Sodium in PDB 4kld: Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S

All present enzymatic activity of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S, PDB code: 4kld 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)	23.15 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%)	19.7 / 25.1

The structure of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S (pdb code 4kld). 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 Substrate Complex with CA2+, 0 S, PDB code: 4kld:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 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 Substrate Complex with CA2+, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:THR101 2.3 25.2 1.0 OP1 P:DG9 2.4 23.6 1.0 O A:HOH531 2.4 27.0 1.0 O A:ILE106 2.5 21.8 1.0 O A:VAL103 2.6 18.6 1.0 O P:HOH111 2.7 31.7 1.0 C A:THR101 3.4 24.9 1.0 P P:DG9 3.4 26.2 1.0 OP2 P:DG9 3.4 31.4 1.0 C A:VAL103 3.5 23.9 1.0 C A:ILE106 3.6 23.1 1.0 N A:ILE106 3.9 17.2 1.0 CA A:THR101 4.0 20.8 1.0 N A:GLY105 4.1 21.7 1.0 N A:VAL103 4.2 26.3 1.0 CA A:SER104 4.2 23.2 1.0 N A:SER104 4.2 21.5 1.0 C A:ARG102 4.3 25.9 1.0 CA A:ILE106 4.3 18.7 1.0 N A:ARG102 4.4 20.9 1.0 O3' P:DC8 4.4 26.5 1.0 CA A:VAL103 4.5 21.9 1.0 C A:SER104 4.5 21.8 1.0 O5' P:DG9 4.5 30.5 1.0 N A:GLY107 4.6 20.0 1.0 CA A:ARG102 4.6 22.4 1.0 CB A:THR101 4.6 22.4 1.0 O A:ARG102 4.6 28.6 1.0 CB A:ILE106 4.7 19.9 1.0 C A:GLY105 4.8 23.9 1.0 CA A:GLY107 4.8 18.2 1.0 O A:LEU100 4.9 17.1 1.0 CA A:GLY105 4.9 26.1 1.0 O A:HOH613 5.0 42.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 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 Substrate Complex with CA2+, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O D:HOH101 2.3 28.9 1.0 O A:VAL65 2.4 30.9 1.0 O A:LYS60 2.4 28.0 1.0 O A:HOH567 2.5 31.7 1.0 OP1 D:DC3 2.6 21.9 1.0 O A:LEU62 2.7 26.1 1.0 C A:VAL65 3.5 27.9 1.0 C A:LYS60 3.5 29.3 1.0 P D:DC3 3.6 25.3 1.0 C A:LEU62 3.7 25.7 1.0 OP2 D:DC3 3.7 26.4 1.0 N A:VAL65 3.8 23.9 1.0 CA A:VAL65 4.1 26.1 1.0 C A:LYS61 4.2 32.0 1.0 N A:GLY64 4.2 31.4 1.0 N A:LEU62 4.3 28.1 1.0 CA A:LYS60 4.3 22.4 1.0 O A:LYS61 4.3 29.9 1.0 CA A:PRO63 4.3 29.0 1.0 CB A:VAL65 4.4 21.1 1.0 N A:PRO63 4.4 28.7 1.0 CG A:LYS60 4.4 34.5 1.0 N A:LYS61 4.5 27.6 1.0 N A:GLY66 4.5 23.5 1.0 O3' D:DT2 4.5 27.1 1.0 CA A:LEU62 4.6 24.1 1.0 CA A:LYS61 4.6 35.1 1.0 C A:PRO63 4.7 33.0 1.0 CA A:GLY66 4.8 22.4 1.0 O5' D:DC3 4.8 28.4 1.0 C A:GLY64 4.9 24.1 1.0 CB A:LYS60 5.0 29.4 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