Magnesium in PDB 3h4d: Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp

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

The structure of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp, PDB code: 3h4d was solved by R.Jain, D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.68 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.915, 97.915, 203.392, 90.00, 90.00, 120.00
R / Rfree (%)	25.4 / 27

The structure of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Magnesium atom in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp (pdb code 3h4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp, PDB code: 3h4d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Human Dna Polymerase Iota with Template U/T 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 Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:64.0 occ:1.00 O1A T:DGT875 2.1 45.8 0.7 OD2 A:ASP34 2.2 26.6 1.0 O A:LEU35 2.3 27.9 1.0 O2B T:DGT875 2.7 40.4 0.7 O1G T:DGT875 2.8 42.3 0.7 MG A:MG872 2.9 58.6 1.0 OD2 A:ASP126 3.0 33.3 1.0 CG A:ASP126 3.2 33.3 1.0 PA T:DGT875 3.4 46.6 0.7 C A:LEU35 3.4 26.3 1.0 CG A:ASP34 3.4 27.4 1.0 OD1 A:ASP126 3.5 36.6 1.0 PB T:DGT875 3.6 47.3 0.7 N A:LEU35 3.6 26.4 1.0 O3A T:DGT875 3.7 45.5 0.7 O A:HOH452 3.8 45.6 1.0 CA A:LEU35 3.9 27.9 1.0 C5' T:DGT875 4.0 47.5 0.7 CB A:ASP126 4.0 29.8 1.0 OD1 A:ASP34 4.0 28.4 1.0 PG T:DGT875 4.1 44.4 0.7 O5' T:DGT875 4.1 45.2 0.7 O3B T:DGT875 4.2 42.6 0.7 C A:ASP34 4.2 25.4 1.0 O A:HOH475 4.3 39.6 1.0 CB A:LEU35 4.5 29.4 1.0 O2A T:DGT875 4.5 48.9 0.7 N A:ASP36 4.6 26.3 1.0 CB A:ASP34 4.6 25.3 1.0 CA A:ASP34 4.6 24.4 1.0 O A:ASP126 4.7 26.5 1.0 O1B T:DGT875 4.8 41.2 0.7 N A:CYS37 4.9 24.5 1.0 O A:ASP34 4.9 25.5 1.0 CA A:ASP36 4.9 26.4 1.0 O3G T:DGT875 4.9 40.7 0.7 CG A:GLU127 5.0 22.4 1.0 C A:ASP36 5.0 25.9 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Human Dna Polymerase Iota with Template U/T 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 Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:58.6 occ:1.00 O1A T:DGT875 2.0 45.8 0.7 OE2 A:GLU127 2.4 26.6 1.0 MG A:MG871 2.9 64.0 1.0 OD2 A:ASP34 3.0 26.6 1.0 PA T:DGT875 3.0 46.6 0.7 OD1 A:ASP126 3.1 36.6 1.0 OD1 A:ASP34 3.1 28.4 1.0 O2A T:DGT875 3.2 48.9 0.7 CD A:GLU127 3.2 26.4 1.0 CG A:ASP34 3.3 27.4 1.0 CG A:GLU127 3.3 22.4 1.0 C3' P:DOC873 3.4 37.8 1.0 O A:HOH475 3.5 39.6 1.0 OD2 A:ASP126 3.6 33.3 1.0 CG A:ASP126 3.7 33.3 1.0 O5' T:DGT875 4.1 45.2 0.7 O3A T:DGT875 4.2 45.5 0.7 O1G T:DGT875 4.2 42.3 0.7 OE1 A:GLU127 4.4 25.5 1.0 O A:HOH6 4.4 26.9 1.0 C2' P:DOC873 4.5 36.5 1.0 C4' P:DOC873 4.5 40.2 1.0 CB A:ASP34 4.7 25.3 1.0 CB A:GLU127 4.8 22.4 1.0 C5' T:DGT875 4.8 47.5 0.7 O2B T:DGT875 5.0 40.4 0.7

R.Jain, D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Replication Across Template T/U By Human Dna Polymerase-Iota. Structure V. 17 974 2009.
ISSN: ISSN 0969-2126
PubMed: 19604477
DOI: 10.1016/J.STR.2009.04.011