Sodium in PDB 4klf: Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S

All present enzymatic activity of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S, PDB code: 4klf was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.20 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.750, 79.956, 55.320, 90.00, 107.52, 90.00
R / Rfree (%)	17.9 / 23.1

The structure of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S (pdb code 4klf). 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 Matched Reactant Complex with MG2+, 20 S, PDB code: 4klf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S


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 Matched Reactant Complex with MG2+, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:30.0 occ:1.00 O P:HOH107 2.4 24.1 1.0 O A:THR101 2.4 22.9 1.0 OP1 P:DG9 2.5 24.3 1.0 O A:VAL103 2.5 19.5 1.0 O A:ILE106 2.6 19.9 1.0 O P:HOH124 2.6 30.0 1.0 C A:THR101 3.3 17.4 1.0 C A:VAL103 3.4 18.2 1.0 P P:DG9 3.5 22.6 1.0 C A:ILE106 3.5 17.7 1.0 OP2 P:DG9 3.6 23.9 1.0 O A:HOH640 3.8 34.1 1.0 N A:ILE106 3.9 20.4 1.0 CA A:THR101 3.9 18.1 1.0 CA A:SER104 4.0 18.7 1.0 N A:SER104 4.0 16.7 1.0 N A:GLY105 4.1 14.1 1.0 N A:VAL103 4.1 17.8 1.0 CA A:ILE106 4.2 15.3 1.0 C A:ARG102 4.3 22.6 1.0 N A:ARG102 4.4 21.9 1.0 C A:SER104 4.4 19.6 1.0 CA A:VAL103 4.4 18.2 1.0 CB A:THR101 4.5 18.1 1.0 N A:GLY107 4.5 18.6 1.0 O3' P:DC8 4.5 23.0 1.0 CA A:ARG102 4.6 20.6 1.0 CB A:ILE106 4.6 21.1 1.0 C A:GLY105 4.7 18.5 1.0 CA A:GLY107 4.8 20.0 1.0 O5' P:DG9 4.8 21.7 1.0 O A:ARG102 4.8 22.3 1.0 O A:LEU100 4.9 20.5 1.0 CA A:GLY105 5.0 20.4 1.0 O A:HOH748 5.0 35.8 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S


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 Matched Reactant Complex with MG2+, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:30.0 occ:1.00 O A:LEU62 2.3 28.1 1.0 O A:VAL65 2.4 22.5 1.0 O A:LYS60 2.4 28.9 1.0 O A:HOH632 2.4 31.4 1.0 OP1 D:DC3 2.7 28.0 1.0 O D:HOH101 2.7 32.0 1.0 C A:LEU62 3.2 28.6 1.0 C A:LYS60 3.4 25.2 1.0 C A:VAL65 3.5 25.7 1.0 P D:DC3 3.7 25.1 1.0 N A:VAL65 3.8 21.7 1.0 N A:LEU62 3.9 24.9 1.0 O D:HOH109 3.9 43.2 1.0 OP2 D:DC3 3.9 23.8 1.0 N A:PRO63 4.0 32.6 1.0 C A:LYS61 4.0 32.0 1.0 CA A:PRO63 4.1 33.3 1.0 CA A:VAL65 4.1 17.9 1.0 N A:GLY64 4.1 24.4 1.0 CA A:LEU62 4.2 26.6 1.0 CA A:LYS60 4.2 25.0 1.0 O A:LYS61 4.3 33.7 1.0 N A:LYS61 4.3 31.2 1.0 CB A:VAL65 4.3 22.0 1.0 C A:PRO63 4.5 29.3 1.0 CA A:LYS61 4.5 30.5 1.0 CG A:LYS60 4.5 33.2 1.0 N A:GLY66 4.5 24.7 1.0 O3' D:DT2 4.6 26.1 1.0 O A:ALA59 4.7 27.3 1.0 C A:GLY64 4.8 24.8 1.0 CA A:GLY66 4.8 29.8 1.0 CB A:LYS60 5.0 32.3 1.0 O5' D:DC3 5.0 27.4 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048