Sodium in PDB 5v1o: Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp

All present enzymatic activity of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp:
2.7.7.7;

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp, PDB code: 5v1o was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.80 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.574, 79.685, 55.416, 90.00, 107.76, 90.00
R / Rfree (%)	17.9 / 21.5

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp (pdb code 5v1o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp, PDB code: 5v1o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp


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 Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:16.0 occ:1.00 O A:ILE106 2.3 13.7 1.0 O A:THR101 2.3 14.0 1.0 OP1 P:DG9 2.4 16.4 1.0 O A:VAL103 2.4 14.8 1.0 O P:HOH207 2.5 20.7 1.0 O A:HOH726 2.7 20.7 1.0 C A:THR101 3.3 12.6 1.0 C A:ILE106 3.4 16.3 1.0 C A:VAL103 3.4 14.4 1.0 P P:DG9 3.4 15.2 1.0 OP2 P:DG9 3.6 14.5 1.0 N A:ILE106 3.7 16.2 1.0 CA A:THR101 3.8 14.7 1.0 N A:GLY105 4.0 11.2 1.0 CA A:ILE106 4.1 12.5 1.0 CA A:SER104 4.1 15.5 1.0 N A:VAL103 4.1 13.9 1.0 N A:SER104 4.1 11.6 1.0 C A:ARG102 4.3 17.1 1.0 N A:ARG102 4.3 12.9 1.0 O3' P:DC8 4.3 15.3 1.0 N A:GLY107 4.4 13.5 1.0 CB A:THR101 4.4 15.0 1.0 C A:SER104 4.4 15.9 1.0 O A:HOH727 4.4 35.2 1.0 CA A:VAL103 4.4 14.0 1.0 CB A:ILE106 4.5 15.3 1.0 CA A:ARG102 4.6 15.4 1.0 C A:GLY105 4.6 15.9 1.0 O5' P:DG9 4.7 18.2 1.0 CA A:GLY107 4.7 13.0 1.0 O A:ARG102 4.7 15.9 1.0 O A:LEU100 4.8 13.6 1.0 CA A:GLY105 4.9 14.1 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp


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 Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:23.4 occ:1.00 O A:LEU62 2.3 23.4 1.0 O A:LYS60 2.4 21.2 1.0 O A:VAL65 2.4 20.8 1.0 O A:HOH723 2.4 29.0 1.0 O D:HOH101 2.6 31.0 1.0 OP1 D:DC3 2.7 26.4 1.0 C A:LEU62 3.3 21.8 1.0 C A:LYS60 3.4 24.0 1.0 C A:VAL65 3.5 23.0 1.0 P D:DC3 3.7 24.9 1.0 OP2 D:DC3 3.8 23.9 1.0 O D:HOH106 3.9 40.2 1.0 N A:VAL65 3.9 21.7 1.0 N A:LEU62 4.0 23.8 1.0 C A:LYS61 4.0 30.6 1.0 CA A:PRO63 4.0 22.4 1.0 N A:PRO63 4.1 24.9 1.0 CA A:LYS60 4.2 22.8 1.0 CA A:VAL65 4.2 22.4 1.0 N A:GLY64 4.2 23.8 1.0 CA A:LEU62 4.3 23.0 1.0 O A:LYS61 4.3 28.5 1.0 CG A:LYS60 4.4 28.6 1.0 N A:LYS61 4.4 23.9 1.0 CB A:VAL65 4.4 18.9 1.0 CA A:LYS61 4.5 25.4 1.0 C A:PRO63 4.5 26.6 1.0 N A:GLY66 4.6 17.0 1.0 O3' D:DT2 4.6 24.4 1.0 O A:ALA59 4.8 23.2 1.0 CA A:GLY66 4.9 23.2 1.0 O5' D:DC3 4.9 28.7 1.0 CB A:LYS60 4.9 25.4 1.0 C A:GLY64 4.9 24.1 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:24.9 occ:1.00 OD2 A:ASP190 2.1 28.0 1.0 OD1 A:ASP192 2.1 13.7 1.0 OD2 A:ASP256 2.2 16.5 1.0 OP1 P:DC11 2.4 12.7 1.0 O3' P:8OG10 2.5 12.1 1.0 O A:HOH501 2.5 27.6 1.0 CG A:ASP190 2.9 16.8 1.0 P P:DC11 3.0 14.8 1.0 OD1 A:ASP190 3.1 13.8 1.0 CG A:ASP192 3.2 9.2 1.0 CG A:ASP256 3.3 14.8 1.0 MG A:MG401 3.5 11.8 1.0 OD2 A:ASP192 3.5 13.3 1.0 C3' P:8OG10 3.7 13.4 1.0 CB A:ASP256 3.8 13.6 1.0 C4' P:8OG10 3.9 15.3 1.0 OP2 P:DC11 4.0 28.2 1.0 C5' P:8OG10 4.1 14.4 1.0 O5' P:DC11 4.1 11.3 1.0 C5' P:DC11 4.3 10.4 1.0 OD1 A:ASP256 4.3 12.5 1.0 CB A:ASP190 4.3 13.5 1.0 CB A:ASP192 4.4 8.9 1.0 C2' P:8OG10 4.6 14.9 1.0 O P:HOH208 4.6 23.2 1.0 O A:MET191 4.7 12.6 1.0 O5' P:8OG10 4.7 14.1 1.0 NH2 A:ARG254 4.8 14.3 1.0 CA A:ASP192 4.8 14.3 1.0 N A:ASP256 4.9 13.3 1.0 C A:MET191 4.9 15.5 1.0 OP1 P:8OG10 4.9 15.6 1.0 CA A:ASP256 5.0 10.5 1.0

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293