Sodium in PDB 5yve: Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator

The structure of Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator, PDB code: 5yve was solved by Y.Wang, M.Hattori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.59 / 3.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	119.613, 119.613, 235.691, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 29.6

The structure of Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator (pdb code 5yve). 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 Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator, PDB code: 5yve:

Sodium binding site 1 out of 1 in the Crystal Structure of Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator


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 Human P2X3 Receptor in Complex with the Af-219 Negative Allosteric Modulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:0.9 occ:0.00 O A:ILE323 4.1 0.7 1.0 CG1 A:VAL326 4.1 0.9 1.0 CG2 A:ILE323 4.1 0.7 1.0 N A:ALA327 4.5 0.7 1.0 CB A:VAL326 4.6 0.2 1.0 CA A:ILE323 4.8 0.5 1.0 CB A:ALA327 4.8 0.9 1.0 CA A:ALA327 4.8 0.9 1.0 C A:ILE323 4.9 0.4 1.0 CB A:ILE323 5.0 0.0 1.0

J.Wang, Y.Wang, W.W.Cui, Y.Huang, Y.Yang, Y.Liu, W.S.Zhao, X.Y.Cheng, W.S.Sun, P.Cao, M.X.Zhu, R.Wang, M.Hattori, Y.Yu. Druggable Negative Allosteric Site of P2X3 Receptors. Proc. Natl. Acad. Sci. V. 115 4939 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29674445
DOI: 10.1073/PNAS.1800907115