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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

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