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Magnesium in PDB 3ohb: Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion

Enzymatic activity of Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion

All present enzymatic activity of Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion:
2.7.7.7;

Protein crystallography data

The structure of Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion, PDB code: 3ohb 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) 47.54 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.958, 228.268, 85.932, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion (pdb code 3ohb). 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 Extending From An 8-Oxog Lesion, PDB code: 3ohb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ohb

Go back to Magnesium Binding Sites List in 3ohb
Magnesium binding site 1 out of 2 in the Yeast Dna Polymerase Eta Extending From An 8-Oxog 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 Extending From An 8-Oxog Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg515

b:15.6
occ:1.00
OD1 A:ASP30 2.0 18.8 1.0
O1B A:DCP514 2.1 13.6 1.0
O1A A:DCP514 2.1 16.6 1.0
O1G A:DCP514 2.1 19.0 1.0
O A:MET31 2.2 16.0 1.0
OD1 A:ASP155 2.2 17.2 1.0
CG A:ASP30 3.1 18.0 1.0
PB A:DCP514 3.1 14.3 1.0
CG A:ASP155 3.3 16.4 1.0
PA A:DCP514 3.3 18.5 1.0
C A:MET31 3.4 15.2 1.0
PG A:DCP514 3.4 17.5 1.0
OD2 A:ASP30 3.5 24.0 1.0
O3A A:DCP514 3.5 16.2 1.0
OD2 A:ASP155 3.6 16.9 1.0
O3B A:DCP514 3.6 17.3 1.0
O A:HOH667 3.7 15.8 1.0
O A:HOH708 4.0 19.5 1.0
C5' A:DCP514 4.0 16.1 1.0
N A:MET31 4.0 15.1 1.0
O2G A:DCP514 4.1 13.5 1.0
O5' A:DCP514 4.1 17.8 1.0
CA A:MET31 4.2 16.2 1.0
C A:ASP30 4.3 14.6 1.0
N A:ASN32 4.3 14.6 1.0
N A:ALA33 4.4 14.6 1.0
CB A:ASP30 4.4 14.5 1.0
O2B A:DCP514 4.5 16.6 1.0
CA A:ASN32 4.5 15.0 1.0
O2A A:DCP514 4.5 19.1 1.0
CB A:ASP155 4.6 17.8 1.0
MG A:MG516 4.6 47.6 1.0
O3G A:DCP514 4.6 20.5 1.0
CB A:MET31 4.6 16.8 1.0
C A:ASN32 4.6 14.6 1.0
N A:PHE34 4.7 14.5 1.0
O A:ASP30 4.7 13.8 1.0
CB A:PHE34 4.8 14.6 1.0
CA A:ASP30 4.8 14.3 1.0
O A:HOH875 4.9 35.5 1.0

Magnesium binding site 2 out of 2 in 3ohb

Go back to Magnesium Binding Sites List in 3ohb
Magnesium binding site 2 out of 2 in the Yeast Dna Polymerase Eta Extending From An 8-Oxog 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 Extending From An 8-Oxog Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg516

b:47.6
occ:1.00
O A:HOH875 2.6 35.5 1.0
OE1 A:GLU156 2.8 30.8 1.0
OD2 A:ASP30 2.8 24.0 1.0
O1A A:DCP514 3.0 16.6 1.0
O A:HOH687 3.2 38.1 1.0
C3' P:DOC11 3.3 24.6 1.0
OD2 A:ASP155 3.3 16.9 1.0
CD A:GLU156 3.4 25.4 1.0
CG A:GLU156 3.4 22.1 1.0
C4' P:DOC11 3.4 23.8 1.0
PA A:DCP514 3.6 18.5 1.0
O2A A:DCP514 3.6 19.1 1.0
C5' P:DOC11 3.8 24.2 1.0
CG A:ASP30 4.0 18.0 1.0
O5' A:DCP514 4.0 17.8 1.0
OG A:SER153 4.1 23.8 1.0
NZ A:LYS272 4.2 31.5 1.0
O A:HOH708 4.3 19.5 1.0
C2' P:DOC11 4.3 25.9 1.0
OD1 A:ASP30 4.4 18.8 1.0
CG A:ASP155 4.4 16.4 1.0
OE2 A:GLU156 4.5 28.0 1.0
MG A:MG515 4.6 15.6 1.0
C5' A:DCP514 4.6 16.1 1.0
CB A:GLU156 4.8 16.6 1.0
OD1 A:ASP155 4.8 17.2 1.0
O4' P:DOC11 4.8 25.3 1.0
O5' P:DOC11 4.8 25.5 1.0

Reference:

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
Page generated: Mon Dec 14 08:35:02 2020

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