Magnesium in PDB 5kft: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 40S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 40S:
2.7.7.7;

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 40S, PDB code: 5kft 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)	19.93 / 1.52
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.430, 98.430, 82.000, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.1

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 40S 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 40S (pdb code 5kft). 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 40S, PDB code: 5kft:
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 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.9 occ:0.90 K A:K507 0.0 18.8 0.1 OD2 A:ASP13 2.2 23.7 0.8 OE2 A:GLU116 2.2 28.5 1.0 O3' P:DT8 2.3 20.6 1.0 OD2 A:ASP115 2.4 15.2 1.0 O1A A:DTP506 2.5 13.7 1.0 O A:HOH737 2.5 25.5 1.0 OD1 A:ASP13 3.0 13.6 0.2 C3' P:DT8 3.2 24.2 1.0 CD A:GLU116 3.2 29.3 1.0 CG A:ASP13 3.3 17.7 0.8 CG A:ASP115 3.3 11.9 1.0 CG A:ASP13 3.5 16.7 0.2 MG A:MG503 3.5 11.3 0.4 CA A:CA502 3.5 11.2 0.6 OD2 A:ASP13 3.6 16.2 0.2 OD1 A:ASP115 3.6 14.1 1.0 PA A:DTP506 3.7 12.7 1.0 OD1 A:ASP13 3.7 21.1 0.8 OG A:SER113 3.7 18.2 1.0 C4' P:DT8 4.0 21.4 1.0 CB A:GLU116 4.0 22.3 1.0 OE1 A:GLU116 4.0 28.4 1.0 CG A:GLU116 4.1 17.3 1.0 O5' A:DTP506 4.2 11.9 1.0 O2A A:DTP506 4.2 16.7 1.0 C5' A:DTP506 4.3 12.3 1.0 O A:HOH681 4.4 27.3 1.0 C5' P:DT8 4.4 24.5 0.4 O P:HOH101 4.4 17.1 0.5 NZ A:LYS224 4.4 23.0 0.7 C2' P:DT8 4.5 23.4 1.0 CB A:ASP13 4.5 13.4 0.8 C5' P:DT8 4.5 25.0 0.6 C A:ASP115 4.6 14.1 1.0 O A:ASP115 4.6 14.6 1.0 CB A:ASP13 4.7 13.8 0.2 CB A:ASP115 4.7 10.7 1.0 N A:GLU116 4.7 11.5 1.0 CB A:SER113 4.8 16.7 1.0 O1G A:DTP506 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:11.3 occ:0.40 CA A:CA502 0.0 11.2 0.6 OD1 A:ASP115 2.3 14.1 1.0 O1G A:DTP506 2.3 12.4 1.0 OD1 A:ASP13 2.3 21.1 0.8 O1B A:DTP506 2.3 10.8 1.0 O A:MET14 2.3 12.7 1.0 OD1 A:ASP13 2.3 13.6 0.2 O1A A:DTP506 2.4 13.7 1.0 CG A:ASP13 2.9 17.7 0.8 OD2 A:ASP13 2.9 23.7 0.8 CG A:ASP115 3.3 11.9 1.0 PB A:DTP506 3.3 11.8 1.0 CG A:ASP13 3.4 16.7 0.2 PA A:DTP506 3.4 12.7 1.0 C A:MET14 3.5 11.1 1.0 PG A:DTP506 3.5 12.1 1.0 MG A:MG501 3.5 20.9 0.9 K A:K507 3.5 18.8 0.1 O3A A:DTP506 3.6 11.9 1.0 OD2 A:ASP115 3.7 15.2 1.0 O3B A:DTP506 3.8 11.0 1.0 NZ A:LYS231 3.8 15.6 1.0 O A:HOH681 3.9 27.3 1.0 OD2 A:ASP13 3.9 16.2 0.2 N A:MET14 3.9 12.0 1.0 C5' A:DTP506 4.1 12.3 1.0 O A:HOH737 4.1 25.5 1.0 O2G A:DTP506 4.2 12.6 1.0 CA A:MET14 4.2 11.2 1.0 C A:ASP13 4.2 12.5 0.2 C A:ASP13 4.3 12.4 0.8 O5' A:DTP506 4.3 11.9 1.0 CB A:ASP13 4.3 13.4 0.8 N A:ASP15 4.5 9.0 1.0 N A:CYS16 4.5 9.8 1.0 CB A:ASP13 4.6 13.8 0.2 CA A:ASP15 4.6 9.9 1.0 CB A:ASP115 4.6 10.7 1.0 O A:ASP13 4.6 12.9 0.2 O A:ASP13 4.6 12.9 0.8 O2B A:DTP506 4.7 11.5 1.0 O2A A:DTP506 4.7 16.7 1.0 CE A:LYS231 4.7 22.5 1.0 O3G A:DTP506 4.7 12.8 1.0 CB A:MET14 4.7 12.3 1.0 CA A:ASP13 4.8 13.7 0.2 C A:ASP15 4.8 10.7 1.0 CA A:ASP13 4.8 13.8 0.8 N A:PHE17 4.8 10.8 1.0 O A:ASP115 4.9 14.6 1.0 CB A:PHE17 4.9 9.3 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