Sodium in PDB 8c25: Purine Nucleoside Phosphorylase in Complex with Js-375

All present enzymatic activity of Purine Nucleoside Phosphorylase in Complex with Js-375:
2.4.2.1;

The structure of Purine Nucleoside Phosphorylase in Complex with Js-375, PDB code: 8c25 was solved by S.Djukic, P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.28 / 1.56
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	125.12, 125.12, 125.12, 90, 90, 90
R / Rfree (%)	15.3 / 18.5

The structure of Purine Nucleoside Phosphorylase in Complex with Js-375 also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Purine Nucleoside Phosphorylase in Complex with Js-375 (pdb code 8c25). 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 Purine Nucleoside Phosphorylase in Complex with Js-375, PDB code: 8c25:

Sodium binding site 1 out of 1 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:27.9 occ:1.00 O A:HOH492 2.2 27.3 1.0 O A:HOH415 2.3 23.7 1.0 OE1 A:GLU212 2.4 24.2 1.0 O A:VAL100 2.4 17.4 1.0 O A:HOH593 2.5 28.2 1.0 C A:VAL100 3.5 15.2 1.0 CD A:GLU212 3.5 18.6 1.0 O A:HOH558 3.5 41.5 1.0 CA A:VAL100 3.8 15.7 1.0 CG A:GLU212 3.9 12.8 1.0 CG1 A:VAL100 4.1 17.0 1.0 CG A:ARG88 4.1 15.5 1.0 O A:HOH557 4.2 21.8 0.7 O A:HOH625 4.2 22.4 1.0 O A:ILE89 4.3 23.1 1.0 CD A:ARG88 4.4 12.8 1.0 O A:TYR99 4.4 25.5 1.0 CB A:ARG88 4.4 20.9 1.0 CG A:PRO103 4.4 17.7 1.0 NE A:ARG88 4.4 12.3 1.0 CB A:VAL100 4.5 14.7 1.0 CD A:PRO103 4.5 18.3 1.0 OE2 A:GLU212 4.5 23.6 1.0 N A:ILE89 4.6 19.6 1.0 CD2 A:LEU85 4.6 9.8 0.3 CA A:ARG88 4.6 17.5 1.0 N A:VAL101 4.7 14.7 1.0 O A:HOH547 4.9 27.2 1.0 N A:VAL100 4.9 16.8 1.0 CB A:PRO103 5.0 18.0 1.0

J.Skacel, S.Djukic, O.Baszczynski, F.Kalcic, T.Bilek, K.Chalupsky, J.Kozak, A.Dvorakova, E.Tloust'ova, Z.Kral'ova, M.Smidkova, J.Voldrich, M.Rumlova, P.Pachl, J.Brynda, T.Vuckova, M.Fabry, J.Snasel, I.Pichova, P.Rezacova, H.Mertlikova-Kaiserova, Z.Janeba. Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37134237
DOI: 10.1021/ACS.JMEDCHEM.2C02097