Magnesium in PDB 4o3s: Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair

All present enzymatic activity of Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair:
2.7.7.7;

The structure of Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair, PDB code: 4o3s 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)	42.57 / 1.72
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.312, 98.312, 81.596, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair (pdb code 4o3s). 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 Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair, PDB code: 4o3s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair


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 Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:9.4 occ:1.00 OD2 A:ASP13 2.1 21.6 1.0 O1B A:0KX501 2.2 14.1 1.0 OD2 A:ASP115 2.2 17.7 1.0 O2A A:0KX501 2.2 17.1 1.0 O1G A:0KX501 2.2 15.5 1.0 O A:MET14 2.3 14.3 1.0 CG A:ASP13 3.0 18.3 1.0 PB A:0KX501 3.2 15.2 1.0 CG A:ASP115 3.2 18.4 1.0 OD1 A:ASP13 3.3 29.1 1.0 PA A:0KX501 3.4 16.6 1.0 MG A:MG503 3.4 26.1 1.0 C A:MET14 3.4 13.3 1.0 PG A:0KX501 3.5 15.7 1.0 N3A A:0KX501 3.6 16.4 1.0 OD1 A:ASP115 3.6 18.1 1.0 O3B A:0KX501 3.7 14.8 1.0 O A:HOH683 3.8 28.9 1.0 N A:MET14 3.9 13.1 1.0 NZ A:LYS231 4.0 15.6 1.0 C5' A:0KX501 4.0 15.3 1.0 O5' A:0KX501 4.2 15.8 1.0 CA A:MET14 4.2 12.4 1.0 O A:HOH668 4.2 25.7 1.0 O3G A:0KX501 4.2 16.2 1.0 C A:ASP13 4.3 15.5 1.0 CB A:ASP13 4.3 14.1 1.0 N A:ASP15 4.5 13.2 1.0 CB A:ASP115 4.5 16.1 1.0 CE A:LYS231 4.6 25.1 1.0 O2B A:0KX501 4.6 13.2 1.0 O1A A:0KX501 4.6 21.5 1.0 O2G A:0KX501 4.6 16.7 1.0 CB A:MET14 4.7 14.9 1.0 N A:CYS16 4.7 11.9 1.0 CA A:ASP15 4.7 13.2 1.0 N A:PHE17 4.7 12.4 1.0 O A:ASP13 4.7 15.4 1.0 O3' P:DC8 4.8 18.6 0.4 C A:ASP15 4.8 13.3 1.0 CA A:ASP13 4.8 15.3 1.0 CB A:PHE17 4.8 12.5 1.0 O A:ASP115 4.9 13.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair


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 Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Dc Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:26.1 occ:1.00 O3' P:DC8 2.0 18.6 0.4 OD1 A:ASP13 2.1 29.1 1.0 OE2 A:GLU116 2.2 38.0 1.0 OD1 A:ASP115 2.2 18.1 1.0 O A:HOH668 2.3 25.7 1.0 O2A A:0KX501 2.3 17.1 1.0 O3' P:DC8 2.7 20.8 0.6 CG A:GLU116 2.8 28.6 1.0 CD A:GLU116 2.8 30.5 1.0 C3' P:DC8 3.0 22.6 0.6 C3' P:DC8 3.1 22.5 0.4 CG A:ASP13 3.1 18.3 1.0 CG A:ASP115 3.1 18.4 1.0 OD2 A:ASP115 3.4 17.7 1.0 MG A:MG502 3.4 9.4 1.0 OD2 A:ASP13 3.5 21.6 1.0 PA A:0KX501 3.5 16.6 1.0 OG A:SER113 3.9 21.0 1.0 C4' P:DC8 3.9 21.5 0.6 O1A A:0KX501 4.0 21.5 1.0 O5' A:0KX501 4.0 15.8 1.0 C4' P:DC8 4.0 21.1 0.4 OE1 A:GLU116 4.0 32.2 1.0 O A:HOH683 4.1 28.9 1.0 C5' A:0KX501 4.2 15.3 1.0 CB A:GLU116 4.2 20.8 1.0 C2' P:DC8 4.3 23.1 0.6 C2' P:DC8 4.3 23.1 0.4 C5' P:DC8 4.4 24.0 0.4 C5' P:DC8 4.4 22.1 0.6 CB A:ASP13 4.4 14.1 1.0 NZ A:LYS224 4.4 24.2 0.6 C A:ASP115 4.5 15.9 1.0 O A:ASP115 4.5 13.8 1.0 CB A:ASP115 4.6 16.1 1.0 N A:GLU116 4.7 14.5 1.0 O1G A:0KX501 4.8 15.5 1.0 O1B A:0KX501 4.9 14.1 1.0 N3A A:0KX501 4.9 16.4 1.0 CA A:GLU116 5.0 16.1 1.0 CA A:ASP115 5.0 15.2 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