Sodium in PDB 4gp7: Polynucleotide Kinase

All present enzymatic activity of Polynucleotide Kinase:
2.7.1.78;

The structure of Polynucleotide Kinase, PDB code: 4gp7 was solved by L.K.Wang, U.Das, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.306, 66.781, 119.546, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 23

The structure of Polynucleotide Kinase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Polynucleotide Kinase (pdb code 4gp7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Polynucleotide Kinase, PDB code: 4gp7:

Sodium binding site 1 out of 1 in the Polynucleotide Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Polynucleotide Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:52.7 occ:1.00 CD2 B:PHE100 2.3 63.2 1.0 CD2 B:TYR151 2.4 29.6 1.0 CE2 B:TYR151 2.5 31.4 1.0 CG B:TYR151 3.0 13.7 1.0 CE2 B:PHE100 3.1 33.2 1.0 CZ B:TYR151 3.1 34.5 1.0 CG B:PHE100 3.3 47.5 1.0 CD1 B:TYR151 3.5 12.4 1.0 CE1 B:TYR151 3.6 10.7 1.0 CB B:PHE100 3.6 21.2 1.0 CB B:ARG150 3.6 23.9 1.0 CB B:TYR151 3.9 8.5 1.0 OH B:TYR151 4.0 40.9 1.0 CG B:PRO6 4.0 19.9 1.0 N B:TYR151 4.0 6.7 1.0 CD B:PRO6 4.1 24.6 1.0 C B:ARG150 4.2 10.8 1.0 CG2 B:VAL102 4.2 10.6 1.0 CZ B:PHE100 4.4 57.3 1.0 O B:HOH1169 4.5 37.1 1.0 CA B:ARG150 4.5 11.4 1.0 CA B:TYR151 4.5 1.6 1.0 CD1 B:PHE100 4.6 53.6 1.0 CG B:ARG150 4.7 37.7 1.0 O B:PRO101 4.7 12.3 1.0 O B:ARG150 4.7 11.7 1.0 CA B:PHE100 4.8 12.1 1.0 OG1 A:THR4 5.0 21.7 1.0 C B:PHE100 5.0 11.4 1.0

L.K.Wang, U.Das, P.Smith, S.Shuman. Structure and Mechanism of the Polynucleotide Kinase Component of the Bacterial Pnkp-HEN1 Rna Repair System. Rna V. 18 2277 2012.
ISSN: ISSN 1355-8382
PubMed: 23118415
DOI: 10.1261/RNA.036061.112