Sodium in PDB 8i5y: Structure of Human NAV1.7 in Complex with Vixotrigine

The structure of Structure of Human NAV1.7 in Complex with Vixotrigine also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Structure of Human NAV1.7 in Complex with Vixotrigine (pdb code 8i5y). 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 Human NAV1.7 in Complex with Vixotrigine, PDB code: 8i5y:

Sodium binding site 1 out of 1 in the Structure of Human NAV1.7 in Complex with Vixotrigine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human NAV1.7 in Complex with Vixotrigine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2009 b:7.2 occ:1.00 OD1 A:ASP361 2.4 10.7 1.0 OE2 A:GLU930 2.9 12.8 1.0 CG A:ASP361 3.1 5.2 1.0 O A:HOH2105 3.2 12.5 1.0 OD2 A:ASP361 3.2 7.6 1.0 CB A:GLU927 3.6 1.7 1.0 CA A:GLU927 3.6 1.5 1.0 CG2 A:ILE929 3.7 2.9 1.0 N A:TRP928 3.7 13.0 1.0 CD A:GLU930 3.8 11.2 1.0 N A:ILE929 3.8 0.0 1.0 CB A:TYR362 3.9 24.6 1.0 C A:GLU927 3.9 8.4 1.0 CG A:GLU930 3.9 2.9 1.0 N A:GLU930 3.9 9.2 1.0 CG A:GLU927 4.0 0.0 1.0 CB A:GLU930 4.3 6.2 1.0 OE1 A:GLU927 4.3 14.1 1.0 CD A:GLU927 4.3 10.4 1.0 N A:TYR362 4.4 20.3 1.0 CB A:ASP361 4.5 5.3 1.0 C A:ASP361 4.5 8.7 1.0 C A:TRP928 4.6 1.0 1.0 CG A:TYR362 4.6 24.1 1.0 CA A:ILE929 4.6 4.0 1.0 CB A:ILE929 4.6 9.0 1.0 CA A:TRP928 4.7 5.0 1.0 O A:GLU927 4.7 10.8 1.0 CA A:TYR362 4.7 17.8 1.0 C A:ILE929 4.8 0.0 1.0 CA A:GLU930 4.8 0.0 1.0 CA A:ASP361 4.8 2.5 1.0 NH2 A:ARG922 4.9 13.3 1.0 O A:ASP361 5.0 18.2 1.0

Q.Wu, J.Huang, X.Fan, K.Wang, X.Jin, G.Huang, J.Li, X.Pan, N.Yan. Structural Mapping of Na V 1.7 Antagonists. Nat Commun V. 14 3224 2023.
ISSN: ESSN 2041-1723
PubMed: 37270609
DOI: 10.1038/S41467-023-38942-3