Sodium in PDB 5j0o: Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus:
2.7.7.7;

The structure of Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus, PDB code: 5j0o was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.100, 79.500, 54.700, 90.00, 105.34, 90.00
R / Rfree (%)	21 / 26.4

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus (pdb code 5j0o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus, PDB code: 5j0o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:16.4 occ:1.00 O A:THR101 2.3 14.4 1.0 O A:ILE106 2.3 14.3 1.0 OP1 P:DG9 2.4 14.1 1.0 O A:VAL103 2.5 12.6 1.0 O P:HOH110 2.6 19.9 1.0 O A:HOH722 2.7 23.1 1.0 C A:THR101 3.3 15.8 1.0 C A:ILE106 3.3 13.7 1.0 P P:DG9 3.4 16.7 1.0 C A:VAL103 3.5 15.8 1.0 OP2 P:DG9 3.6 13.5 1.0 N A:ILE106 3.7 12.8 1.0 O A:HOH583 3.7 29.4 1.0 CA A:THR101 3.8 15.5 1.0 CA A:ILE106 4.0 13.1 1.0 CA A:SER104 4.0 14.0 1.0 N A:GLY105 4.0 14.1 1.0 N A:SER104 4.1 14.8 1.0 N A:VAL103 4.1 12.9 1.0 N A:GLY107 4.3 11.3 1.0 CB A:THR101 4.3 15.4 1.0 O P:HOH138 4.3 42.8 1.0 N A:ARG102 4.3 16.4 1.0 C A:SER104 4.3 13.2 1.0 C A:ARG102 4.4 16.8 1.0 CB A:ILE106 4.4 14.1 1.0 O3' P:DC8 4.4 15.8 1.0 CA A:VAL103 4.5 15.5 1.0 CA A:GLY107 4.5 13.3 1.0 O5' P:DG9 4.6 14.6 1.0 C A:GLY105 4.6 12.3 1.0 CA A:ARG102 4.7 16.9 1.0 O P:HOH114 4.8 36.0 1.0 O A:ARG102 4.9 15.1 1.0 O A:LEU100 4.9 15.2 1.0 O A:HOH578 4.9 22.8 1.0 CA A:GLY105 5.0 12.5 1.0

Sodium binding site 2 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:23.5 occ:1.00 O D:HOH117 2.2 30.8 1.0 O A:VAL65 2.3 23.9 1.0 O A:LYS60 2.3 27.4 1.0 O A:LEU62 2.5 24.5 1.0 OP1 D:DC3 2.6 21.2 1.0 O A:HOH710 2.6 26.5 1.0 C A:VAL65 3.3 22.4 1.0 C A:LYS60 3.5 27.7 1.0 C A:LEU62 3.6 25.0 1.0 P D:DC3 3.6 21.4 1.0 N A:VAL65 3.7 22.5 1.0 OP2 D:DC3 3.8 18.6 1.0 CA A:VAL65 4.0 21.6 1.0 N A:GLY64 4.1 24.6 1.0 CG A:LYS60 4.1 32.2 1.0 CA A:LYS60 4.2 26.8 1.0 N A:LEU62 4.2 24.2 1.0 CA A:PRO63 4.3 25.6 1.0 CB A:VAL65 4.3 21.2 1.0 N A:PRO63 4.3 25.0 1.0 C A:LYS61 4.3 26.6 1.0 N A:GLY66 4.4 21.6 1.0 O3' D:DT2 4.5 18.9 1.0 CA A:LEU62 4.5 24.4 1.0 N A:LYS61 4.5 28.1 1.0 C A:PRO63 4.6 25.0 1.0 CA A:GLY66 4.7 20.2 1.0 O A:LYS61 4.7 27.2 1.0 C A:GLY64 4.7 22.5 1.0 CA A:LYS61 4.7 27.1 1.0 CB A:LYS60 4.8 28.3 1.0 O5' D:DC3 4.9 19.2 1.0

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006