Magnesium in PDB 3q8q: Human Dna Polymerase Iota Incorporating Datp Opposite 8-Oxo-Guanine

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

The structure of Human Dna Polymerase Iota Incorporating Datp Opposite 8-Oxo-Guanine, PDB code: 3q8q 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)	32.65 / 2.03
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.731, 98.731, 202.271, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 25.3

The binding sites of Magnesium atom in the Human Dna Polymerase Iota Incorporating Datp Opposite 8-Oxo-Guanine (pdb code 3q8q). 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 Datp Opposite 8-Oxo-Guanine, PDB code: 3q8q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Iota Incorporating Datp 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 Datp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg421 b:27.5 occ:1.00 OP1 P:DC872 2.5 31.7 1.0 O B:LYS237 2.5 39.8 1.0 O B:HOH553 2.6 41.4 1.0 O B:ILE242 2.6 43.5 1.0 O B:HOH445 2.6 39.5 1.0 O B:ILE239 2.8 26.2 1.0 C B:ILE242 3.5 43.4 1.0 C B:ILE239 3.5 34.4 1.0 C B:LYS237 3.7 46.0 1.0 P P:DC872 3.7 30.4 1.0 O P:HOH261 3.8 54.1 1.0 N B:ILE242 4.0 41.6 1.0 OP2 P:DC872 4.0 28.7 1.0 CA B:PRO240 4.0 36.6 1.0 N B:PRO240 4.1 31.0 1.0 CD B:LYS237 4.1 67.5 1.0 N B:GLY241 4.2 34.6 1.0 CA B:ILE242 4.3 34.2 1.0 N B:ILE239 4.3 27.7 1.0 C B:GLU238 4.4 33.5 1.0 N B:GLY243 4.4 46.4 1.0 CA B:LYS237 4.4 47.6 1.0 CG B:LYS237 4.5 68.2 1.0 CA B:GLY243 4.5 56.4 1.0 C B:PRO240 4.5 32.8 1.0 CA B:ILE239 4.6 29.5 1.0 N B:GLU238 4.6 42.1 1.0 CA B:GLU238 4.7 42.3 1.0 O B:GLU238 4.7 31.9 1.0 CB B:ILE242 4.8 39.5 1.0 NZ B:LYS237 4.8 78.7 1.0 O3' P:DC871 4.8 31.0 1.0 O5' P:DC872 4.8 29.5 1.0 CE B:LYS237 4.9 75.8 1.0 C B:GLY241 4.9 40.1 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Iota Incorporating Datp 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 Datp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg422 b:43.9 occ:1.00 O B:LEU35 2.1 32.3 1.0 OD1 B:ASP34 2.3 27.8 1.0 O1G T:DTP1 2.4 42.0 0.8 O2B T:DTP1 2.5 43.0 0.8 O2A T:DTP1 2.6 43.3 0.8 C B:LEU35 3.3 24.4 1.0 PB T:DTP1 3.3 48.2 0.8 O3A T:DTP1 3.3 49.1 0.8 OD1 B:ASP126 3.4 46.3 1.0 CG B:ASP34 3.5 29.7 1.0 PA T:DTP1 3.6 52.1 0.8 CG B:ASP126 3.6 40.9 1.0 PG T:DTP1 3.7 48.2 0.8 N B:LEU35 3.8 22.9 1.0 O3B T:DTP1 3.8 45.9 0.8 OD2 B:ASP126 3.9 38.0 1.0 O B:HOH487 3.9 38.7 1.0 O B:HOH569 4.0 42.6 1.0 CA B:LEU35 4.0 21.2 1.0 OD2 B:ASP34 4.1 34.6 1.0 C B:ASP34 4.1 23.0 1.0 CB B:ASP126 4.2 29.9 1.0 O5' T:DTP1 4.3 48.5 0.8 N B:ASP36 4.3 26.4 1.0 N B:CYS37 4.4 33.4 1.0 O3G T:DTP1 4.5 44.2 0.8 O B:ASP34 4.5 24.6 1.0 CA B:ASP36 4.5 35.8 1.0 CB B:ASP34 4.6 23.0 1.0 CB B:LEU35 4.6 22.1 1.0 O B:ASP126 4.7 25.5 1.0 CA B:ASP34 4.7 17.9 1.0 C B:ASP36 4.7 33.3 1.0 O1B T:DTP1 4.8 50.5 0.8 O2G T:DTP1 4.8 48.1 0.8 O1A T:DTP1 4.9 47.7 0.8 N B:PHE38 5.0 30.7 1.0

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