Sodium in PDB 5wnx: Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp, PDB code: 5wnx was solved by M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.243, 79.203, 55.625, 90.00, 107.36, 90.00
R / Rfree (%)	20.6 / 29

The structure of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp (pdb code 5wnx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp, PDB code: 5wnx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:48.5 occ:1.00 O A:THR101 2.4 36.4 1.0 OP1 P:DG9 2.7 39.1 1.0 O P:HOH101 2.9 31.8 1.0 O A:ILE106 2.9 37.8 1.0 OP2 P:DG9 3.1 36.8 1.0 P P:DG9 3.3 38.9 1.0 C A:THR101 3.5 31.6 1.0 O A:VAL103 3.7 41.1 1.0 C A:ILE106 4.0 39.7 1.0 CA A:THR101 4.1 39.0 1.0 CB A:THR101 4.2 33.9 1.0 O5' P:DG9 4.3 40.1 1.0 C A:VAL103 4.6 34.7 1.0 N A:ARG102 4.6 30.1 1.0 CA A:GLY107 4.6 30.1 1.0 O3' P:DC8 4.6 44.6 1.0 N A:GLY107 4.7 30.2 1.0 N A:GLY105 4.8 33.1 1.0 CA A:ARG102 4.8 37.5 1.0 N A:ILE106 4.8 34.4 1.0 CA A:SER104 4.9 36.2 1.0 C A:ARG102 4.9 39.1 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:47.6 occ:1.00 O A:VAL65 2.3 49.7 1.0 O A:LYS60 2.4 45.3 1.0 O A:LEU62 2.5 42.1 1.0 OP1 D:DC3 2.7 49.4 1.0 OP2 D:DC3 3.2 48.1 1.0 C A:VAL65 3.4 43.9 1.0 P D:DC3 3.4 57.1 1.0 C A:LYS60 3.5 48.4 1.0 C A:LEU62 3.6 43.2 1.0 N A:VAL65 3.9 38.6 1.0 CA A:PRO63 4.0 47.4 1.0 N A:GLY64 4.1 47.8 1.0 CA A:VAL65 4.2 44.1 1.0 CA A:LYS60 4.2 51.1 1.0 N A:PRO63 4.2 43.9 1.0 CG A:LYS60 4.3 52.1 1.0 C A:LYS61 4.3 45.4 1.0 N A:LEU62 4.4 44.2 1.0 O3' D:DT2 4.4 65.5 1.0 N A:GLY66 4.4 46.3 1.0 C A:PRO63 4.4 47.4 1.0 CB A:VAL65 4.5 46.2 1.0 O A:LYS61 4.6 47.1 1.0 N A:LYS61 4.6 49.2 1.0 CA A:LEU62 4.6 44.9 1.0 CA A:GLY66 4.7 42.6 1.0 CA A:LYS61 4.8 47.1 1.0 O5' D:DC3 4.8 55.4 1.0 C A:GLY64 4.8 47.1 1.0 CB A:LYS60 4.9 45.1 1.0 O A:ALA59 4.9 39.9 1.0

M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal. Structures of A Dna Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. V. 30 1993 2017.
ISSN: ISSN 1520-5010
PubMed: 28862449
DOI: 10.1021/ACS.CHEMRESTOX.7B00173