Magnesium in PDB 4o3r: Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Da Pair

All present enzymatic activity of Crystal Structure of Human Polymerase Eta Extending An 8-Oxog Dna Lesion: Post Insertion of 8-Oxog-Da 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-Da Pair, PDB code: 4o3r 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)	42.70 / 1.62
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.613, 98.613, 81.842, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 20.4

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-Da Pair (pdb code 4o3r). 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-Da Pair, PDB code: 4o3r:
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-Da 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-Da Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:7.3 occ:1.00 OD2 A:ASP13 2.2 16.4 1.0 OD2 A:ASP115 2.2 15.2 1.0 O1B A:0KX501 2.2 11.3 1.0 O2A A:0KX501 2.3 13.3 1.0 O1G A:0KX501 2.3 12.2 1.0 O A:MET14 2.3 10.3 1.0 CG A:ASP115 3.2 14.3 1.0 MG A:MG503 3.3 31.9 1.0 PB A:0KX501 3.3 11.9 1.0 CG A:ASP13 3.4 21.6 1.0 PA A:0KX501 3.4 13.4 1.0 C A:MET14 3.5 11.9 1.0 PG A:0KX501 3.5 12.6 1.0 OD1 A:ASP115 3.6 15.3 1.0 N3A A:0KX501 3.7 12.5 1.0 O A:HOH1012 3.7 31.0 1.0 O3B A:0KX501 3.7 11.7 1.0 NZ A:LYS231 3.9 12.8 1.0 O A:HOH981 3.9 28.7 1.0 N A:MET14 3.9 10.7 1.0 OD1 A:ASP13 3.9 29.7 1.0 C5' A:0KX501 4.0 12.8 1.0 O5' A:0KX501 4.1 11.9 1.0 CA A:MET14 4.2 12.0 1.0 C A:ASP13 4.2 11.8 1.0 O3G A:0KX501 4.3 13.3 1.0 N A:ASP15 4.5 11.0 1.0 CB A:ASP115 4.5 11.4 1.0 CB A:ASP13 4.6 10.4 1.0 O A:ASP13 4.6 12.6 1.0 N A:CYS16 4.6 9.8 1.0 CE A:LYS231 4.6 19.7 1.0 CB A:MET14 4.6 13.3 1.0 O2B A:0KX501 4.7 11.4 1.0 O1A A:0KX501 4.7 17.0 1.0 O3' P:DA8 4.7 16.1 0.4 CA A:ASP15 4.7 10.0 1.0 O2G A:0KX501 4.7 14.0 1.0 CA A:ASP13 4.7 11.1 1.0 N A:PHE17 4.8 11.3 1.0 C A:ASP15 4.8 10.9 1.0 CB A:PHE17 4.8 8.6 1.0 O A:ASP115 4.9 12.7 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-Da 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-Da Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:31.9 occ:1.00 O3' P:DA8 2.1 16.1 0.4 O2A A:0KX501 2.4 13.3 1.0 OD1 A:ASP115 2.4 15.3 1.0 O A:HOH981 2.5 28.7 1.0 CG A:GLU116 2.8 18.1 1.0 O3' P:DA8 2.9 17.7 0.6 C3' P:DA8 3.0 19.0 0.6 OD2 A:ASP13 3.0 16.4 1.0 OD1 A:ASP13 3.2 29.7 1.0 C3' P:DA8 3.2 20.6 0.4 CD A:GLU116 3.2 24.5 1.0 CG A:ASP13 3.2 21.6 1.0 MG A:MG502 3.3 7.3 1.0 CG A:ASP115 3.3 14.3 1.0 OE2 A:GLU116 3.5 31.1 1.0 OD2 A:ASP115 3.5 15.2 1.0 PA A:0KX501 3.6 13.4 1.0 C4' P:DA8 3.9 17.9 0.6 O A:HOH1012 3.9 31.0 1.0 O5' A:0KX501 4.0 11.9 1.0 OE1 A:GLU116 4.0 36.0 1.0 C4' P:DA8 4.1 17.9 0.4 O1A A:0KX501 4.1 17.0 1.0 OG A:SER113 4.1 16.6 1.0 C5' P:DA8 4.2 24.9 0.6 CB A:GLU116 4.2 13.8 1.0 C5' A:0KX501 4.3 12.8 1.0 C2' P:DA8 4.3 19.3 0.6 C2' P:DA8 4.4 19.3 0.4 NZ A:LYS224 4.4 23.5 0.4 CB A:ASP13 4.4 10.4 1.0 C5' P:DA8 4.5 21.7 0.4 O A:ASP115 4.5 12.7 1.0 C A:ASP115 4.6 12.3 1.0 O1G A:0KX501 4.7 12.2 1.0 CB A:ASP115 4.7 11.4 1.0 N A:GLU116 4.7 11.8 1.0 CA A:GLU116 4.9 12.6 1.0 CA A:ASP13 4.9 11.1 1.0 O1B A:0KX501 4.9 11.3 1.0 N3A A:0KX501 5.0 12.5 1.0 O P:HOH116 5.0 29.0 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