:ASP13 2.7 21.4 0.5 O3' P:DA8 3.0 31.1 0.6 CG A:ASP13 3.1 21.4 0.5 OD2 A:ASP13 3.1 30.2 0.5 CG A:ASP13 3.1 21.6 0.5 CA A:CA502 3.2 18.1 0.3 MG A:MG503 3.2 18.0 0.7 CD A:GLU116 3.3 32.8 1.0 C3' P:DA8 3.4 29.8 0.6 PA A:DTP507 3.4 27.7 0.6 CG A:ASP115 3.4 27.4 1.0 OD2 A:ASP13 3.5 19.3 0.5 OD2 A:ASP115 3.5 20.9 1.0 OP2 P:DA9 3.6 24.5 0.4 C3' P:DA8 3.7 29.0 0.4 O A:HOH779 3.7 35.3 1.0 O1A A:DTP507 3.9 23.5 0.6 O5' P:DA9 3.9 25.4 0.4 OE1 A:GLU116 4.0 37.7 1.0 C4' P:DA8 4.1 28.3 0.6 CG A:GLU116 4.1 35.5 1.0 O5' A:DTP507 4.1 25.5 0.6 CB A:GLU116 4.1 24.4 1.0 C4' P:DA8 4.1 28.4 0.4 C5' P:DA8 4.2 31.8 0.6 C5' P:DA9 4.2 21.3 0.4 OG A:SER113 4.2 27.3 1.0 C5' A:DTP507 4.3 21.1 0.6 CB A:ASP13 4.3 17.5 0.5 CB A:ASP13 4.4 17.4 0.5 C5' P:DA8 4.5 31.6 0.4 O3A A:DTP507 4.5 22.9 0.6 O5 A:DPO508 4.6 19.0 0.4 NZ A:LYS224 4.6 29.3 0.8 O3G A:DTP507 4.7 18.9 0.6 O1 A:DPO508 4.7 18.9 0.4 O A:ASP115 4.7 17.6 1.0 C A:ASP115 4.7 25.8 1.0 C2' P:DA8 4.8 27.7 0.6 C2' P:DA8 4.8 27.5 0.4 CB A:ASP115 4.8 14.3 1.0 O1B A:DTP507 4.9 18.3 0.6 O2 A:DPO508 4.9 22.1 0.4 N A:GLU116 4.9 16.6 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:18.0 occ:0.70 CA A:CA502 0.0 18.1 0.3 O1 A:DPO508 2.2 18.9 0.4 O5 A:DPO508 2.2 19.0 0.4 OP1 P:DA9 2.2 24.8 0.4 O1B A:DTP507 2.3 18.3 0.6 OD2 A:ASP115 2.3 20.9 1.0 O3G A:DTP507 2.3 18.9 0.6 O A:MET14 2.3 19.1 1.0 OD1 A:ASP13 2.3 21.4 0.5 O2A A:DTP507 2.4 24.7 0.6 OD2 A:ASP13 2.4 19.3 0.5 CG A:ASP13 3.0 21.4 0.5 OD1 A:ASP13 3.0 26.3 0.5 CG A:ASP13 3.1 21.6 0.5 PB A:DTP507 3.1 18.3 0.6 MG A:MG501 3.2 26.3 0.5 P1 A:DPO508 3.2 18.4 0.4 CG A:ASP115 3.3 27.4 1.0 O3A A:DTP507 3.3 22.9 0.6 OD2 A:ASP13 3.3 30.2 0.5 PA A:DTP507 3.3 27.7 0.6 P2 A:DPO508 3.4 21.0 0.4 PG A:DTP507 3.5 21.0 0.6 O2 A:DPO508 3.5 22.1 0.4 C A:MET14 3.5 11.6 1.0 O4 A:DPO508 3.6 20.3 0.4 O3B A:DTP507 3.6 20.3 0.6 OD1 A:ASP115 3.6 23.3 1.0 P P:DA9 3.7 29.0 0.4 O A:HOH779 