Atomistry » Magnesium » PDB 3rer-3rqx » 3rjh
Atomistry »
  Magnesium »
    PDB 3rer-3rqx »
      3rjh »

Magnesium in PDB 3rjh: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.35 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.530, 79.910, 55.460, 90.00, 108.04, 90.00
R / Rfree (%) 20.4 / 25.9

Other elements in 3rjh:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site (pdb code 3rjh). 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 Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3rjh

Go back to Magnesium Binding Sites List in 3rjh
Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site


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 Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:15.2
occ:1.00
 O1G A:6CF401 1.9 15.9 1.0
O1A A:6CF401 1.9 11.4 1.0
OD1 A:ASP190 1.9 23.1 1.0
O2B A:6CF401 2.0 9.2 1.0
OD2 A:ASP192 2.0 17.5 1.0
O A:HOH503 2.2 19.6 1.0
CG A:ASP190 2.9 23.2 1.0
CG A:ASP192 3.0 15.9 1.0
P2 A:6CF401 3.1 13.6 1.0
P3 A:6CF401 3.1 22.7 1.0
P1 A:6CF401 3.1 18.3 1.0
OD2 A:ASP190 3.3 24.6 1.0
MG A:MG403 3.3 17.4 1.0
OD1 A:ASP192 3.4 14.7 1.0
C3A A:6CF401 3.4 17.2 1.0
O3B A:6CF401 3.5 15.8 1.0
O3G A:6CF401 3.6 16.9 1.0
O A:HOH504 3.7 15.4 1.0
F2A A:6CF401 3.8 17.1 1.0
C5' A:6CF401 3.9 18.3 1.0
O5' A:6CF401 4.0 16.1 1.0
O A:ASP190 4.1 23.0 1.0
CB A:ASP190 4.3 21.2 1.0
O2A A:6CF401 4.3 16.2 1.0
O A:HOH512 4.3 19.8 1.0
C A:ASP190 4.3 21.6 1.0
CB A:ASP192 4.4 19.9 1.0
O1B A:6CF401 4.4 14.0 1.0
O2G A:6CF401 4.4 19.9 1.0
O A:HOH505 4.4 19.4 1.0
N A:ASP190 4.4 21.2 1.0
CA A:GLY179 4.5 18.7 1.0
CA A:ASP190 4.6 21.9 1.0
F1A A:6CF401 4.7 12.3 1.0
O3' P:DA10 4.8 21.0 1.0
N A:SER180 4.8 20.5 1.0
N A:ASP192 4.9 20.4 1.0
N A:MET191 5.0 19.6 1.0

Magnesium binding site 2 out of 2 in 3rjh

Go back to Magnesium Binding Sites List in 3rjh
Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site


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 Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:17.4
occ:1.00
 OD2 A:ASP190 2.0 24.6 1.0
OD2 A:ASP256 2.0 23.8 1.0
OD1 A:ASP192 2.0 14.7 1.0
O1A A:6CF401 2.2 11.4 1.0
O3' P:DA10 2.2 21.0 1.0
O A:HOH505 2.2 19.4 1.0
CG A:ASP192 3.0 15.9 1.0
CG A:ASP190 3.0 23.2 1.0
CG A:ASP256 3.2 22.1 1.0
P1 A:6CF401 3.2 18.3 1.0
MG A:MG402 3.3 15.2 1.0
OD2 A:ASP192 3.3 17.5 1.0
OD1 A:ASP190 3.4 23.1 1.0
C3' P:DA10 3.5 24.1 1.0
O2A A:6CF401 3.5 16.2 1.0
O5' A:6CF401 3.7 16.1 1.0
CB A:ASP256 3.9 20.3 1.0
O A:HOH504 3.9 15.4 1.0
C4' P:DA10 4.1 23.5 1.0
C5' P:DA10 4.2 22.2 1.0
C5' A:6CF401 4.2 18.3 1.0
OD1 A:ASP256 4.2 17.6 1.0
CB A:ASP190 4.4 21.2 1.0
CB A:ASP192 4.4 19.9 1.0
O1G A:6CF401 4.5 15.9 1.0
OP1 P:DA10 4.5 25.0 1.0
O5' P:DA10 4.6 22.9 1.0
NH2 A:ARG254 4.7 21.6 1.0
C2' P:DA10 4.7 22.4 1.0
O2B A:6CF401 4.7 9.2 1.0
C3A A:6CF401 4.8 17.2 1.0
O A:MET191 4.9 17.9 1.0
CA A:ASP192 5.0 20.1 1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108
Page generated: Thu Aug 15 10:30:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy