Sodium in PDB 5wo0: Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp

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

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp, PDB code: 5wo0 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)	31.79 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.728, 79.637, 55.289, 90.00, 107.28, 90.00
R / Rfree (%)	20 / 23.1

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

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp (pdb code 5wo0). 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-Fodutp, PDB code: 5wo0:
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-Fodutp


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-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ P:Na401 b:17.5 occ:1.00 O A:THR101 2.4 17.8 1.0 OP1 P:DG9 2.4 18.0 1.0 O A:ILE106 2.4 17.1 1.0 O P:HOH503 2.4 27.2 1.0 O A:VAL103 2.5 16.6 1.0 O A:HOH725 2.5 22.7 1.0 C A:THR101 3.3 15.8 1.0 C A:VAL103 3.4 15.7 1.0 P P:DG9 3.4 18.9 1.0 C A:ILE106 3.4 15.5 1.0 OP2 P:DG9 3.6 22.1 1.0 N A:ILE106 3.8 16.4 1.0 CA A:THR101 3.9 16.9 1.0 CA A:SER104 4.0 17.1 1.0 N A:GLY105 4.0 15.3 1.0 N A:SER104 4.1 14.9 1.0 N A:VAL103 4.1 15.6 1.0 CA A:ILE106 4.2 14.5 1.0 C A:ARG102 4.3 22.0 1.0 C A:SER104 4.4 13.9 1.0 N A:ARG102 4.4 14.5 1.0 CB A:THR101 4.4 16.6 1.0 N A:GLY107 4.4 15.9 1.0 O3' P:DC8 4.4 19.4 1.0 CA A:VAL103 4.4 16.6 1.0 CB A:ILE106 4.6 18.5 1.0 CA A:ARG102 4.6 19.7 1.0 O5' P:DG9 4.6 19.4 1.0 CA A:GLY107 4.7 18.3 1.0 C A:GLY105 4.7 16.5 1.0 O A:ARG102 4.8 20.5 1.0 O A:LEU100 4.9 17.1 1.0 CA A:GLY105 4.9 20.2 1.0

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


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-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:24.3 occ:1.00 O A:HOH735 2.4 33.1 1.0 O A:LEU62 2.4 22.7 1.0 O A:LYS60 2.4 26.6 1.0 O A:VAL65 2.4 23.9 1.0 O D:HOH209 2.5 31.9 1.0 OP1 D:DC3 2.7 23.8 1.0 C A:LEU62 3.3 22.1 1.0 C A:LYS60 3.5 25.4 1.0 C A:VAL65 3.5 22.7 1.0 P D:DC3 3.7 24.9 1.0 OP2 D:DC3 3.8 22.3 1.0 O D:HOH213 3.9 34.9 1.0 N A:VAL65 3.9 17.3 1.0 N A:LEU62 3.9 25.6 1.0 CA A:PRO63 4.0 26.4 1.0 C A:LYS61 4.0 28.2 1.0 N A:PRO63 4.0 26.4 1.0 N A:GLY64 4.1 22.8 1.0 CA A:VAL65 4.2 20.9 1.0 O A:LYS61 4.2 28.8 1.0 CA A:LYS60 4.2 24.0 1.0 CA A:LEU62 4.2 24.7 1.0 N A:LYS61 4.4 25.9 1.0 CB A:VAL65 4.4 23.7 1.0 C A:PRO63 4.4 25.1 1.0 CG A:LYS60 4.5 31.6 1.0 CA A:LYS61 4.5 27.2 1.0 N A:GLY66 4.6 20.7 1.0 O3' D:DT2 4.6 23.3 1.0 C A:GLY64 4.9 23.8 1.0 O A:ALA59 4.9 21.7 1.0 O5' D:DC3 4.9 31.2 1.0 CA A:GLY66 4.9 25.2 1.0 CB A:LYS60 5.0 27.0 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