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Sodium 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
Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rjk

Go back to Sodium Binding Sites List in 3rjk
Sodium 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 Sodium with other atoms in the Na 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:Na341

b:21.5
occ:1.00
 O A:HOH644 2.3 37.3 1.0
OP1 P:DG9 2.3 15.0 1.0
O A:THR101 2.4 16.4 1.0
O A:VAL103 2.5 13.4 1.0
O A:HOH390 2.6 20.1 1.0
O A:ILE106 2.6 12.0 1.0
C A:THR101 3.4 17.0 1.0
C A:VAL103 3.4 14.0 1.0
P P:DG9 3.5 15.9 1.0
C A:ILE106 3.6 13.2 1.0
N A:ILE106 3.7 13.2 1.0
OP2 P:DG9 3.7 17.7 1.0
N A:GLY105 3.8 13.6 1.0
CA A:SER104 3.8 14.5 1.0
N A:SER104 4.0 14.9 1.0
N A:VAL103 4.1 14.7 1.0
CA A:THR101 4.1 17.4 1.0
CA A:ILE106 4.2 12.2 1.0
C A:SER104 4.2 13.2 1.0
C A:ARG102 4.3 13.6 1.0
N A:ARG102 4.3 14.4 1.0
O3' P:DC8 4.4 15.2 1.0
CA A:VAL103 4.4 14.6 1.0
N A:GLY107 4.5 13.1 1.0
CA A:ARG102 4.5 13.6 1.0
CB A:ILE106 4.6 13.1 1.0
C A:GLY105 4.6 13.1 1.0
O5' P:DG9 4.7 17.5 1.0
CB A:THR101 4.7 17.8 1.0
O A:ARG102 4.7 14.8 1.0
CA A:GLY107 4.8 13.6 1.0
CA A:GLY105 4.8 14.5 1.0
O A:LEU100 4.9 16.8 1.0

Sodium binding site 2 out of 2 in 3rjk

Go back to Sodium Binding Sites List in 3rjk
Sodium 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 Sodium with other atoms in the Na 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:Na342

b:31.8
occ:1.00
 O A:VAL65 2.2 23.8 1.0
O A:HOH672 2.4 27.7 1.0
O A:LYS60 2.5 24.5 1.0
OP1 D:DC3 2.5 26.3 1.0
O A:LEU62 2.6 23.8 1.0
O A:HOH573 2.9 33.3 1.0
C A:VAL65 3.4 22.1 1.0
C A:LYS60 3.5 26.3 1.0
P D:DC3 3.5 24.8 1.0
OP2 D:DC3 3.7 24.1 1.0
C A:LEU62 3.7 25.1 1.0
N A:VAL65 3.9 20.8 1.0
CA A:VAL65 4.1 20.1 1.0
CA A:LYS60 4.1 25.1 1.0
CG A:LYS60 4.2 26.9 1.0
CA A:PRO63 4.3 25.3 1.0
N A:GLY64 4.3 23.2 1.0
C A:LYS61 4.3 26.6 1.0
CB A:VAL65 4.4 20.0 1.0
N A:LEU62 4.4 25.7 1.0
N A:PRO63 4.4 25.2 1.0
N A:GLY66 4.4 22.4 1.0
N A:LYS61 4.4 26.7 1.0
O A:LYS61 4.5 26.2 1.0
O3' D:DT2 4.5 25.1 1.0
CA A:GLY66 4.6 22.6 1.0
CA A:LYS61 4.7 27.1 1.0
CA A:LEU62 4.7 25.5 1.0
C A:PRO63 4.7 23.8 1.0
O5' D:DC3 4.8 28.0 1.0
NZ A:LYS60 4.8 30.8 1.0
CB A:LYS60 4.8 25.9 1.0
C A:GLY64 4.9 21.7 1.0
O A:ALA59 5.0 22.3 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: Mon Oct 7 12:49:16 2024

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