Atomistry » Magnesium » PDB 3fzn-3g8c » 3g6v
Atomistry »
  Magnesium »
    PDB 3fzn-3g8c »
      3g6v »

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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 3g6v

Go back to Magnesium Binding Sites List in 3g6v
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 3g6v

Go back to Magnesium Binding Sites List in 3g6v
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

Reference:

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
Page generated: Mon Dec 14 08:10:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy