Sodium in PDB 3v72: Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna

All present enzymatic activity of Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna:
2.7.7.7;

The structure of Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna, PDB code: 3v72 was solved by C.L.Gridley, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.76 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.193, 73.763, 118.367, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 29.1

The structure of Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna (pdb code 3v72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna, PDB code: 3v72:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:84.5 occ:1.00 OG A:SER180 2.5 81.8 1.0 OG A:SER188 2.6 0.2 1.0 CB A:SER188 3.0 91.1 1.0 N A:PHE181 3.1 46.6 1.0 N A:SER180 3.3 55.0 1.0 CB A:SER180 3.7 72.3 1.0 CA A:SER180 3.7 59.2 1.0 C A:SER180 3.8 53.2 1.0 CB A:PHE181 4.1 38.0 1.0 C A:GLY179 4.1 64.2 1.0 CA A:PHE181 4.1 46.5 1.0 CA A:SER188 4.3 81.3 1.0 CA A:GLY179 4.4 55.8 1.0 O A:ASP190 4.6 52.7 1.0 O A:SER180 4.8 60.3 1.0 O A:SER187 4.8 60.6 1.0 N A:GLY189 4.9 70.4 1.0 O A:CYS178 4.9 48.5 1.0 O A:GLY179 5.0 65.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rat Dna Polymerase Beta Mutator E295K: Enzyme- Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:52.9 occ:1.00 O A:THR101 2.9 41.2 1.0 OP1 P:DG6 3.0 38.9 1.0 O A:ILE106 3.0 37.3 1.0 O A:HOH518 3.1 54.0 1.0 O A:VAL103 3.1 38.7 1.0 OP2 P:DG6 3.4 43.6 1.0 P P:DG6 3.5 42.8 1.0 C A:VAL103 3.7 34.9 1.0 C A:ILE106 3.9 34.8 1.0 N A:ILE106 3.9 29.4 1.0 C A:THR101 3.9 31.8 1.0 O A:HOH561 3.9 52.5 1.0 N A:GLY105 4.0 34.0 1.0 CA A:THR104 4.0 37.9 1.0 N A:THR104 4.1 33.8 1.0 N A:VAL103 4.1 51.2 1.0 CA A:ILE106 4.3 34.8 1.0 C A:ARG102 4.5 51.0 1.0 C A:THR104 4.5 33.0 1.0 O3' P:DA5 4.5 34.3 1.0 CA A:VAL103 4.6 32.8 1.0 CA A:THR101 4.6 25.9 1.0 N A:ARG102 4.7 40.8 1.0 O5' P:DG6 4.7 38.9 1.0 CA A:ARG102 4.8 42.3 1.0 CB A:ILE106 4.8 36.1 1.0 C A:GLY105 4.8 31.2 1.0 N A:GLY107 4.9 25.0 1.0 CA A:GLY105 5.0 23.6 1.0

Y.Li, C.L.Gridley, J.Jaeger, J.B.Sweasy, T.Schlick. Unfavorable Electrostatic and Steric Interactions in Dna Polymerase Beta E295K Mutant Interfere with the Enzyme S Pathway J.Am.Chem.Soc. V. 134 9999 2012.
ISSN: ISSN 0002-7863
PubMed: 22651551
DOI: 10.1021/JA300361R