Magnesium in PDB 4o3p: Crystal Structure of Human Polymerase Eta Inserting Dctp Opposite An 8-Oxog Containing Dna Template

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

The structure of Crystal Structure of Human Polymerase Eta Inserting Dctp Opposite An 8-Oxog Containing Dna Template, PDB code: 4o3p 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)	42.52 / 1.72
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.198, 98.198, 81.551, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.8

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta Inserting Dctp Opposite An 8-Oxog Containing Dna Template (pdb code 4o3p). 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 Dctp Opposite An 8-Oxog Containing Dna Template, PDB code: 4o3p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Dctp 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 Dctp Opposite An 8-Oxog Containing Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:9.1 occ:1.00 OD2 A:ASP13 2.0 11.5 1.0 O1G A:0KX501 2.1 9.9 1.0 O1B A:0KX501 2.1 9.1 1.0 OD2 A:ASP115 2.1 9.4 1.0 O A:MET14 2.1 10.7 1.0 O2A A:0KX501 2.2 10.7 1.0 CG A:ASP13 3.0 10.5 1.0 PB A:0KX501 3.1 10.7 1.0 CG A:ASP115 3.2 13.3 1.0 PA A:0KX501 3.3 10.9 1.0 C A:MET14 3.3 9.2 1.0 PG A:0KX501 3.3 11.4 1.0 OD1 A:ASP13 3.4 14.0 1.0 N3A A:0KX501 3.4 11.6 1.0 MG A:MG503 3.5 12.2 1.0 O3B A:0KX501 3.6 9.7 1.0 OD1 A:ASP115 3.6 10.4 1.0 NZ A:LYS231 3.8 9.6 1.0 N A:MET14 3.8 7.9 1.0 O A:HOH602 3.8 17.8 1.0 O3G A:0KX501 4.0 10.6 1.0 C5' A:0KX501 4.0 9.6 1.0 CA A:MET14 4.0 9.2 1.0 O5' A:0KX501 4.2 10.0 1.0 C A:ASP13 4.2 8.5 1.0 CB A:ASP13 4.3 10.0 1.0 O A:HOH601 4.3 13.6 1.0 N A:ASP15 4.4 9.1 1.0 CB A:ASP115 4.5 10.2 1.0 CE A:LYS231 4.5 16.9 1.0 O2B A:0KX501 4.5 10.9 1.0 CA A:ASP15 4.5 7.8 1.0 O1A A:0KX501 4.5 13.6 1.0 CB A:MET14 4.6 10.8 1.0 N A:CYS16 4.6 9.6 1.0 O2G A:0KX501 4.6 12.9 1.0 O A:ASP13 4.6 10.7 1.0 C A:ASP15 4.7 10.2 1.0 N A:PHE17 4.7 9.6 1.0 CA A:ASP13 4.7 9.4 1.0 CB A:PHE17 4.8 8.0 1.0 O A:ASP115 4.9 11.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Dctp 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 Dctp Opposite An 8-Oxog Containing Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:12.2 occ:1.00 OD1 A:ASP13 2.1 14.0 1.0 OD1 A:ASP115 2.1 10.4 1.0 OE1 A:GLU116 2.1 15.1 1.0 O2A A:0KX501 2.2 10.7 1.0 O A:HOH601 2.2 13.6 1.0 O3' P:DT8 2.2 14.9 0.3 O3' P:DT8 2.3 15.2 0.7 CG A:ASP115 3.0 13.3 1.0 CG A:ASP13 3.1 10.5 1.0 CD A:GLU116 3.1 18.7 1.0 C3' P:DT8 3.2 12.1 0.7 PA A:0KX501 3.3 10.9 1.0 C3' P:DT8 3.3 12.2 0.3 OD2 A:ASP115 3.3 9.4 1.0 OD2 A:ASP13 3.5 11.5 1.0 MG A:MG502 3.5 9.1 1.0 O1A A:0KX501 3.7 13.6 1.0 OG A:SER113 3.7 13.3 1.0 O5' A:0KX501 3.8 10.0 1.0 OE2 A:GLU116 3.8 19.4 1.0 C5' A:0KX501 4.1 9.6 1.0 CG A:GLU116 4.1 13.5 1.0 O A:HOH602 4.1 17.8 1.0 C4' P:DT8 4.1 13.1 0.7 CB A:GLU116 4.2 11.9 1.0 C4' P:DT8 4.2 13.2 0.3 NZ A:LYS224 4.2 11.9 0.8 O P:HOH102 4.3 13.4 1.0 CB A:ASP13 4.4 10.0 1.0 CB A:ASP115 4.4 10.2 1.0 C2' P:DT8 4.4 13.1 0.7 C2' P:DT8 4.5 13.4 0.3 C A:ASP115 4.5 11.3 1.0 O A:ASP115 4.6 11.0 1.0 C5' P:DT8 4.7 11.8 0.3 O1G A:0KX501 4.7 9.9 1.0 N3A A:0KX501 4.7 11.6 1.0 N A:GLU116 4.8 8.9 1.0 CB A:SER113 4.8 14.1 1.0 C5' P:DT8 4.8 16.2 0.7 O A:HOH741 4.8 25.9 1.0 O1B A:0KX501 4.9 9.1 1.0 CA A:ASP115 4.9 11.1 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