Magnesium in PDB 5kfv: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S:
2.7.7.7;

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S, PDB code: 5kfv was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 1.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.280, 98.280, 81.930, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.9

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S (pdb code 5kfv). 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 Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S, PDB code: 5kfv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.3 occ:0.90 K A:K507 0.0 17.0 0.1 OE2 A:GLU116 2.2 22.3 1.0 OD2 A:ASP13 2.2 23.7 1.0 O A:HOH804 2.2 20.0 1.0 O3' P:DT8 2.3 15.8 1.0 OD1 A:ASP115 2.4 13.7 1.0 O1A A:DTP506 2.4 15.1 1.0 C3' P:DT8 3.2 20.5 1.0 CD A:GLU116 3.2 21.6 1.0 CG A:ASP13 3.3 17.2 1.0 CG A:ASP115 3.4 13.8 1.0 MG A:MG503 3.5 11.3 0.5 CA A:CA502 3.5 11.2 0.5 PA A:DTP506 3.6 13.3 1.0 OD2 A:ASP115 3.6 12.8 1.0 OG A:SER113 3.7 16.7 1.0 OD1 A:ASP13 3.9 22.1 1.0 OE1 A:GLU116 4.0 23.8 1.0 C4' P:DT8 4.0 21.0 1.0 O2A A:DTP506 4.0 15.5 1.0 CB A:GLU116 4.1 17.8 1.0 O5' A:DTP506 4.1 11.6 1.0 CG A:GLU116 4.1 12.6 1.0 C5' A:DTP506 4.3 13.6 1.0 O A:HOH731 4.3 21.3 1.0 NZ A:LYS224 4.3 18.5 0.8 C5' P:DT8 4.4 21.5 0.5 O P:HOH101 4.4 20.7 1.0 CB A:ASP13 4.5 9.7 1.0 C2' P:DT8 4.5 20.6 1.0 C5' P:DT8 4.5 22.6 0.5 C A:ASP115 4.7 11.7 1.0 O A:ASP115 4.7 12.0 1.0 CB A:ASP115 4.8 11.9 1.0 CB A:SER113 4.8 16.2 1.0 N A:GLU116 4.8 11.8 1.0 O1G A:DTP506 4.9 12.7 1.0 O3A A:DTP506 4.9 12.9 1.0 O5' P:DT8 5.0 23.5 0.5

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 140S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:11.3 occ:0.50 CA A:CA502 0.0 11.2 0.5 OD1 A:ASP13 2.2 22.1 1.0 O1G A:DTP506 2.2 12.7 1.0 O1B A:DTP506 2.2 11.0 1.0 OD2 A:ASP115 2.3 12.8 1.0 O1A A:DTP506 2.3 15.1 1.0 O A:MET14 2.3 12.7 1.0 CG A:ASP13 2.8 17.2 1.0 OD2 A:ASP13 2.8 23.7 1.0 PB A:DTP506 3.3 11.7 1.0 CG A:ASP115 3.3 13.8 1.0 PA A:DTP506 3.4 13.3 1.0 C A:MET14 3.5 11.8 1.0 PG A:DTP506 3.5 12.5 1.0 MG A:MG501 3.5 17.3 0.9 K A:K507 3.5 17.0 0.1 O3A A:DTP506 3.6 12.9 1.0 OD1 A:ASP115 3.6 13.7 1.0 O3B A:DTP506 3.8 10.8 1.0 NZ A:LYS231 3.8 16.0 1.0 O A:HOH731 3.8 21.3 1.0 N A:MET14 3.9 10.3 1.0 C5' A:DTP506 4.1 13.6 1.0 O2G A:DTP506 4.2 11.7 1.0 CA A:MET14 4.2 10.7 1.0 CB A:ASP13 4.2 9.7 1.0 C A:ASP13 4.2 11.8 1.0 O5' A:DTP506 4.3 11.6 1.0 O A:HOH804 4.3 20.0 1.0 N A:ASP15 4.5 10.4 1.0 O A:ASP13 4.5 11.1 1.0 N A:CYS16 4.5 9.9 1.0 CB A:ASP115 4.6 11.9 1.0 O2B A:DTP506 4.6 12.1 1.0 O2A A:DTP506 4.6 15.5 1.0 CA A:ASP15 4.6 9.6 1.0 CE A:LYS231 4.6 24.0 1.0 O3G A:DTP506 4.7 12.4 1.0 CB A:MET14 4.7 11.1 1.0 CA A:ASP13 4.7 12.8 1.0 C A:ASP15 4.8 10.7 1.0 N A:PHE17 4.8 10.3 1.0 O A:ASP115 4.9 12.0 1.0 CB A:PHE17 4.9 9.2 1.0

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633