Sodium in PDB 4kls: Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min, PDB code: 4kls 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)	24.13 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.920, 78.607, 55.034, 90.00, 112.88, 90.00
R / Rfree (%)	22.6 / 28.5

The structure of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min (pdb code 4kls). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min, PDB code: 4kls:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


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 Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:21.6 occ:1.00 O A:ILE106 2.4 15.9 1.0 OP1 P:DG9 2.4 27.0 1.0 O A:THR101 2.4 23.1 1.0 O P:HOH201 2.4 24.6 1.0 O A:HOH508 2.5 30.7 1.0 O A:VAL103 2.5 16.3 1.0 C A:THR101 3.4 17.4 1.0 C A:ILE106 3.4 14.2 1.0 C A:VAL103 3.4 21.1 1.0 P P:DG9 3.4 25.0 1.0 OP2 P:DG9 3.7 22.2 1.0 N A:ILE106 3.8 16.1 1.0 O A:HOH572 3.9 33.0 1.0 CA A:THR101 3.9 19.4 1.0 N A:GLY105 3.9 19.0 1.0 CA A:SER104 4.0 22.0 1.0 N A:SER104 4.1 19.5 1.0 CA A:ILE106 4.1 15.0 1.0 N A:VAL103 4.3 16.3 1.0 C A:SER104 4.3 22.4 1.0 N A:GLY107 4.4 17.6 1.0 CB A:THR101 4.4 20.2 1.0 C A:ARG102 4.4 20.0 1.0 CA A:VAL103 4.5 24.0 1.0 N A:ARG102 4.5 18.9 1.0 O3' P:DC8 4.5 24.1 1.0 CB A:ILE106 4.5 13.6 1.0 O5' P:DG9 4.6 22.3 1.0 CA A:GLY107 4.6 18.0 1.0 C A:GLY105 4.7 19.3 1.0 CA A:ARG102 4.8 26.1 1.0 O A:ARG102 4.8 22.9 1.0 O A:LEU100 4.9 21.1 1.0 CA A:GLY105 4.9 17.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


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 Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:27.6 occ:1.00 N A:HIS34 3.5 24.3 1.0 C A:ALA32 3.5 23.2 1.0 CA A:ALA32 3.5 21.4 1.0 CB A:ALA32 3.6 21.9 1.0 CB A:HIS34 3.7 27.9 1.0 N A:ILE33 3.8 16.8 1.0 N A:LYS35 3.8 19.2 1.0 O A:ALA32 3.9 22.8 1.0 CA A:HIS34 4.0 26.6 1.0 CD2 A:HIS34 4.0 28.3 1.0 CG A:LYS35 4.1 24.8 1.0 CG A:HIS34 4.2 27.1 1.0 C A:HIS34 4.3 22.3 1.0 C A:ILE33 4.5 25.6 1.0 O6 D:DG1 4.5 31.1 1.0 O A:HOH564 4.6 32.2 1.0 CA A:ILE33 4.7 25.9 1.0 CB A:LYS35 4.7 22.7 1.0 CA A:LYS35 4.8 18.3 1.0 N A:ALA32 5.0 21.9 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:30.0 occ:1.00 O A:HOH545 2.3 26.3 1.0 O A:LYS60 2.4 23.9 1.0 O A:VAL65 2.4 24.8 1.0 O A:LEU62 2.4 21.4 1.0 O D:HOH102 2.5 23.2 1.0 OP1 D:DC3 2.7 20.8 1.0 C A:LEU62 3.3 26.5 1.0 C A:LYS60 3.4 29.7 1.0 C A:VAL65 3.5 26.0 1.0 P D:DC3 3.8 24.1 1.0 N A:VAL65 3.9 25.4 1.0 OP2 D:DC3 3.9 21.5 1.0 N A:LEU62 3.9 22.5 1.0 C A:LYS61 4.0 27.1 1.0 N A:PRO63 4.1 26.7 1.0 CA A:VAL65 4.1 22.2 1.0 CA A:PRO63 4.1 22.7 1.0 CA A:LYS60 4.2 24.2 1.0 CA A:LEU62 4.2 23.9 1.0 CB A:VAL65 4.2 27.0 1.0 O A:LYS61 4.3 31.7 1.0 N A:GLY64 4.4 26.1 1.0 CG A:LYS60 4.4 38.0 1.0 N A:LYS61 4.4 24.3 1.0 C A:PRO63 4.6 28.4 1.0 CA A:LYS61 4.6 27.2 1.0 N A:GLY66 4.6 23.1 1.0 O A:ALA59 4.7 23.2 1.0 O3' D:DT2 4.7 23.6 1.0 CA A:GLY66 4.9 22.7 1.0 C A:GLY64 4.9 27.7 1.0 CB A:LYS60 4.9 29.0 1.0 NZ A:LYS60 4.9 27.8 1.0 CD A:LYS60 4.9 33.2 1.0 CG1 A:VAL65 5.0 30.1 1.0 O5' D:DC3 5.0 25.5 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