Magnesium in PDB 4o3o: Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template

All present enzymatic activity of Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template:
2.7.7.7;

The structure of Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template, PDB code: 4o3o was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.68 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.567, 98.567, 81.555, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template (pdb code 4o3o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template, PDB code: 4o3o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.4 occ:1.00 OD2 A:ASP13 2.0 18.4 1.0 O3G A:DZ4501 2.1 17.1 1.0 O1B A:DZ4501 2.1 14.9 1.0 OD2 A:ASP115 2.1 14.1 1.0 O A:MET14 2.1 15.2 1.0 O1A A:DZ4501 2.2 16.6 1.0 CG A:ASP13 3.0 18.8 1.0 PB A:DZ4501 3.1 15.8 1.0 CG A:ASP115 3.1 17.4 1.0 C A:MET14 3.3 14.1 1.0 PA A:DZ4501 3.3 17.3 1.0 PG A:DZ4501 3.3 17.9 1.0 OD1 A:ASP13 3.4 19.1 1.0 N3A A:DZ4501 3.4 17.5 1.0 MG A:MG503 3.5 13.7 1.0 OD1 A:ASP115 3.6 16.2 1.0 O3B A:DZ4501 3.6 15.7 1.0 NZ A:LYS231 3.7 16.1 1.0 N A:MET14 3.8 14.3 1.0 O A:HOH604 3.9 23.1 1.0 C5' A:DZ4501 4.0 14.7 1.0 CA A:MET14 4.0 13.8 1.0 O1G A:DZ4501 4.0 16.9 1.0 O5' A:DZ4501 4.1 16.9 1.0 C A:ASP13 4.2 16.7 1.0 CB A:ASP13 4.3 15.2 1.0 N A:ASP15 4.3 13.6 1.0 O A:HOH603 4.4 19.4 1.0 CB A:ASP115 4.4 17.0 1.0 CE A:LYS231 4.5 21.9 1.0 O2B A:DZ4501 4.5 16.2 1.0 CB A:MET14 4.5 18.3 1.0 O2G A:DZ4501 4.5 20.4 1.0 O2A A:DZ4501 4.5 19.4 1.0 CA A:ASP15 4.6 15.0 1.0 O A:ASP13 4.6 16.3 1.0 N A:CYS16 4.6 15.1 1.0 C A:ASP15 4.7 16.6 1.0 CA A:ASP13 4.7 15.3 1.0 N A:PHE17 4.7 13.9 1.0 CB A:PHE17 4.8 15.4 1.0 O A:ASP115 4.9 16.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Polymerase Eta Inserting Datp Opposite An 8-Oxog Containing Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.7 occ:1.00 OD1 A:ASP115 2.0 16.2 1.0 OD1 A:ASP13 2.1 19.1 1.0 OE2 A:GLU116 2.1 21.5 1.0 O1A A:DZ4501 2.2 16.6 1.0 O A:HOH603 2.2 19.4 1.0 O3' P:DT8 2.3 20.1 0.2 O3' P:DT8 2.3 20.4 0.8 CG A:ASP115 3.0 17.4 1.0 CG A:ASP13 3.1 18.8 1.0 CD A:GLU116 3.2 25.2 1.0 C3' P:DT8 3.3 17.9 0.8 PA A:DZ4501 3.3 17.3 1.0 C3' P:DT8 3.3 18.1 0.2 OD2 A:ASP115 3.4 14.1 1.0 OD2 A:ASP13 3.5 18.4 1.0 MG A:MG502 3.5 13.4 1.0 O2A A:DZ4501 3.7 19.4 1.0 O5' A:DZ4501 3.8 16.9 1.0 OG A:SER113 3.8 17.2 1.0 OE1 A:GLU116 3.8 24.8 1.0 C5' A:DZ4501 4.0 14.7 1.0 C4' P:DT8 4.1 19.3 0.2 C4' P:DT8 4.1 18.9 0.8 CG A:GLU116 4.1 19.0 1.0 O A:HOH604 4.1 23.1 1.0 CB A:GLU116 4.2 19.6 1.0 NZ A:LYS224 4.2 19.5 0.5 O P:HOH102 4.3 19.0 1.0 CB A:ASP13 4.4 15.2 1.0 CB A:ASP115 4.4 17.0 1.0 C2' P:DT8 4.5 19.8 0.8 C5' P:DT8 4.5 20.7 0.2 C2' P:DT8 4.6 19.9 0.2 C A:ASP115 4.6 16.1 1.0 O A:ASP115 4.6 16.8 1.0 O3G A:DZ4501 4.7 17.1 1.0 N3A A:DZ4501 4.7 17.5 1.0 N A:GLU116 4.8 17.4 1.0 CB A:SER113 4.8 18.4 1.0 C5' P:DT8 4.8 20.9 0.8 O1B A:DZ4501 4.8 14.9 1.0 CA A:ASP115 4.9 17.2 1.0

A.Patra, L.D.Nagy, Q.Zhang, Y.Su, L.Muller, F.P.Guengerich, M.Egli. Kinetics, Structure, and Mechanism of 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine Bypass By Human Dna Polymerase Eta J.Biol.Chem. V. 289 16867 2014.
ISSN: ISSN 0021-9258
PubMed: 24759104
DOI: 10.1074/JBC.M114.551820