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Magnesium in PDB 3rjk: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site, PDB code: 3rjk 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) 22.32 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.650, 79.970, 55.510, 90.00, 107.75, 90.00
R / Rfree (%) 20 / 25.8

Other elements in 3rjk:

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

Fluorine (F) 2 atoms
Chlorine (Cl) 3 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 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site (pdb code 3rjk). 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 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site, PDB code: 3rjk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3rjk

Go back to Magnesium Binding Sites List in 3rjk
Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in 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 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:16.4
occ:1.00
 OD1 A:ASP190 1.9 12.9 1.0
O2B A:6CF338 2.0 10.4 1.0
O3G A:6CF338 2.0 12.8 1.0
O1A A:6CF338 2.1 7.8 1.0
OD2 A:ASP192 2.1 11.8 1.0
O A:HOH354 2.3 11.6 1.0
CG A:ASP190 3.0 14.4 1.0
CG A:ASP192 3.0 8.1 1.0
P2 A:6CF338 3.1 11.0 1.0
P3 A:6CF338 3.2 17.2 1.0
P1 A:6CF338 3.2 11.6 1.0
OD1 A:ASP192 3.3 11.7 1.0
OD2 A:ASP190 3.4 17.8 1.0
O3B A:6CF338 3.5 11.8 1.0
C3A A:6CF338 3.5 12.6 1.0
O2G A:6CF338 3.5 14.4 1.0
MG A:MG340 3.5 9.3 1.0
O A:HOH399 3.8 16.3 1.0
F2A A:6CF338 3.9 13.8 1.0
C5' A:6CF338 3.9 12.3 1.0
O A:ASP190 4.0 14.6 1.0
O5' A:6CF338 4.0 12.4 1.0
C A:ASP190 4.2 14.0 1.0
CB A:ASP190 4.3 14.1 1.0
N A:ASP190 4.3 14.3 1.0
O1G A:6CF338 4.4 18.2 1.0
CB A:ASP192 4.4 13.0 1.0
O A:HOH360 4.4 14.9 1.0
O1B A:6CF338 4.4 9.4 1.0
O2A A:6CF338 4.5 14.3 1.0
O A:HOH373 4.5 16.1 1.0
CA A:ASP190 4.5 13.3 1.0
CA A:GLY179 4.6 12.9 1.0
F1A A:6CF338 4.7 11.8 1.0
N A:SER180 4.7 14.9 1.0
N A:ASP192 4.8 12.6 1.0
N A:MET191 4.9 11.8 1.0
O3' P:DC10 5.0 16.3 1.0

Magnesium binding site 2 out of 2 in 3rjk

Go back to Magnesium Binding Sites List in 3rjk
Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in 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 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:9.3
occ:1.00
 OD2 A:ASP256 1.9 13.3 1.0
OD2 A:ASP190 2.0 17.8 1.0
OD1 A:ASP192 2.1 11.7 1.0
O A:HOH373 2.2 16.1 1.0
O3' P:DC10 2.3 16.3 1.0
O1A A:6CF338 2.4 7.8 1.0
CG A:ASP190 3.0 14.4 1.0
CG A:ASP256 3.1 15.5 1.0
CG A:ASP192 3.2 8.1 1.0
OD1 A:ASP190 3.4 12.9 1.0
P1 A:6CF338 3.4 11.6 1.0
C3' P:DC10 3.5 15.8 1.0
MG A:MG339 3.5 16.4 1.0
OD2 A:ASP192 3.7 11.8 1.0
O2A A:6CF338 3.7 14.3 1.0
CB A:ASP256 3.8 14.7 1.0
O5' A:6CF338 3.8 12.4 1.0
C5' P:DC10 4.1 16.4 1.0
C4' P:DC10 4.1 17.3 1.0
OD1 A:ASP256 4.1 16.3 1.0
O A:HOH399 4.2 16.3 1.0
C5' A:6CF338 4.3 12.3 1.0
CB A:ASP190 4.4 14.1 1.0
OP1 P:DC10 4.4 20.0 1.0
O P:HOH465 4.5 48.3 1.0
CB A:ASP192 4.5 13.0 1.0
O5' P:DC10 4.5 18.3 1.0
NH2 A:ARG254 4.6 21.8 1.0
O3G A:6CF338 4.8 12.8 1.0
C2' P:DC10 4.8 15.8 1.0
O A:MET191 4.8 12.4 1.0
O2B A:6CF338 5.0 10.4 1.0
N A:ASP256 5.0 12.1 1.0
CA A:ASP192 5.0 11.2 1.0
C3A A:6CF338 5.0 12.6 1.0
CA A:ASP256 5.0 12.4 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 10:31:09 2024

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