Magnesium in PDB 3q8r: Human Dna Polymerase Iota Incorporating Dgtp Opposite 8-Oxo-Guanine

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

The structure of Human Dna Polymerase Iota Incorporating Dgtp Opposite 8-Oxo-Guanine, PDB code: 3q8r 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)	39.24 / 2.45
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.290, 98.290, 202.582, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 28

The binding sites of Magnesium atom in the Human Dna Polymerase Iota Incorporating Dgtp Opposite 8-Oxo-Guanine (pdb code 3q8r). 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 Dgtp Opposite 8-Oxo-Guanine, PDB code: 3q8r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Iota Incorporating Dgtp 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 Dgtp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg422 b:44.9 occ:1.00 O B:LYS237 2.5 46.6 1.0 O B:ILE242 2.5 52.6 1.0 OP1 P:DC872 2.6 50.2 1.0 O B:ILE239 2.6 37.7 1.0 O P:HOH51 2.7 42.8 1.0 O B:HOH495 2.8 50.5 1.0 C B:ILE242 3.3 51.5 1.0 C B:ILE239 3.5 49.6 1.0 C B:LYS237 3.6 50.8 1.0 P P:DC872 3.6 51.0 1.0 N B:ILE242 3.9 56.3 1.0 OP2 P:DC872 3.9 44.5 1.0 CA B:PRO240 4.0 47.5 1.0 CA B:ILE242 4.1 45.5 1.0 N B:PRO240 4.1 51.7 1.0 N B:GLY243 4.2 58.8 1.0 N B:GLY241 4.3 44.1 1.0 N B:ILE239 4.4 31.5 1.0 CA B:GLY243 4.4 50.0 1.0 CA B:LYS237 4.4 47.5 1.0 C B:GLU238 4.4 40.0 1.0 CB B:ILE242 4.5 47.3 1.0 C B:PRO240 4.6 46.9 1.0 N B:GLU238 4.6 47.1 1.0 CA B:ILE239 4.6 42.0 1.0 CA B:GLU238 4.7 37.8 1.0 O3' P:DC871 4.7 49.6 1.0 O B:GLU238 4.7 43.0 1.0 O5' P:DC872 4.7 46.6 1.0 O P:HOH45 4.7 49.1 1.0 CB B:LYS237 4.8 41.3 1.0 C B:GLY241 5.0 59.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Iota Incorporating Dgtp 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 Dgtp Opposite 8-Oxo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg423 b:60.2 occ:1.00 O2G B:DGT421 2.3 61.0 0.8 OD1 B:ASP34 2.5 43.2 1.0 O B:LEU35 2.7 41.9 1.0 O2A B:DGT421 2.8 54.9 0.8 O1B B:DGT421 2.8 52.3 0.8 PG B:DGT421 3.0 59.0 0.8 O3A B:DGT421 3.0 58.5 0.8 O1G B:DGT421 3.1 57.2 0.8 CG B:ASP34 3.2 35.2 1.0 PB B:DGT421 3.2 63.1 0.8 O3B B:DGT421 3.3 61.6 0.8 OD2 B:ASP34 3.4 42.2 1.0 O B:HOH538 3.4 69.5 1.0 PA B:DGT421 3.5 65.5 0.8 C B:LEU35 3.7 35.6 1.0 CA B:ASP36 4.3 40.3 1.0 O1A B:DGT421 4.3 63.5 0.8 N B:ASP36 4.3 32.6 1.0 O3G B:DGT421 4.4 62.8 0.8 CB B:ASP34 4.4 35.1 1.0 N B:LEU35 4.4 34.5 1.0 C B:ASP34 4.4 33.8 1.0 NZ B:LYS214 4.5 62.5 1.0 N B:CYS37 4.5 41.5 1.0 O B:ASP34 4.6 38.5 1.0 O2B B:DGT421 4.7 53.2 0.8 CA B:LEU35 4.7 33.3 1.0 O5' B:DGT421 4.8 55.6 0.8 C B:ASP36 4.8 40.7 1.0 CA B:ASP34 4.9 33.8 1.0 OD1 B:ASP126 5.0 47.8 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