Magnesium in PDB 3gv8: Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp

All present enzymatic activity of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp:
2.7.7.7;

The structure of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp, PDB code: 3gv8 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)	23.84 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.070, 98.070, 203.380, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 24.8

The binding sites of Magnesium atom in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp (pdb code 3gv8). 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 in Complex with T Template Dna and Incoming Dgtp, PDB code: 3gv8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp


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 in Complex with T Template Dna and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg871 b:40.8 occ:1.00 OD1 B:ASP126 2.1 49.2 1.0 O B:LEU35 2.2 38.2 1.0 O2A B:DGT421 2.3 47.8 1.0 O2G B:DGT421 2.3 46.6 1.0 O1B B:DGT421 2.4 41.9 1.0 OD1 B:ASP34 2.4 40.9 1.0 O B:HOH632 3.0 48.6 1.0 CG B:ASP126 3.2 41.8 1.0 PB B:DGT421 3.3 47.5 1.0 C B:LEU35 3.4 35.6 1.0 MG B:MG422 3.5 54.6 1.0 PA B:DGT421 3.5 53.4 1.0 PG B:DGT421 3.5 49.4 1.0 CG B:ASP34 3.6 39.9 1.0 OD2 B:ASP126 3.6 40.1 1.0 O3A B:DGT421 3.7 47.8 1.0 O B:HOH592 3.8 44.8 1.0 N B:LEU35 3.8 34.7 1.0 O3B B:DGT421 3.9 48.9 1.0 O B:HOH589 4.1 45.5 1.0 C B:ASP34 4.1 34.6 1.0 CA B:LEU35 4.1 36.4 1.0 OD2 B:ASP34 4.2 42.8 1.0 O1G B:DGT421 4.2 43.0 1.0 O5' B:DGT421 4.3 49.7 1.0 CB B:ASP126 4.4 36.8 1.0 N B:ASP36 4.4 35.0 1.0 N B:CYS37 4.5 33.5 1.0 O B:ASP34 4.6 34.4 1.0 O B:ASP126 4.7 35.2 1.0 CB B:ASP34 4.7 35.4 1.0 CA B:ASP36 4.7 35.2 1.0 C B:ASP36 4.7 34.5 1.0 O3G B:DGT421 4.7 50.2 1.0 CA B:ASP34 4.7 35.4 1.0 O2B B:DGT421 4.7 44.4 1.0 O1A B:DGT421 4.8 49.6 1.0 CB B:LEU35 4.8 35.6 1.0 N B:PHE38 4.9 33.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dgtp


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 in Complex with T Template Dna and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg422 b:54.6 occ:1.00 CG B:ASP126 2.0 41.8 1.0 OD2 B:ASP126 2.1 40.1 1.0 O5' B:DGT421 2.2 49.7 1.0 OD1 B:ASP126 2.4 49.2 1.0 C4' B:DGT421 2.6 50.1 1.0 O B:HOH631 2.6 45.9 1.0 CB B:ASP126 2.8 36.8 1.0 O2A B:DGT421 2.8 47.8 1.0 C5' B:DGT421 2.9 52.4 1.0 PA B:DGT421 3.0 53.4 1.0 O1B B:DGT421 3.0 41.9 1.0 O4' B:DGT421 3.3 49.9 1.0 MG B:MG871 3.5 40.8 1.0 O3A B:DGT421 3.6 47.8 1.0 O B:HOH632 3.8 48.6 1.0 PB B:DGT421 3.8 47.5 1.0 C3' B:DGT421 3.9 47.8 1.0 CB B:PHE38 3.9 32.8 1.0 O B:HOH485 3.9 31.2 1.0 CA B:ASP126 4.0 35.5 1.0 O3' B:DGT421 4.1 37.1 1.0 N B:ASP126 4.3 34.2 1.0 O1A B:DGT421 4.3 49.6 1.0 O2B B:DGT421 4.4 44.4 1.0 C2' P:DC873 4.4 36.2 1.0 C1' B:DGT421 4.6 49.1 1.0 C B:ASP126 4.6 35.0 1.0 C3' P:DC873 4.8 37.4 1.0 N B:PHE38 4.8 33.5 1.0 CG B:PHE38 4.8 33.9 1.0 O B:LEU35 4.9 38.2 1.0 CD2 B:PHE38 4.9 32.6 1.0 O B:ASP126 4.9 35.2 1.0 C2' B:DGT421 5.0 48.1 1.0 CA B:PHE38 5.0 33.3 1.0 OD1 B:ASP34 5.0 40.9 1.0

K.N.Kirouac, H.Ling. Structural Basis of Error-Prone Replication and Stalling at A Thymine Base By Human Dna Polymerase Iota Embo J. V. 28 1644 2009.
ISSN: ISSN 0261-4189
PubMed: 19440206
DOI: 10.1038/EMBOJ.2009.122