Magnesium in PDB 5kfu: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 80S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 80S:
2.7.7.7;

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 80S, PDB code: 5kfu 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)	19.92 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.350, 98.350, 81.940, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.1

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 80S 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 80S (pdb code 5kfu). 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 80S, PDB code: 5kfu:
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 80S


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 80S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.3 occ:0.90 K A:K507 0.0 17.8 0.1 OE2 A:GLU116 2.2 27.2 1.0 OD2 A:ASP13 2.2 24.2 0.9 O A:HOH819 2.3 22.5 1.0 O3' P:DT8 2.4 17.9 1.0 OD1 A:ASP115 2.4 14.4 1.0 O1A A:DTP506 2.4 12.9 1.0 OD1 A:ASP13 3.1 15.2 0.1 OD2 A:ASP13 3.1 18.0 0.1 C3' P:DT8 3.2 23.6 1.0 CD A:GLU116 3.2 27.5 1.0 CG A:ASP13 3.3 17.2 0.9 CG A:ASP115 3.3 13.1 1.0 CG A:ASP13 3.4 17.1 0.1 CA A:CA502 3.5 10.7 0.6 MG A:MG503 3.5 10.8 0.5 OD2 A:ASP115 3.6 13.9 1.0 PA A:DTP506 3.6 12.3 1.0 OD1 A:ASP13 3.7 20.5 0.9 OG A:SER113 3.8 18.1 1.0 OE1 A:GLU116 4.0 27.4 1.0 C4' P:DT8 4.0 19.9 1.0 CB A:GLU116 4.0 20.4 1.0 CG A:GLU116 4.1 16.4 1.0 O5' A:DTP506 4.1 11.2 1.0 O2A A:DTP506 4.1 16.6 1.0 C5' A:DTP506 4.3 13.4 1.0 NZ A:LYS224 4.3 20.3 0.8 O A:HOH657 4.3 24.1 1.0 C5' P:DT8 4.4 24.6 0.5 O P:HOH103 4.5 21.8 0.8 CB A:ASP13 4.5 12.9 0.9 C2' P:DT8 4.5 22.6 1.0 C5' P:DT8 4.5 25.1 0.5 CB A:ASP13 4.6 13.1 0.1 C A:ASP115 4.6 12.7 1.0 O A:ASP115 4.7 14.0 1.0 CB A:ASP115 4.7 11.4 1.0 CB A:SER113 4.8 16.9 1.0 N A:GLU116 4.8 11.3 1.0 O1G A:DTP506 4.8 12.2 1.0 O3A A:DTP506 5.0 12.2 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 80S


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 80S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:10.8 occ:0.45 CA A:CA502 0.0 10.7 0.6 O1G A:DTP506 2.2 12.2 1.0 OD2 A:ASP115 2.2 13.9 1.0 OD1 A:ASP13 2.3 20.5 0.9 O1B A:DTP506 2.3 11.0 1.0 O A:MET14 2.3 12.5 1.0 O1A A:DTP506 2.3 12.9 1.0 OD1 A:ASP13 2.4 15.2 0.1 CG A:ASP13 2.9 17.2 0.9 CG A:ASP13 3.0 17.1 0.1 OD2 A:ASP13 3.0 24.2 0.9 OD2 A:ASP13 3.0 18.0 0.1 CG A:ASP115 3.3 13.1 1.0 PB A:DTP506 3.3 11.5 1.0 PA A:DTP506 3.5 12.3 1.0 C A:MET14 3.5 11.0 1.0 PG A:DTP506 3.5 11.8 1.0 MG A:MG501 3.5 18.3 0.9 K A:K507 3.5 17.8 0.1 O3A A:DTP506 3.6 12.2 1.0 OD1 A:ASP115 3.7 14.4 1.0 O3B A:DTP506 3.8 10.1 1.0 NZ A:LYS231 3.8 15.1 1.0 O A:HOH657 3.8 24.1 1.0 N A:MET14 3.9 11.1 1.0 C5' A:DTP506 4.1 13.4 1.0 O2G A:DTP506 4.1 13.3 1.0 CA A:MET14 4.2 11.8 1.0 C A:ASP13 4.2 11.2 0.9 O A:HOH819 4.3 22.5 1.0 O5' A:DTP506 4.3 11.2 1.0 CB A:ASP13 4.3 12.9 0.9 C A:ASP13 4.3 11.4 0.1 CB A:ASP13 4.4 13.1 0.1 N A:ASP15 4.5 8.9 1.0 N A:CYS16 4.5 9.6 1.0 CA A:ASP15 4.6 8.8 1.0 CB A:ASP115 4.6 11.4 1.0 O A:ASP13 4.6 12.1 0.9 CE A:LYS231 4.7 22.8 1.0 O2B A:DTP506 4.7 12.3 1.0 O3G A:DTP506 4.7 12.8 1.0 O A:ASP13 4.7 12.2 0.1 O2A A:DTP506 4.7 16.6 1.0 CB A:MET14 4.7 12.3 1.0 C A:ASP15 4.7 11.4 1.0 CA A:ASP13 4.8 13.9 0.9 N A:PHE17 4.8 9.7 1.0 CA A:ASP13 4.8 13.8 0.1 O A:ASP115 4.9 14.0 1.0 CB A:PHE17 4.9 9.5 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