Sodium in PDB 4klh: Dna Polymerase Beta Matched Product Complex with MN2+, 40 S

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S, PDB code: 4klh 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)	25.09 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.900, 80.200, 55.100, 90.00, 107.90, 90.00
R / Rfree (%)	20.5 / 26.9

The structure of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S also contains other interesting chemical elements:

Manganese	(Mn)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 S (pdb code 4klh). 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 Product Complex with MN2+, 40 S, PDB code: 4klh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 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 Product Complex with MN2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:30.0 occ:1.00 OP1 P:DG9 2.4 26.1 1.0 O P:HOH213 2.5 30.1 1.0 O A:THR101 2.5 26.3 1.0 O A:VAL103 2.5 19.5 1.0 O A:ILE106 2.5 20.8 1.0 O A:HOH635 2.6 31.4 1.0 C A:VAL103 3.4 19.9 1.0 C A:THR101 3.4 23.7 1.0 P P:DG9 3.5 25.1 1.0 C A:ILE106 3.5 21.9 1.0 OP2 P:DG9 3.7 20.9 1.0 N A:ILE106 3.8 19.9 1.0 N A:GLY105 3.9 19.5 1.0 CA A:SER104 3.9 22.1 1.0 O A:HOH675 3.9 41.8 1.0 N A:SER104 4.0 17.1 1.0 CA A:THR101 4.1 22.4 1.0 N A:VAL103 4.1 20.4 1.0 CA A:ILE106 4.2 14.5 1.0 C A:SER104 4.3 24.6 1.0 C A:ARG102 4.3 23.7 1.0 N A:ARG102 4.4 20.5 1.0 CA A:VAL103 4.4 16.8 1.0 O3' P:DC8 4.5 21.0 1.0 N A:GLY107 4.5 21.7 1.0 CB A:ILE106 4.6 15.8 1.0 CA A:ARG102 4.6 21.5 1.0 CB A:THR101 4.7 23.4 1.0 C A:GLY105 4.7 24.5 1.0 O5' P:DG9 4.7 25.0 1.0 O A:ARG102 4.7 23.2 1.0 CA A:GLY107 4.7 25.2 1.0 CA A:GLY105 4.9 22.7 1.0 O A:LEU100 5.0 22.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 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 Product Complex with MN2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:30.0 occ:1.00 O A:LYS60 2.4 30.2 1.0 O A:LEU62 2.4 35.7 1.0 O A:HOH582 2.5 32.0 1.0 O D:HOH108 2.5 30.0 1.0 O A:VAL65 2.5 29.5 1.0 OP1 D:DC3 2.6 28.2 1.0 C A:LEU62 3.2 25.4 1.0 C A:LYS60 3.4 35.4 1.0 C A:VAL65 3.6 30.8 1.0 P D:DC3 3.7 29.6 1.0 O D:HOH107 3.8 43.2 1.0 CA A:PRO63 3.9 30.0 1.0 N A:LEU62 3.9 28.0 1.0 N A:PRO63 3.9 31.7 1.0 OP2 D:DC3 3.9 28.7 1.0 N A:VAL65 4.0 28.1 1.0 C A:LYS61 4.0 36.2 1.0 CA A:LEU62 4.2 22.2 1.0 CA A:LYS60 4.2 28.0 1.0 N A:GLY64 4.2 32.3 1.0 CA A:VAL65 4.3 22.7 1.0 O A:LYS61 4.4 37.0 1.0 CG A:LYS60 4.4 37.7 1.0 N A:LYS61 4.4 28.6 1.0 C A:PRO63 4.4 29.9 1.0 CB A:VAL65 4.5 21.1 1.0 CA A:LYS61 4.5 35.2 1.0 O3' D:DT2 4.6 34.7 1.0 N A:GLY66 4.7 28.3 1.0 O A:ALA59 4.8 29.0 1.0 CA A:GLY66 4.9 30.3 1.0 CB A:LYS60 4.9 31.8 1.0 NZ A:LYS60 4.9 33.9 1.0 O5' D:DC3 4.9 34.9 1.0 C A:GLY64 5.0 29.7 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