Magnesium in PDB 3g6y: Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position

All present enzymatic activity of Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position, PDB code: 3g6y 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)	36.61 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.114, 98.114, 202.823, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 25.3

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position (pdb code 3g6y). 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 Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position, PDB code: 3g6y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position


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 Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:12.2 occ:1.00 OD1 A:ASP126 2.0 32.4 1.0 O A:LEU35 2.3 16.8 1.0 O1A A:TTP875 2.3 26.7 1.0 OD2 A:ASP34 2.4 19.7 1.0 O2B A:TTP875 2.4 19.0 1.0 O1G A:TTP875 2.4 27.1 1.0 CG A:ASP126 3.1 23.9 1.0 PB A:TTP875 3.3 25.9 1.0 MG A:MG872 3.4 74.6 1.0 C A:LEU35 3.4 16.2 1.0 OD2 A:ASP126 3.5 24.3 1.0 CG A:ASP34 3.6 17.1 1.0 PA A:TTP875 3.6 29.9 1.0 PG A:TTP875 3.7 29.7 1.0 N A:LEU35 3.8 15.2 1.0 O A:HOH930 3.8 25.4 1.0 O3A A:TTP875 3.8 28.5 1.0 O3B A:TTP875 3.9 28.9 1.0 C5' A:TTP875 4.1 29.9 1.0 CA A:LEU35 4.1 17.4 1.0 OD1 A:ASP34 4.1 17.3 1.0 C A:ASP34 4.2 15.5 1.0 O A:HOH975 4.2 36.4 1.0 O3G A:TTP875 4.3 26.9 1.0 CB A:ASP126 4.4 19.5 1.0 O5' A:TTP875 4.4 29.3 1.0 N A:ASP36 4.5 16.2 1.0 O A:ASP34 4.6 14.3 1.0 N A:CYS37 4.6 14.5 1.0 O1B A:TTP875 4.6 21.4 1.0 CB A:LEU35 4.7 17.5 1.0 O2A A:TTP875 4.7 30.4 1.0 CB A:ASP34 4.7 14.2 1.0 CA A:ASP36 4.7 16.0 1.0 CA A:ASP34 4.7 14.3 1.0 O A:ASP126 4.8 15.1 1.0 C A:ASP36 4.8 15.5 1.0 N A:PHE38 4.8 12.7 1.0 O2G A:TTP875 4.9 26.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position


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 Dna Polymerase Iota:Dna:Dttp with An Abasic Site at the Templating Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:74.6 occ:1.00 O1A A:TTP875 2.2 26.7 1.0 OE2 A:GLU127 2.3 19.5 1.0 OD1 A:ASP34 2.7 17.3 1.0 OD2 A:ASP34 3.0 19.7 1.0 CG A:ASP34 3.1 17.1 1.0 CD A:GLU127 3.2 15.2 1.0 O A:HOH975 3.2 36.4 1.0 PA A:TTP875 3.3 29.9 1.0 MG A:MG871 3.4 12.2 1.0 CG A:GLU127 3.5 11.2 1.0 OD2 A:ASP126 3.5 24.3 1.0 O2A A:TTP875 3.6 30.4 1.0 C3' P:DOC873 3.7 18.8 1.0 O1G A:TTP875 4.2 27.1 1.0 OD1 A:ASP126 4.2 32.4 1.0 CG A:ASP126 4.3 23.9 1.0 OE1 A:GLU127 4.3 17.9 1.0 O5' A:TTP875 4.3 29.3 1.0 C4' P:DOC873 4.5 22.7 1.0 CB A:ASP34 4.6 14.2 1.0 O3A A:TTP875 4.6 28.5 1.0 O A:HOH901 4.7 13.8 1.0 C5' P:DOC873 4.8 22.0 1.0 C5' A:TTP875 4.8 29.9 1.0 C2' P:DOC873 4.9 19.6 1.0 CB A:GLU127 5.0 11.6 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