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Sodium 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
Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3rjh

Go back to Sodium Binding Sites List in 3rjh
Sodium 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 Sodium with other atoms in the Na 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:Na404

b:22.7
occ:1.00
 OP1 P:DG9 2.3 25.0 1.0
O A:HOH524 2.4 23.9 1.0
O A:THR101 2.5 24.7 1.0
O A:ILE106 2.5 23.4 1.0
O A:VAL103 2.5 19.4 1.0
O A:HOH584 2.6 40.0 1.0
P P:DG9 3.3 24.9 1.0
C A:ILE106 3.4 22.1 1.0
C A:THR101 3.4 24.9 1.0
C A:VAL103 3.5 20.4 1.0
OP2 P:DG9 3.5 28.3 1.0
N A:ILE106 3.6 23.0 1.0
N A:GLY105 3.8 20.8 1.0
CA A:SER104 3.8 22.4 1.0
O A:HOH683 4.0 39.3 1.0
CA A:ILE106 4.0 21.8 1.0
N A:SER104 4.0 20.5 1.0
CA A:THR101 4.1 25.3 1.0
C A:SER104 4.1 21.6 1.0
N A:VAL103 4.2 21.9 1.0
O3' P:DC8 4.2 22.9 1.0
N A:GLY107 4.4 21.9 1.0
C A:ARG102 4.4 23.7 1.0
CB A:ILE106 4.4 20.8 1.0
N A:ARG102 4.4 21.7 1.0
C A:GLY105 4.5 21.0 1.0
O5' P:DG9 4.5 27.1 1.0
CA A:VAL103 4.5 20.0 1.0
CA A:GLY107 4.7 22.6 1.0
CA A:ARG102 4.7 23.5 1.0
CB A:THR101 4.7 26.3 1.0
CA A:GLY105 4.7 21.9 1.0
O A:LEU100 4.8 24.2 1.0
O A:ARG102 4.8 23.1 1.0
O A:HOH682 4.9 42.6 1.0

Sodium binding site 2 out of 2 in 3rjh

Go back to Sodium Binding Sites List in 3rjh
Sodium 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 Sodium with other atoms in the Na 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:Na405

b:38.3
occ:1.00
 O D:HOH108 2.3 39.2 1.0
O A:LYS60 2.4 34.4 1.0
O A:LEU62 2.6 30.6 1.0
OP1 D:DC3 2.6 35.1 1.0
O A:VAL65 2.7 32.4 1.0
O A:HOH595 2.7 32.8 1.0
C A:LYS60 3.5 34.0 1.0
C A:LEU62 3.5 32.0 1.0
P D:DC3 3.7 35.8 1.0
C A:VAL65 3.8 31.6 1.0
OP2 D:DC3 3.9 32.5 1.0
CA A:PRO63 4.1 32.2 1.0
N A:VAL65 4.1 30.8 1.0
C A:LYS61 4.2 35.2 1.0
N A:PRO63 4.2 31.4 1.0
N A:LEU62 4.2 33.8 1.0
CA A:LYS60 4.3 32.3 1.0
CG A:LYS60 4.3 35.7 1.0
N A:GLY64 4.3 31.8 1.0
N A:LYS61 4.4 34.9 1.0
O A:LYS61 4.4 36.2 1.0
CA A:VAL65 4.4 30.7 1.0
CA A:LYS61 4.5 36.2 1.0
CA A:LEU62 4.6 31.4 1.0
CB A:VAL65 4.6 31.0 1.0
C A:PRO63 4.7 31.8 1.0
O3' D:DT2 4.8 33.3 1.0
O5' D:DC3 4.8 38.2 1.0
N A:GLY66 4.8 32.3 1.0
NZ A:LYS60 4.9 45.0 1.0
CB A:LYS60 4.9 32.9 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: Tue Dec 15 06:23:50 2020

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