Sodium in PDB 5wiv: Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride

The structure of Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride, PDB code: 5wiv was solved by D.Wacker, S.Wang, A.Levit, T.Che, R.M.Betz, J.D.Mccorvy, A.J.Venkatakrishnan, X.-P.Huang, R.O.Dror, B.K.Shoichet, B.L.Roth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 2.14
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.861, 162.836, 83.181, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.7

The structure of Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride (pdb code 5wiv). 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 Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride, PDB code: 5wiv:

Sodium binding site 1 out of 1 in the Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Sodium-Bound Human D4 Dopamine Receptor in Complex with Nemonapride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1224 b:67.5 occ:1.00 O A:HOH1357 2.3 49.9 1.0 OG A:SER122 2.3 45.2 1.0 OD1 A:ASP80 2.4 59.9 1.0 O A:HOH1349 2.5 54.4 1.0 CB A:SER122 3.3 41.7 1.0 OG A:SER441 3.5 45.9 1.0 CG A:ASP80 3.6 53.9 1.0 O A:HOH1320 3.7 45.5 1.0 O A:HOH1366 3.7 45.3 1.0 OD2 A:ASP80 4.2 51.7 1.0 O A:LEU118 4.3 43.0 1.0 CA A:SER122 4.6 45.0 1.0 OD1 A:ASN440 4.7 44.0 1.0 CB A:ALA79 4.7 44.3 1.0 CA A:ASP80 4.7 46.3 1.0 CB A:SER441 4.7 47.3 1.0 N A:ASP80 4.8 46.4 1.0 CB A:ASP80 4.8 49.4 1.0 C A:ALA79 4.9 43.7 1.0 CE2 A:PHE403 4.9 48.0 1.0 CA A:SER441 5.0 44.8 1.0

S.Wang, D.Wacker, A.Levit, T.Che, R.M.Betz, J.D.Mccorvy, A.J.Venkatakrishnan, X.P.Huang, R.O.Dror, B.K.Shoichet, B.L.Roth. D4 Dopamine Receptor High-Resolution Structures Enable the Discovery of Selective Agonists. Science V. 358 381 2017.
ISSN: ESSN 1095-9203
PubMed: 29051383
DOI: 10.1126/SCIENCE.AAN5468