Magnesium in PDB 3gv7: Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dttp

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

The structure of Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dttp, PDB code: 3gv7 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)	27.04 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.190, 97.190, 201.940, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 25.8

The binding sites of Magnesium atom in the Human Dna Polymerase Iota in Complex with T Template Dna and Incoming Dttp (pdb code 3gv7). 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 Dttp, PDB code: 3gv7:
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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg871 b:32.2 occ:1.00 OD1 B:ASP126 2.0 44.6 1.0 O B:LEU35 2.2 41.6 1.0 O1G B:TTP421 2.2 44.8 1.0 O2A B:TTP421 2.3 40.8 1.0 OD1 B:ASP34 2.3 47.9 1.0 O1B B:TTP421 2.3 38.6 1.0 O B:HOH496 2.6 66.9 1.0 CG B:ASP126 3.1 40.0 1.0 PB B:TTP421 3.3 42.1 1.0 C B:LEU35 3.4 41.7 1.0 CG B:ASP34 3.4 43.9 1.0 PG B:TTP421 3.5 46.0 1.0 PA B:TTP421 3.5 45.3 1.0 OD2 B:ASP126 3.6 40.5 1.0 O3A B:TTP421 3.7 44.1 1.0 O B:HOH610 3.7 54.1 1.0 N B:LEU35 3.8 42.0 1.0 MG B:MG422 3.8 59.5 1.0 O3B B:TTP421 3.9 45.1 1.0 OD2 B:ASP34 4.0 50.5 1.0 CA B:LEU35 4.1 42.5 1.0 C B:ASP34 4.2 41.1 1.0 C5' B:TTP421 4.2 44.7 1.0 O2G B:TTP421 4.2 44.2 1.0 O5' B:TTP421 4.4 44.0 1.0 CB B:ASP126 4.4 38.1 1.0 N B:ASP36 4.4 41.1 1.0 CB B:ASP34 4.6 42.4 1.0 O B:ASP34 4.6 41.1 1.0 O3G B:TTP421 4.6 45.6 1.0 N B:CYS37 4.6 41.6 1.0 CA B:ASP36 4.7 41.2 1.0 CA B:ASP34 4.7 41.4 1.0 CB B:LEU35 4.7 42.6 1.0 O2B B:TTP421 4.7 42.3 1.0 C B:ASP36 4.7 41.4 1.0 O1A B:TTP421 4.7 41.5 1.0 O B:ASP126 4.8 38.6 1.0 N B:PHE38 4.8 41.6 1.0 OE2 B:GLU127 4.9 47.8 1.0

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


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg422 b:59.5 occ:1.00 O B:HOH662 2.8 62.0 1.0 O1G B:TTP421 2.9 44.8 1.0 OD2 B:ASP34 2.9 50.5 1.0 O B:HOH496 3.3 66.9 1.0 O2A B:TTP421 3.4 40.8 1.0 O3G B:TTP421 3.6 45.6 1.0 CG B:ASP34 3.6 43.9 1.0 OD1 B:ASP34 3.7 47.9 1.0 MG B:MG871 3.8 32.2 1.0 PG B:TTP421 3.8 46.0 1.0 O1A B:TTP421 4.1 41.5 1.0 NZ B:LYS77 4.1 64.3 1.0 O B:HOH527 4.1 43.2 1.0 PA B:TTP421 4.1 45.3 1.0 NZ B:LYS214 4.2 48.6 1.0 O B:HOH610 4.4 54.1 1.0 OE2 B:GLU127 4.4 47.8 1.0 O3A B:TTP421 4.5 44.1 1.0 O3B B:TTP421 4.8 45.1 1.0 O2G B:TTP421 5.0 44.2 1.0 CE B:LYS214 5.0 51.3 1.0 CB B:ASP34 5.0 42.4 1.0 O B:HOH661 5.0 67.6 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