Magnesium in PDB 3g6v: Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota

All present enzymatic activity of Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota:
2.7.7.7;

The structure of Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota, PDB code: 3g6v was solved by D.T.Nair, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.22 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.150, 98.150, 203.315, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 25.1

The binding sites of Magnesium atom in the Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota (pdb code 3g6v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota, PDB code: 3g6v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:16.2 occ:1.00 O1A A:ATP875 2.1 28.9 1.0 OD1 A:ASP126 2.1 35.6 1.0 O2B A:ATP875 2.4 18.2 1.0 O A:LEU35 2.4 17.7 1.0 OD2 A:ASP34 2.4 17.3 1.0 O1G A:ATP875 2.5 24.1 1.0 CG A:ASP126 3.0 24.7 1.0 OD2 A:ASP126 3.3 22.7 1.0 MG A:MG872 3.3 58.6 1.0 PB A:ATP875 3.4 26.9 1.0 PA A:ATP875 3.5 31.2 1.0 C A:LEU35 3.6 17.1 1.0 CG A:ASP34 3.6 17.2 1.0 O3A A:ATP875 3.7 28.2 1.0 PG A:ATP875 3.8 27.1 1.0 N A:LEU35 3.8 14.6 1.0 O A:HOH929 4.0 30.6 1.0 O3B A:ATP875 4.0 28.2 1.0 C5' A:ATP875 4.1 29.3 1.0 O A:HOH932 4.2 29.3 1.0 OD1 A:ASP34 4.2 21.5 1.0 CA A:LEU35 4.2 16.6 1.0 C A:ASP34 4.2 15.6 1.0 CB A:ASP126 4.3 18.5 1.0 O5' A:ATP875 4.4 27.2 1.0 O3G A:ATP875 4.5 21.1 1.0 O A:ASP126 4.5 15.4 1.0 N A:ASP36 4.6 15.7 1.0 CB A:LEU35 4.7 17.7 1.0 O2A A:ATP875 4.7 33.4 1.0 N A:CYS37 4.7 14.5 1.0 CA A:ASP34 4.7 14.1 1.0 O A:ASP34 4.8 15.6 1.0 O1B A:ATP875 4.8 21.9 1.0 CB A:ASP34 4.8 14.2 1.0 CA A:ASP36 4.9 17.4 1.0 C A:ASP36 4.9 16.4 1.0 O2G A:ATP875 5.0 27.3 1.0 N A:PHE38 5.0 12.8 1.0

Magnesium binding site 2 out of 2 in the Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase-Iota within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:58.6 occ:1.00 OE2 A:GLU127 2.4 17.6 1.0 O1A A:ATP875 2.4 28.9 1.0 O A:HOH932 2.7 29.3 1.0 OD1 A:ASP34 2.7 21.5 1.0 OD2 A:ASP34 3.0 17.3 1.0 CG A:ASP34 3.2 17.2 1.0 MG A:MG871 3.3 16.2 1.0 CD A:GLU127 3.3 18.9 1.0 PA A:ATP875 3.5 31.2 1.0 CG A:GLU127 3.6 12.2 1.0 O2A A:ATP875 3.6 33.4 1.0 C3' P:DOC873 3.9 21.0 1.0 O1G A:ATP875 3.9 24.1 1.0 OD2 A:ASP126 4.0 22.7 1.0 OE1 A:GLU127 4.4 18.0 1.0 O3A A:ATP875 4.5 28.2 1.0 CB A:ASP34 4.6 14.2 1.0 C4' P:DOC873 4.6 23.2 1.0 O5' A:ATP875 4.6 27.2 1.0 OD1 A:ASP126 4.6 35.6 1.0 CG A:ASP126 4.7 24.7 1.0 C5' P:DOC873 4.7 25.9 1.0 NZ A:LYS207 5.0 24.6 1.0 O A:HOH911 5.0 15.2 1.0

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase Iota Structure V. 17 530 2009.
ISSN: ISSN 0969-2126
PubMed: 19368886
DOI: 10.1016/J.STR.2009.02.015