Sodium in PDB 3v7l: Apo Structure of Rat Dna Polymerase Beta K72E Variant

All present enzymatic activity of Apo Structure of Rat Dna Polymerase Beta K72E Variant:
2.7.7.7;

The structure of Apo Structure of Rat Dna Polymerase Beta K72E Variant, PDB code: 3v7l was solved by S.Rangarajan, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.53 / 2.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.425, 71.386, 82.905, 90.00, 90.52, 90.00
R / Rfree (%)	25.6 / 33.5

The structure of Apo Structure of Rat Dna Polymerase Beta K72E Variant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Apo Structure of Rat Dna Polymerase Beta K72E Variant (pdb code 3v7l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo Structure of Rat Dna Polymerase Beta K72E Variant, PDB code: 3v7l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apo Structure of Rat Dna Polymerase Beta K72E Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Structure of Rat Dna Polymerase Beta K72E Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na336 b:11.0 occ:1.00 N A:ILE106 3.4 41.2 1.0 O A:ILE106 3.5 40.2 1.0 OG1 A:THR101 3.7 34.1 1.0 C A:ILE106 3.8 43.4 1.0 CA A:ILE106 4.1 44.4 1.0 C A:GLY105 4.2 33.7 1.0 CA A:GLY105 4.3 22.9 1.0 N A:GLY105 4.4 25.2 1.0 N A:GLY107 4.6 42.6 1.0 CB A:THR101 4.9 29.8 1.0

Sodium binding site 2 out of 2 in the Apo Structure of Rat Dna Polymerase Beta K72E Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Structure of Rat Dna Polymerase Beta K72E Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na337 b:24.8 occ:1.00 O1 A:SO4340 3.1 6.9 1.0 CB A:SER180 3.7 10.9 1.0 CB A:ALA185 4.0 0.8 1.0 O A:SER187 4.3 2.2 1.0 NH2 A:ARG149 4.3 0.9 1.0 S A:SO4340 4.3 17.9 1.0 O2 A:SO4340 4.3 17.4 1.0 OG A:SER180 4.4 11.1 1.0 CA A:SER180 4.9 4.5 1.0

S.Rangarajan, C.L.Gridley, S.Firbank, S.Dalal, J.B.Sweasy, J.Jaeger. Crystallographic Studies of K72E Mutant Dna Polymerase Explain Loss of Lyase Function and Reveal Changes in the Overall Conformational State of the Polymerase Domain To Be Published.