Sodium in PDB 4klt: Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min, PDB code: 4klt 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)	25.76 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.082, 78.596, 54.980, 90.00, 112.43, 90.00
R / Rfree (%)	22.9 / 29.3

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min (pdb code 4klt). 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+, 30 Min, PDB code: 4klt:
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+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:49.0 occ:1.00 O A:THR101 2.3 27.6 1.0 O A:ILE106 2.4 12.2 1.0 OP1 P:DG9 2.4 23.7 1.0 O P:HOH102 2.6 21.6 1.0 O A:VAL103 2.6 12.3 1.0 O P:HOH129 3.1 30.0 1.0 C A:THR101 3.3 17.9 1.0 C A:ILE106 3.4 17.2 1.0 P P:DG9 3.4 24.6 1.0 C A:VAL103 3.6 23.9 1.0 O A:HOH596 3.6 39.1 1.0 OP2 P:DG9 3.7 18.6 1.0 N A:ILE106 3.8 24.8 1.0 CA A:THR101 3.8 17.9 1.0 N A:GLY105 4.0 18.4 1.0 CA A:ILE106 4.0 13.8 1.0 CA A:SER104 4.1 21.3 1.0 N A:SER104 4.2 21.3 1.0 CB A:THR101 4.3 21.2 1.0 N A:VAL103 4.4 20.2 1.0 N A:GLY107 4.4 23.6 1.0 C A:SER104 4.4 19.8 1.0 N A:ARG102 4.5 16.6 1.0 CB A:ILE106 4.5 17.6 1.0 O3' P:DC8 4.5 26.7 1.0 C A:ARG102 4.5 21.9 1.0 CA A:VAL103 4.6 25.0 1.0 O5' P:DG9 4.6 23.5 1.0 CA A:GLY107 4.7 18.4 1.0 C A:GLY105 4.7 19.9 1.0 CA A:ARG102 4.8 16.0 1.0 O A:LEU100 4.9 17.3 1.0 O A:ARG102 4.9 18.8 1.0 CA A:GLY105 4.9 17.8 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 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 Product Complex with MN2+, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.0 occ:1.00 O A:VAL65 2.2 23.6 1.0 O A:LEU62 2.2 26.5 1.0 O A:HOH687 2.4 30.0 1.0 O D:HOH105 2.5 25.2 1.0 O A:LYS60 2.5 18.4 1.0 OP1 D:DC3 2.6 20.0 1.0 C A:LEU62 3.2 18.3 1.0 C A:VAL65 3.3 25.8 1.0 C A:LYS60 3.6 27.7 1.0 P D:DC3 3.7 21.4 1.0 N A:VAL65 3.8 23.4 1.0 OP2 D:DC3 3.8 15.5 1.0 N A:LEU62 4.0 30.2 1.0 CA A:VAL65 4.0 20.4 1.0 N A:PRO63 4.0 26.9 1.0 CA A:PRO63 4.1 20.6 1.0 CB A:VAL65 4.1 24.5 1.0 C A:LYS61 4.2 26.5 1.0 CA A:LYS60 4.2 23.4 1.0 CA A:LEU62 4.2 21.7 1.0 CD A:LYS60 4.4 36.5 1.0 N A:GLY66 4.4 24.2 1.0 N A:GLY64 4.4 21.0 1.0 O A:LYS61 4.4 27.9 1.0 O3' D:DT2 4.5 23.1 1.0 C A:PRO63 4.5 21.6 1.0 CG A:LYS60 4.5 28.4 1.0 N A:LYS61 4.6 25.9 1.0 CA A:GLY66 4.6 19.2 1.0 O A:ALA59 4.7 21.3 1.0 CA A:LYS61 4.8 24.2 1.0 CG1 A:VAL65 4.8 21.6 1.0 NZ A:LYS60 4.8 27.0 1.0 C A:GLY64 4.9 16.4 1.0 O5' D:DC3 4.9 29.9 1.0 CB A:LYS60 5.0 28.6 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