Sodium in PDB 4klu: Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H

All present enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H:
2.7.7.7;

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H, PDB code: 4klu 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)	31.99 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.222, 80.105, 55.812, 90.00, 109.64, 90.00
R / Rfree (%)	21.2 / 25.1

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H (pdb code 4klu). 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 Mismatched Product Complex with MN2+, 15 H, PDB code: 4klu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H


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 Mismatched Product Complex with MN2+, 15 H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.0 occ:1.00 O A:THR101 2.3 14.6 1.0 O A:VAL103 2.4 11.9 1.0 O A:ILE106 2.4 14.4 1.0 OP1 P:DG9 2.5 17.9 1.0 O A:HOH604 2.6 18.3 1.0 O P:HOH101 2.7 18.6 1.0 C A:THR101 3.3 16.0 1.0 C A:VAL103 3.4 15.5 1.0 C A:ILE106 3.4 14.9 1.0 P P:DG9 3.5 15.5 1.0 O A:HOH570 3.6 32.3 1.0 OP2 P:DG9 3.7 18.1 1.0 N A:ILE106 3.7 10.8 1.0 CA A:THR101 3.9 14.8 1.0 CA A:SER104 3.9 18.7 1.0 N A:SER104 4.0 14.6 1.0 N A:GLY105 4.0 13.3 1.0 CA A:ILE106 4.0 11.9 1.0 N A:VAL103 4.1 14.4 1.0 C A:ARG102 4.3 17.1 1.0 C A:SER104 4.3 16.1 1.0 N A:ARG102 4.4 14.9 1.0 CA A:VAL103 4.4 16.3 1.0 CB A:THR101 4.4 19.5 1.0 N A:GLY107 4.4 15.2 1.0 CB A:ILE106 4.4 13.5 1.0 O3' P:DC8 4.6 17.1 1.0 CA A:ARG102 4.6 17.0 1.0 CA A:GLY107 4.6 13.2 1.0 O A:ARG102 4.6 15.0 1.0 O5' P:DG9 4.7 18.7 1.0 C A:GLY105 4.7 13.4 1.0 O A:LEU100 4.8 13.5 1.0 O P:HOH131 4.9 37.8 1.0 CA A:GLY105 5.0 16.5 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 15 H


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 Mismatched Product Complex with MN2+, 15 H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.0 occ:1.00 O A:LEU62 2.3 25.4 1.0 O A:VAL65 2.3 23.7 1.0 O A:LYS60 2.4 26.8 1.0 O D:HOH206 2.4 28.9 1.0 O A:HOH617 2.4 32.3 1.0 OP1 D:DC3 3.0 23.8 1.0 C A:LEU62 3.3 27.7 1.0 C A:LYS60 3.4 29.8 1.0 C A:VAL65 3.5 22.9 1.0 N A:VAL65 3.8 21.8 1.0 P D:DC3 4.0 25.2 1.0 N A:LEU62 4.0 25.9 1.0 OP2 D:DC3 4.0 20.0 1.0 CA A:VAL65 4.0 20.8 1.0 CA A:PRO63 4.1 27.2 1.0 C A:LYS61 4.1 34.5 1.0 N A:PRO63 4.1 26.6 1.0 CA A:LYS60 4.2 27.1 1.0 N A:GLY64 4.2 26.2 1.0 CB A:VAL65 4.2 21.4 1.0 CA A:LEU62 4.3 29.3 1.0 O A:LYS61 4.3 32.5 1.0 N A:LYS61 4.4 30.0 1.0 CG A:LYS60 4.4 31.1 1.0 C A:PRO63 4.5 28.5 1.0 N A:GLY66 4.5 20.4 1.0 CA A:LYS61 4.6 35.1 1.0 O3' D:DT2 4.7 22.0 1.0 O A:ALA59 4.8 24.3 1.0 CA A:GLY66 4.8 21.8 1.0 C A:GLY64 4.8 23.9 1.0 CB A:LYS60 4.9 28.3 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