Sodium in PDB 5v1j: Dna Polymerase Beta Open Product Complex with 8-Oxog:C and Inserted Dctp

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

The structure of Dna Polymerase Beta Open Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1j 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)	31.76 / 2.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.273, 79.795, 55.887, 90.00, 110.29, 90.00
R / Rfree (%)	21.7 / 28.5

The binding sites of Sodium atom in the Dna Polymerase Beta Open Product Complex with 8-Oxog:C and Inserted Dctp (pdb code 5v1j). 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 Open Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Open 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 Open Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:39.6 occ:1.00 O A:THR101 2.3 41.9 1.0 OP1 P:DG9 2.4 41.8 1.0 O A:HOH517 2.6 44.4 1.0 O A:ILE106 2.7 40.7 1.0 O A:VAL103 2.9 40.8 1.0 O P:HOH101 3.0 33.5 1.0 P P:DG9 3.4 40.7 1.0 C A:THR101 3.4 36.7 1.0 C A:VAL103 3.5 41.7 1.0 OP2 P:DG9 3.6 40.2 1.0 C A:ILE106 3.7 44.4 1.0 CA A:SER104 3.7 28.9 1.0 N A:SER104 3.8 40.3 1.0 N A:ILE106 3.9 35.3 1.0 N A:GLY105 4.2 44.0 1.0 CA A:THR101 4.2 42.8 1.0 C A:ARG102 4.2 45.7 1.0 N A:VAL103 4.2 44.4 1.0 C A:SER104 4.3 45.0 1.0 O5' P:DG9 4.3 32.5 1.0 CA A:ILE106 4.3 41.9 1.0 N A:ARG102 4.4 36.5 1.0 O A:ARG102 4.5 41.1 1.0 CA A:VAL103 4.5 41.4 1.0 CA A:ARG102 4.6 35.3 1.0 CB A:THR101 4.6 44.4 1.0 N A:GLY107 4.7 35.2 1.0 O3' P:DC8 4.7 37.1 1.0 CB A:ILE106 4.8 42.9 1.0 C A:GLY105 4.8 48.6 1.0 CA A:GLY107 4.9 32.8 1.0 CB A:SER104 5.0 36.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Open 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 Open Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:63.5 occ:1.00 O D:HOH102 2.3 54.8 1.0 O A:LEU62 2.5 54.9 1.0 O A:LYS60 2.7 65.4 1.0 OP1 D:DC3 3.1 42.8 1.0 O A:VAL65 3.1 58.6 1.0 C A:LEU62 3.4 60.1 1.0 C A:LYS60 3.8 57.1 1.0 N A:LEU62 3.8 56.2 1.0 C A:LYS61 4.0 57.6 1.0 P D:DC3 4.1 62.0 1.0 OP2 D:DC3 4.1 43.6 1.0 C A:VAL65 4.2 56.4 1.0 N A:PRO63 4.2 55.2 1.0 CA A:PRO63 4.2 57.7 1.0 CA A:LEU62 4.2 61.1 1.0 O A:LYS61 4.3 55.1 1.0 N A:VAL65 4.3 51.9 1.0 N A:GLY64 4.4 50.3 1.0 CA A:LYS61 4.4 58.2 1.0 N A:LYS61 4.6 59.0 1.0 CA A:VAL65 4.8 54.9 1.0 C A:PRO63 4.8 53.4 1.0 CA A:LYS60 4.8 55.4 1.0 NZ A:LYS60 4.8 63.6 1.0 O3' D:DT2 5.0 63.0 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