Magnesium in PDB 3oha: Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion

All present enzymatic activity of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion:
2.7.7.7;

The structure of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion, PDB code: 3oha was solved by T.D.Silverstein, R.Jain, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.82 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.039, 227.635, 86.077, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.5

The binding sites of Magnesium atom in the Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion (pdb code 3oha). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion, PDB code: 3oha:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:14.3 occ:1.00 OD1 A:ASP30 2.0 19.1 1.0 O1A A:DCP514 2.0 16.4 1.0 O2B A:DCP514 2.1 11.8 1.0 O3G A:DCP514 2.1 17.8 1.0 OD1 A:ASP155 2.2 17.5 1.0 O A:MET31 2.2 14.0 1.0 CG A:ASP30 3.0 14.2 1.0 PB A:DCP514 3.1 14.2 1.0 PA A:DCP514 3.2 17.0 1.0 CG A:ASP155 3.3 16.6 1.0 PG A:DCP514 3.4 16.3 1.0 C A:MET31 3.4 12.8 1.0 OD2 A:ASP30 3.4 19.6 1.0 O3A A:DCP514 3.5 15.8 1.0 O3B A:DCP514 3.6 16.5 1.0 OD2 A:ASP155 3.6 18.6 1.0 O A:HOH756 3.7 9.7 1.0 O A:HOH797 3.9 13.8 1.0 C5' A:DCP514 4.0 16.9 1.0 N A:MET31 4.0 12.2 1.0 O5' A:DCP514 4.1 17.8 1.0 O2G A:DCP514 4.1 14.5 1.0 CA A:MET31 4.2 13.8 1.0 C A:ASP30 4.3 12.3 1.0 CB A:ASP30 4.3 12.0 1.0 N A:ASN32 4.4 13.0 1.0 N A:ALA33 4.4 13.1 1.0 CA A:ASN32 4.5 13.3 1.0 MG A:MG519 4.5 41.1 1.0 O2A A:DCP514 4.5 15.8 1.0 O1B A:DCP514 4.5 16.6 1.0 CB A:ASP155 4.5 16.3 1.0 O1G A:DCP514 4.6 19.2 1.0 CB A:MET31 4.6 14.8 1.0 C A:ASN32 4.6 13.8 1.0 O A:ASP30 4.6 11.6 1.0 N A:PHE34 4.7 12.4 1.0 CA A:ASP30 4.7 12.0 1.0 CB A:PHE34 4.8 12.0 1.0 O A:HOH972 4.9 30.0 1.0

Magnesium binding site 2 out of 2 in the Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg519 b:41.1 occ:1.00 O A:HOH972 2.5 30.0 1.0 OE1 A:GLU156 2.8 25.0 1.0 OD2 A:ASP30 2.8 19.6 1.0 O1A A:DCP514 2.9 16.4 1.0 O A:HOH776 3.2 26.7 1.0 OD2 A:ASP155 3.2 18.6 1.0 C3' P:DOC11 3.3 32.8 1.0 CD A:GLU156 3.4 21.7 1.0 CG A:GLU156 3.4 18.8 1.0 C4' P:DOC11 3.5 31.7 1.0 O2A A:DCP514 3.5 15.8 1.0 PA A:DCP514 3.5 17.0 1.0 O A:HOH948 3.7 17.5 1.0 C5' P:DOC11 3.8 31.7 1.0 CG A:ASP30 3.9 14.2 1.0 O5' A:DCP514 3.9 17.8 1.0 NZ A:LYS272 4.2 30.1 1.0 OG A:SER153 4.2 20.9 1.0 CG A:ASP155 4.3 16.6 1.0 O A:HOH797 4.4 13.8 1.0 OD1 A:ASP30 4.4 19.1 1.0 C2' P:DOC11 4.4 34.4 1.0 OE2 A:GLU156 4.5 23.9 1.0 MG A:MG518 4.5 14.3 1.0 C5' A:DCP514 4.6 16.9 1.0 OD1 A:ASP155 4.6 17.5 1.0 CB A:GLU156 4.8 13.7 1.0 O4' P:DOC11 4.8 30.6 1.0 O5' P:DOC11 4.9 31.1 1.0

T.D.Silverstein, R.Jain, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Basis For Error-Free Replication of Oxidatively Damaged Dna By Yeast Dna Polymerase Eta. Structure V. 18 1463 2010.
ISSN: ISSN 0969-2126
PubMed: 21070945
DOI: 10.1016/J.STR.2010.08.019