Sodium in PDB 3rjj: Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass, PDB code: 3rjj 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)	22.62 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.480, 79.410, 54.910, 90.00, 105.51, 90.00
R / Rfree (%)	20.2 / 26.1

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass (pdb code 3rjj). 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 Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass, PDB code: 3rjj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass within 5.0Å range: probe atom residue distance (Å) B Occ A:Na336 b:7.8 occ:1.00 O A:THR101 2.3 11.4 1.0 OP1 P:DG9 2.3 6.2 1.0 O A:HOH342 2.4 8.9 1.0 O A:VAL103 2.4 9.7 1.0 O A:ILE106 2.4 8.9 1.0 O P:HOH26 2.6 10.8 1.0 C A:THR101 3.3 10.6 1.0 O A:HOH389 3.3 15.1 1.0 C A:VAL103 3.3 9.8 1.0 C A:ILE106 3.4 8.5 1.0 P P:DG9 3.4 9.1 1.0 OP2 P:DG9 3.7 9.5 1.0 N A:ILE106 3.7 6.9 1.0 CA A:THR101 3.9 9.1 1.0 CA A:SER104 3.9 8.1 1.0 N A:GLY105 4.0 7.4 1.0 N A:SER104 4.0 8.5 1.0 N A:VAL103 4.0 9.2 1.0 CA A:ILE106 4.0 8.2 1.0 O P:HOH237 4.2 36.0 1.0 C A:SER104 4.3 7.4 1.0 C A:ARG102 4.3 10.2 1.0 N A:GLY107 4.3 6.8 1.0 N A:ARG102 4.4 10.0 1.0 CA A:VAL103 4.4 9.4 1.0 CB A:THR101 4.4 9.3 1.0 O3' P:DC8 4.4 8.4 1.0 CB A:ILE106 4.5 8.1 1.0 O5' P:DG9 4.5 8.4 1.0 O A:HOH560 4.6 30.1 1.0 C A:GLY105 4.6 6.5 1.0 CA A:GLY107 4.6 8.5 1.0 CA A:ARG102 4.7 9.9 1.0 O A:ARG102 4.9 9.1 1.0 O A:LEU100 4.9 11.6 1.0 CA A:GLY105 4.9 5.4 1.0 O A:HOH621 4.9 14.4 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with Template 8ODG Provides Insight Into Mutagenic Lesion Bypass within 5.0Å range: probe atom residue distance (Å) B Occ A:Na337 b:16.4 occ:1.00 O D:HOH261 1.9 21.7 1.0 O A:VAL65 2.2 17.8 1.0 O A:LYS60 2.3 22.6 1.0 O A:HOH759 2.6 31.4 1.0 OP1 D:DC3 2.7 18.3 1.0 O A:LEU62 2.8 21.5 1.0 C A:VAL65 3.3 14.2 1.0 C A:LYS60 3.4 22.2 1.0 P D:DC3 3.7 15.5 1.0 OP2 D:DC3 3.7 14.0 1.0 C A:LEU62 3.7 21.5 1.0 N A:VAL65 3.8 14.6 1.0 CA A:VAL65 4.1 14.1 1.0 CA A:LYS60 4.1 19.9 1.0 CG A:LYS60 4.2 21.9 1.0 N A:GLY64 4.2 16.9 1.0 N A:LEU62 4.3 22.8 1.0 C A:LYS61 4.3 23.5 1.0 N A:GLY66 4.4 12.7 1.0 CB A:VAL65 4.4 13.1 1.0 CA A:PRO63 4.4 19.9 1.0 N A:LYS61 4.4 23.4 1.0 N A:PRO63 4.4 20.2 1.0 CA A:GLY66 4.6 11.9 1.0 O A:LYS61 4.6 24.7 1.0 O3' D:DT2 4.6 16.2 1.0 CA A:LEU62 4.6 22.0 1.0 CA A:LYS61 4.7 23.7 1.0 C A:PRO63 4.7 17.8 1.0 CB A:LYS60 4.7 20.7 1.0 C A:GLY64 4.7 14.9 1.0 O A:ALA59 4.9 18.4 1.0 O5' D:DC3 4.9 14.3 1.0 NZ A:LYS60 5.0 28.1 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