Sodium in PDB 4lvs: Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min, PDB code: 4lvs 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)	39.67 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.982, 78.506, 55.138, 90.00, 113.24, 90.00
R / Rfree (%)	21.6 / 28.1

The structure of Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 Min (pdb code 4lvs). 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 Substrate Complex with MN2+, 2.5 Min, PDB code: 4lvs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 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 Substrate Complex with MN2+, 2.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O A:THR101 2.4 24.0 1.0 OP1 P:DG9 2.4 31.3 1.0 O A:ILE106 2.5 16.7 1.0 O P:HOH201 2.5 23.6 1.0 O A:VAL103 2.5 17.7 1.0 O A:HOH513 2.7 29.7 1.0 C A:THR101 3.4 17.7 1.0 C A:VAL103 3.4 19.3 1.0 C A:ILE106 3.4 16.7 1.0 P P:DG9 3.5 24.6 1.0 OP2 P:DG9 3.7 26.8 1.0 N A:ILE106 3.8 17.0 1.0 CA A:THR101 3.9 16.9 1.0 CA A:SER104 4.0 18.9 1.0 N A:GLY105 4.0 19.3 1.0 N A:SER104 4.0 20.0 1.0 CA A:ILE106 4.1 15.7 1.0 N A:VAL103 4.2 17.2 1.0 C A:SER104 4.4 22.8 1.0 C A:ARG102 4.4 22.9 1.0 N A:GLY107 4.4 17.7 1.0 CA A:VAL103 4.4 22.9 1.0 CB A:THR101 4.4 23.0 1.0 N A:ARG102 4.4 19.2 1.0 O3' P:DC8 4.5 23.0 1.0 CB A:ILE106 4.5 18.2 1.0 O5' P:DG9 4.6 27.8 1.0 CA A:GLY107 4.6 22.1 1.0 C A:GLY105 4.7 17.9 1.0 CA A:ARG102 4.7 21.3 1.0 O A:ARG102 4.8 23.2 1.0 O A:LEU100 4.8 19.1 1.0 CA A:GLY105 4.9 15.8 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Mismatched Substrate Complex with MN2+, 2.5 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 Substrate Complex with MN2+, 2.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:30.0 occ:1.00 O A:LEU62 2.3 24.9 1.0 O A:VAL65 2.3 29.0 1.0 O A:HOH517 2.4 29.6 1.0 OP1 D:DC3 2.5 25.6 1.0 O A:LYS60 2.5 24.5 1.0 O D:HOH101 2.6 27.9 1.0 C A:LEU62 3.2 30.6 1.0 C A:VAL65 3.4 27.6 1.0 C A:LYS60 3.6 25.6 1.0 P D:DC3 3.6 24.0 1.0 N A:VAL65 3.8 20.4 1.0 OP2 D:DC3 3.8 26.9 1.0 N A:LEU62 3.9 21.9 1.0 N A:PRO63 3.9 34.5 1.0 CA A:VAL65 4.0 18.2 1.0 CA A:PRO63 4.0 30.4 1.0 C A:LYS61 4.1 31.6 1.0 CA A:LEU62 4.2 27.8 1.0 O A:LYS61 4.3 29.7 1.0 CB A:VAL65 4.3 26.5 1.0 CA A:LYS60 4.3 25.1 1.0 N A:GLY64 4.3 28.5 1.0 C A:PRO63 4.5 36.4 1.0 N A:GLY66 4.6 25.6 1.0 N A:LYS61 4.6 28.6 1.0 O3' D:DT2 4.6 24.5 1.0 CG A:LYS60 4.7 37.6 1.0 CA A:LYS61 4.7 31.1 1.0 O5' D:DC3 4.7 31.7 1.0 O A:ALA59 4.8 24.9 1.0 CD A:LYS60 4.8 35.8 1.0 C A:GLY64 4.8 25.9 1.0 CA A:GLY66 4.9 22.7 1.0 NZ A:LYS60 4.9 33.3 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