Sodium in PDB 5wny: Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny 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)	24.65 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.480, 79.747, 55.570, 90.00, 107.23, 90.00
R / Rfree (%)	18.1 / 23.7

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp (pdb code 5wny). 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 5-Fdutp, PDB code: 5wny:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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 5-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:28.1 occ:1.00 OP1 P:DG9 2.3 24.0 1.0 O A:THR101 2.3 24.9 1.0 O A:ILE106 2.3 24.2 1.0 O A:VAL103 2.4 26.4 1.0 O A:HOH674 2.5 34.0 1.0 O P:HOH103 2.6 32.4 1.0 C A:THR101 3.3 23.2 1.0 C A:ILE106 3.3 22.4 1.0 P P:DG9 3.4 29.0 1.0 C A:VAL103 3.4 25.9 1.0 OP2 P:DG9 3.6 24.0 1.0 N A:ILE106 3.7 27.4 1.0 CA A:THR101 3.9 28.4 1.0 CA A:SER104 4.0 26.1 1.0 N A:GLY105 4.0 26.3 1.0 CA A:ILE106 4.0 31.0 1.0 N A:SER104 4.0 18.4 1.0 N A:VAL103 4.1 26.3 1.0 C A:ARG102 4.3 27.6 1.0 C A:SER104 4.3 25.1 1.0 N A:GLY107 4.3 23.2 1.0 N A:ARG102 4.3 22.4 1.0 O3' P:DC8 4.4 27.0 1.0 CA A:VAL103 4.4 30.4 1.0 CB A:THR101 4.4 23.1 1.0 CB A:ILE106 4.5 24.7 1.0 O5' P:DG9 4.5 28.6 1.0 CA A:ARG102 4.6 27.4 1.0 C A:GLY105 4.6 29.8 1.0 CA A:GLY107 4.6 28.7 1.0 O A:ARG102 4.7 26.0 1.0 O A:LEU100 4.8 26.4 1.0 CA A:GLY105 4.8 29.3 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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 5-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:37.8 occ:1.00 O A:LEU62 2.3 38.5 1.0 O A:VAL65 2.4 41.5 1.0 O A:LYS60 2.4 48.5 1.0 O A:HOH634 2.4 39.6 1.0 OP1 D:DC3 2.6 41.2 1.0 C A:LEU62 3.3 33.9 1.0 C A:VAL65 3.4 30.3 1.0 C A:LYS60 3.5 47.5 1.0 P D:DC3 3.6 40.2 1.0 OP2 D:DC3 3.7 33.4 1.0 N A:VAL65 3.8 32.4 1.0 CA A:PRO63 3.9 27.3 1.0 N A:LEU62 4.0 34.8 1.0 C A:LYS61 4.0 45.4 1.0 N A:PRO63 4.0 37.7 1.0 N A:GLY64 4.0 30.5 1.0 CA A:VAL65 4.1 27.5 1.0 O A:LYS61 4.1 39.0 1.0 CA A:LYS60 4.2 35.6 1.0 CA A:LEU62 4.3 36.3 1.0 C A:PRO63 4.4 41.8 1.0 N A:LYS61 4.4 37.3 1.0 CB A:VAL65 4.4 28.4 1.0 N A:GLY66 4.4 33.1 1.0 CG A:LYS60 4.5 51.6 1.0 CA A:LYS61 4.5 35.1 1.0 O3' D:DT2 4.6 44.4 1.0 CA A:GLY66 4.7 36.4 1.0 C A:GLY64 4.8 38.2 1.0 O5' D:DC3 4.8 44.6 1.0 O A:ALA59 4.8 28.4 1.0 CA A:GLY64 5.0 35.8 1.0 CB A:LYS60 5.0 34.9 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