Magnesium in PDB 3q8p: Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine

All present enzymatic activity of Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine:
2.7.7.7;

The structure of Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine, PDB code: 3q8p was solved by K.N.Kirouac, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.73 / 1.95
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	99.161, 99.161, 202.318, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 25.7

The binding sites of Magnesium atom in the Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine (pdb code 3q8p). 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 Iota Incorporating Dctp Opposite 8-Oxo-Guanine, PDB code: 3q8p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine


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 Iota Incorporating Dctp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg422 b:21.9 occ:1.00 O B:LYS237 2.5 30.6 1.0 O B:ILE242 2.5 31.3 1.0 OP1 P:DC872 2.5 27.2 1.0 O P:HOH176 2.6 37.1 1.0 O B:HOH615 2.7 38.8 1.0 O B:ILE239 2.7 26.2 1.0 C B:ILE242 3.4 31.7 1.0 C B:ILE239 3.5 29.0 1.0 C B:LYS237 3.6 34.8 1.0 P P:DC872 3.7 25.1 1.0 O P:HOH94 3.8 42.4 1.0 N B:ILE242 3.9 31.1 1.0 CA B:PRO240 4.0 30.9 1.0 N B:PRO240 4.0 28.0 1.0 OP2 P:DC872 4.0 23.9 1.0 O B:HOH618 4.1 46.4 1.0 N B:GLY241 4.2 27.8 1.0 N B:ILE239 4.2 26.3 1.0 CA B:ILE242 4.2 31.2 1.0 CA B:LYS237 4.3 36.8 1.0 N B:GLY243 4.3 35.9 1.0 C B:GLU238 4.3 26.5 1.0 CA B:GLY243 4.5 39.2 1.0 CA B:ILE239 4.5 27.0 1.0 C B:PRO240 4.5 30.3 1.0 N B:GLU238 4.5 37.1 1.0 CB B:ILE242 4.6 30.7 1.0 CA B:GLU238 4.6 32.7 1.0 O B:GLU238 4.8 29.6 1.0 O5' P:DC872 4.8 26.6 1.0 O B:HOH779 4.8 49.1 1.0 O3' P:DC871 4.8 25.2 1.0 CB B:LYS237 4.9 40.5 1.0 C B:GLY241 4.9 36.0 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Iota Incorporating Dctp Opposite 8-Oxo-Guanine


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 Iota Incorporating Dctp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg423 b:27.9 occ:1.00 O B:LEU35 2.1 25.1 1.0 O2B B:DCP421 2.2 28.2 0.8 OD1 B:ASP126 2.2 28.9 1.0 O2G B:DCP421 2.2 24.6 0.8 OD1 B:ASP34 2.3 25.2 1.0 O1A B:DCP421 3.2 34.5 0.8 CG B:ASP126 3.2 27.4 1.0 C B:LEU35 3.2 23.8 1.0 PB B:DCP421 3.3 31.3 0.8 PG B:DCP421 3.4 30.4 0.8 CG B:ASP34 3.5 27.7 1.0 O3B B:DCP421 3.6 33.8 0.8 N B:LEU35 3.6 22.0 1.0 OD2 B:ASP126 3.7 24.6 1.0 O3A B:DCP421 3.8 34.8 0.8 CA B:LEU35 3.9 23.0 1.0 O B:HOH499 3.9 34.1 1.0 C B:ASP34 4.0 22.8 1.0 O B:HOH623 4.0 37.1 1.0 OD2 B:ASP34 4.1 33.6 1.0 PA B:DCP421 4.1 43.7 0.8 O3G B:DCP421 4.2 29.2 0.8 N B:ASP36 4.3 22.0 1.0 N B:CYS37 4.3 21.3 1.0 O B:ASP34 4.4 21.8 1.0 CB B:ASP126 4.4 22.9 1.0 CA B:ASP36 4.5 25.9 1.0 O1G B:DCP421 4.5 34.6 0.8 CB B:LEU35 4.5 22.1 1.0 CB B:ASP34 4.6 23.7 1.0 O1B B:DCP421 4.6 31.6 0.8 CA B:ASP34 4.6 20.3 1.0 C B:ASP36 4.6 26.4 1.0 O B:ASP126 4.7 17.4 1.0 N B:PHE38 4.8 25.0 1.0 O2A B:DCP421 5.0 41.2 0.8

K.N.Kirouac, H.Ling. Unique Active Site Promotes Error-Free Replication Opposite An 8-Oxo-Guanine Lesion By Human Dna Polymerase Iota. Proc.Natl.Acad.Sci.Usa V. 108 3210 2011.
ISSN: ISSN 0027-8424
PubMed: 21300901
DOI: 10.1073/PNAS.1013909108