Sodium in PDB 5v1i: Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp

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

The structure of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.60 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.564, 79.798, 55.539, 90.00, 107.62, 90.00
R / Rfree (%)	18.4 / 23.7

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

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp (pdb code 5v1i). 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 Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C 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 Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:18.1 occ:1.00 OP1 P:DG9 2.2 16.8 1.0 O A:THR101 2.3 20.2 1.0 O A:ILE106 2.3 15.5 1.0 O P:HOH201 2.4 19.9 1.0 O A:VAL103 2.5 15.9 1.0 O A:HOH674 2.6 23.5 1.0 C A:THR101 3.3 16.0 1.0 C A:ILE106 3.3 21.1 1.0 P P:DG9 3.3 19.3 1.0 C A:VAL103 3.4 21.7 1.0 OP2 P:DG9 3.6 18.8 1.0 N A:ILE106 3.7 16.0 1.0 CA A:THR101 3.8 21.9 1.0 CA A:SER104 3.9 20.5 1.0 N A:GLY105 4.0 21.9 1.0 CA A:ILE106 4.1 16.9 1.0 N A:SER104 4.1 12.7 1.0 N A:VAL103 4.1 21.1 1.0 N A:GLY107 4.3 18.1 1.0 C A:SER104 4.3 19.8 1.0 C A:ARG102 4.3 22.1 1.0 N A:ARG102 4.4 17.0 1.0 CA A:VAL103 4.4 22.0 1.0 O3' P:DC8 4.4 16.0 1.0 CB A:THR101 4.4 17.9 1.0 O5' P:DG9 4.4 19.3 1.0 CB A:ILE106 4.5 16.4 1.0 CA A:GLY107 4.5 22.1 1.0 C A:GLY105 4.6 18.9 1.0 CA A:ARG102 4.7 23.4 1.0 O A:LEU100 4.7 16.7 1.0 O A:ARG102 4.8 23.1 1.0 CA A:GLY105 4.8 22.1 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C 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 Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:28.5 occ:1.00 O A:VAL65 2.4 27.4 1.0 O A:LEU62 2.4 28.0 1.0 O A:HOH676 2.4 32.5 1.0 O A:LYS60 2.4 37.2 1.0 OP1 D:DC3 2.6 31.9 1.0 O D:HOH103 2.7 31.6 1.0 C A:LEU62 3.4 24.5 1.0 C A:VAL65 3.5 27.5 1.0 C A:LYS60 3.5 30.1 1.0 P D:DC3 3.6 35.7 1.0 OP2 D:DC3 3.8 32.8 1.0 N A:VAL65 3.9 23.8 1.0 N A:LEU62 4.0 26.8 1.0 CA A:PRO63 4.1 26.6 1.0 N A:PRO63 4.2 28.4 1.0 C A:LYS61 4.2 31.1 1.0 N A:GLY64 4.2 29.7 1.0 CA A:VAL65 4.2 22.7 1.0 CA A:LYS60 4.3 29.3 1.0 CA A:LEU62 4.4 26.6 1.0 CG A:LYS60 4.4 28.2 1.0 O A:LYS61 4.5 33.3 1.0 N A:LYS61 4.5 25.3 1.0 N A:GLY66 4.5 23.0 1.0 C A:PRO63 4.5 34.8 1.0 CB A:VAL65 4.5 22.9 1.0 O3' D:DT2 4.6 34.3 1.0 CA A:LYS61 4.6 34.4 1.0 CA A:GLY66 4.7 31.0 1.0 C A:GLY64 4.8 25.6 1.0 O5' D:DC3 4.9 35.1 1.0 O A:ALA59 4.9 28.3 1.0 CB A:LYS60 5.0 29.0 1.0 NZ A:LYS60 5.0 45.1 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C 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 Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:25.0 occ:1.00 OD1 A:ASP192 2.2 19.7 1.0 OD2 A:ASP190 2.2 31.1 1.0 OD2 A:ASP256 2.4 23.7 1.0 O3' P:8OG10 2.4 23.9 0.9 OP1 P:DC11 2.6 18.3 1.0 CG A:ASP190 3.1 17.7 1.0 P P:DC11 3.1 21.1 1.0 CG A:ASP192 3.2 16.6 1.0 OD1 A:ASP190 3.2 17.3 1.0 CG A:ASP256 3.3 21.9 1.0 OD2 A:ASP192 3.6 14.2 1.0 C3' P:8OG10 3.6 25.3 0.9 MG A:MG407 3.6 13.2 1.0 CB A:ASP256 3.8 17.9 1.0 C4' P:8OG10 3.9 28.6 0.9 C5' P:8OG10 4.0 23.4 0.9 OP2 P:DC11 4.2 21.9 1.0 O5' P:DC11 4.2 20.5 1.0 OD1 A:ASP256 4.2 18.0 1.0 C5' P:DC11 4.3 17.0 1.0 CB A:ASP190 4.5 13.7 1.0 CB A:ASP192 4.5 16.8 1.0 C2' P:8OG10 4.6 19.2 0.9 O5' P:8OG10 4.6 21.7 0.9 O A:HOH517 4.7 24.8 0.9 NH2 A:ARG254 4.7 15.8 1.0 O A:MET191 4.8 16.0 1.0 CA A:ASP192 4.9 18.6 1.0 O A:HOH568 5.0 29.8 1.0 N A:ASP256 5.0 15.7 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