Sodium in PDB 3rjg: Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus

All present enzymatic activity of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus:
2.7.7.7;

The structure of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus, PDB code: 3rjg 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)	22.20 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.660, 79.590, 55.000, 90.00, 105.79, 90.00
R / Rfree (%)	20.8 / 25.7

The binding sites of Sodium atom in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus (pdb code 3rjg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus, PDB code: 3rjg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na336 b:8.7 occ:1.00 OP1 P:DG9 2.3 8.2 1.0 O A:THR101 2.4 11.4 1.0 O A:ILE106 2.4 9.8 1.0 O A:VAL103 2.5 10.9 1.0 O P:HOH20 2.6 11.4 1.0 O P:HOH11 2.7 16.0 1.0 C A:THR101 3.3 12.5 1.0 O A:HOH345 3.4 17.6 1.0 C A:ILE106 3.4 8.5 1.0 P P:DG9 3.4 12.8 1.0 C A:VAL103 3.4 10.0 1.0 OP2 P:DG9 3.6 10.5 1.0 N A:ILE106 3.7 7.4 1.0 CA A:THR101 3.9 10.6 1.0 CA A:SER104 3.9 7.9 1.0 N A:GLY105 4.0 9.0 1.0 N A:SER104 4.0 8.9 1.0 CA A:ILE106 4.1 8.4 1.0 N A:VAL103 4.1 10.3 1.0 C A:SER104 4.3 8.9 1.0 CB A:THR101 4.3 10.9 1.0 N A:GLY107 4.3 8.8 1.0 C A:ARG102 4.4 11.9 1.0 N A:ARG102 4.4 11.9 1.0 O3' P:DC8 4.4 9.5 1.0 CA A:VAL103 4.5 10.0 1.0 CB A:ILE106 4.5 12.2 1.0 O P:HOH261 4.5 37.5 1.0 O5' P:DG9 4.5 11.1 1.0 CA A:GLY107 4.6 9.2 1.0 C A:GLY105 4.6 8.8 1.0 O A:HOH655 4.6 39.6 1.0 CA A:ARG102 4.7 11.0 1.0 O P:HOH141 4.8 22.4 1.0 O A:ARG102 4.9 11.7 1.0 CA A:GLY105 4.9 7.7 1.0 O A:LEU100 5.0 14.1 1.0

Sodium binding site 2 out of 2 in the Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Da Base-Pair at Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na337 b:17.0 occ:1.00 O D:HOH233 1.9 21.8 1.0 O A:LYS60 2.3 23.5 1.0 O A:LEU62 2.4 23.6 1.0 O A:VAL65 2.4 20.1 1.0 O A:HOH378 2.7 32.3 1.0 OP1 D:DC3 2.8 21.0 1.0 C A:LYS60 3.4 24.6 1.0 C A:LEU62 3.4 23.5 1.0 C A:VAL65 3.5 16.9 1.0 N A:VAL65 3.7 17.5 1.0 P D:DC3 3.8 17.7 1.0 OP2 D:DC3 4.0 15.6 1.0 N A:LEU62 4.0 23.7 1.0 N A:GLY64 4.0 22.2 1.0 CA A:VAL65 4.0 17.1 1.0 C A:LYS61 4.0 25.7 1.0 CA A:PRO63 4.1 22.7 1.0 N A:PRO63 4.1 23.6 1.0 CA A:LYS60 4.2 22.9 1.0 CB A:VAL65 4.2 16.5 1.0 O A:LYS61 4.3 25.4 1.0 N A:LYS61 4.3 25.6 1.0 CA A:LEU62 4.3 23.6 1.0 CA A:LYS61 4.4 26.6 1.0 CG A:LYS60 4.4 25.6 1.0 C A:PRO63 4.5 22.8 1.0 N A:GLY66 4.6 18.1 1.0 O3' D:DT2 4.7 16.8 1.0 C A:GLY64 4.7 19.4 1.0 O A:ALA59 4.7 21.2 1.0 O D:HOH381 4.8 37.9 1.0 CB A:LYS60 4.9 24.2 1.0 CA A:GLY66 5.0 17.0 1.0 CA A:GLY64 5.0 19.9 1.0

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