3.7 35.3 1.0 C5' A:DTP507 4.0 21.1 0.6 N A:MET14 4.1 13.2 1.0 O5' A:DTP507 4.1 25.5 0.6 O A:HOH808 4.2 28.0 1.0 O2G A:DTP507 4.2 18.0 0.6 O7 A:DPO508 4.2 17.9 0.4 NZ A:LYS231 4.2 21.2 1.0 O5' P:DA9 4.3 25.4 0.4 C5' P:DA9 4.3 21.3 0.4 CB A:ASP13 4.4 17.5 0.5 C A:ASP13 4.4 15.3 0.5 CA A:MET14 4.4 16.2 1.0 C A:ASP13 4.4 15.3 0.5 CB A:ASP13 4.4 17.4 0.5 O6 A:DPO508 4.5 21.2 0.4 O2B A:DTP507 4.5 18.6 0.6 OP2 P:DA9 4.5 24.5 0.4 N A:ASP15 4.5 12.6 1.0 N A:CYS16 4.5 14.0 1.0 O3 A:DPO508 4.6 18.4 0.4 O1A A:DTP507 4.6 23.5 0.6 CB A:ASP115 4.6 14.3 1.0 CA A:ASP15 4.6 13.9 1.0 O1G A:DTP507 4.7 21.4 0.6 O3' P:DA8 4.7 22.3 0.4 O A:ASP13 4.8 14.9 0.5 O A:ASP13 4.8 15.0 0.5 N A:PHE17 4.8 12.3 1.0 CA A:ASP13 4.8 15.7 0.5 CA A:ASP13 4.8 15.7 0.5 C A:ASP15 4.8 19.6 1.0 CB A:MET14 4.9 15.4 1.0 CE A:LYS231 4.9 32.1 1.0 CB A:PHE17 4.9 10.6 1.0 O A:ASP115 5.0 17.6 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:31.4 occ:0.40 O1A A:DTP507 2.0 23.5 0.6 OP2 P:DA9 2.1 24.5 0.4 O2 A:DPO508 2.5 22.1 0.4 O A:HOH659 2.6 24.7 1.0 O3A A:DTP507 2.6 22.9 0.6 O A:HOH779 2.7 35.3 1.0 NH1 A:ARG61 2.7 20.9 0.6 PA A:DTP507 2.8 27.7 0.6 O A:HOH1052 3.2 47.6 1.0 P P:DA9 3.4 29.0 0.4 O2A A:DTP507 3.6 24.7 0.6 CZ A:ARG61 3.8 25.2 0.6 OP1 P:DA9 3.8 24.8 0.4 O6 A:DPO508 3.9 21.2 0.4 PB A:DTP507 4.0 18.3 0.6 P1 A:DPO508 4.0 18.4 0.4 NH2 A:ARG61 4.0 18.6 0.6 O5' A:DTP507 4.0 25.5 0.6 O A:HOH794 4.1 32.2 1.0 O1G A:DTP507 4.1 21.4 0.6 O5' P:DA9 4.1 25.4 0.4 O A:HOH808 4.1 28.0 1.0 O3B A:DTP507 4.2 20.3 0.6 O3G A:DTP507 4.3 18.9 0.6 O4 A:DPO508 4.3 20.3 0.4 O5 A:DPO508 4.3 19.0 0.4 O A:HOH976 4.3 25.3 1.0 PG A:DTP507 4.5 21.0 0.6 P2 A:DPO508 4.5 21.0 0.4 O3' P:DA8 4.6 22.3 0.4 O2B A:DTP507 4.7 18.6 0.6 NH1 A:ARG61 4.8 30.6 0.4 O1 A:DPO508 4.8 18.9 0.4 O3 A:DPO508 4.9 18.4 0.4 C3' P:DA8 4.9 29.0 0.4 NE A:ARG61 5.0 27.5 0.6

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