Sodium in PDB 4gxj: R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog

All present enzymatic activity of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog:
2.7.7.7;

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog, PDB code: 4gxj was solved by B.D.Freudenthal, 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)	21.06 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.084, 77.432, 55.125, 90.00, 114.45, 90.00
R / Rfree (%)	23.1 / 29.2

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Manganese	(Mn)	7 atoms

The binding sites of Sodium atom in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog (pdb code 4gxj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog, PDB code: 4gxj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:18.9 occ:1.00 O A:THR101 2.2 22.5 1.0 O A:HOH504 2.3 24.4 1.0 O A:ILE106 2.4 18.4 1.0 O A:VAL103 2.4 23.5 1.0 OP1 P:DG9 2.5 17.5 1.0 O P:HOH202 2.5 27.3 1.0 C A:THR101 3.2 25.7 1.0 C A:VAL103 3.3 22.4 1.0 C A:ILE106 3.4 17.4 1.0 P P:DG9 3.5 23.9 1.0 OP2 P:DG9 3.7 28.8 1.0 N A:ILE106 3.8 18.7 1.0 CA A:THR101 3.8 26.4 1.0 CA A:SER104 3.9 22.9 1.0 N A:GLY105 4.0 16.7 1.0 N A:SER104 4.0 24.8 1.0 N A:VAL103 4.1 19.6 1.0 CA A:ILE106 4.1 16.4 1.0 C A:SER104 4.3 22.2 1.0 CA A:VAL103 4.3 22.8 1.0 CB A:THR101 4.3 27.8 1.0 N A:GLY107 4.3 16.7 1.0 N A:ARG102 4.3 25.5 1.0 C A:ARG102 4.3 22.6 1.0 O3' P:DC8 4.4 22.9 1.0 CB A:ILE106 4.5 13.4 1.0 CA A:GLY107 4.6 22.0 1.0 C A:GLY105 4.7 16.6 1.0 CA A:ARG102 4.7 27.4 1.0 O5' P:DG9 4.7 22.0 1.0 O A:LEU100 4.8 23.3 1.0 O A:ARG102 4.9 25.4 1.0 CA A:GLY105 4.9 16.1 1.0

Sodium binding site 2 out of 2 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:50.5 occ:1.00 N7 D:DG4 2.4 45.8 1.0 C8 D:DG4 3.2 46.6 1.0 C5 D:DG4 3.5 37.4 1.0 O6 D:DG5 3.5 53.1 1.0 O D:HOH203 3.7 45.2 1.0 O6 D:DG4 3.9 42.6 1.0 C2' D:DC3 3.9 45.6 1.0 C6 D:DG4 4.1 37.6 1.0 N4 T:DC1 4.1 44.3 1.0 OP2 D:DG4 4.4 51.4 1.0 N9 D:DG4 4.5 43.9 1.0 C6 D:DG5 4.5 42.8 1.0 C6 D:DC3 4.6 41.0 1.0 C4 D:DG4 4.6 45.2 1.0 C1' D:DC3 4.8 47.6 1.0 N1 D:DC3 4.9 38.0 1.0

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Dna Polymerase Minor Groove Interactions Modulate Mutagenic Bypass of A Templating 8-Oxoguanine Lesion. Nucleic Acids Res. V. 41 1848 2013.
ISSN: ISSN 0305-1048
PubMed: 23267011
DOI: 10.1093/NAR/GKS1276