Sodium in PDB 8y93: Structure of Net-Amitriptyline in Outward-Open State

The structure of Structure of Net-Amitriptyline in Outward-Open State also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of Net-Amitriptyline in Outward-Open State (pdb code 8y93). 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 Net-Amitriptyline in Outward-Open State, PDB code: 8y93:

Sodium binding site 1 out of 1 in the Structure of Net-Amitriptyline in Outward-Open State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Net-Amitriptyline in Outward-Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:30.0 occ:1.00 O A:GLY71 2.3 96.8 1.0 CB A:ASP418 2.9 97.0 1.0 O A:VAL74 2.9 96.0 1.0 O A:LEU415 2.9 96.3 1.0 C A:GLY71 3.2 96.8 1.0 OD2 A:ASP418 3.3 97.0 1.0 CA A:GLY71 3.3 96.8 1.0 CG A:ASP418 3.5 97.0 1.0 C A:LEU415 3.6 96.3 1.0 CA A:LEU415 3.6 96.3 1.0 O A:ALA414 3.6 97.2 1.0 CA A:ASP418 4.0 97.0 1.0 C A:VAL74 4.2 96.0 1.0 N A:SER419 4.2 95.2 1.0 N A:ASP418 4.2 97.0 1.0 OG A:SER419 4.3 95.2 1.0 CD2 A:LEU415 4.4 96.3 1.0 N A:PHE72 4.4 96.5 1.0 C A:ALA414 4.4 97.2 1.0 C A:ASP418 4.5 97.0 1.0 N A:LEU415 4.5 96.3 1.0 CB A:LEU415 4.6 96.3 1.0 OD1 A:ASP418 4.6 97.0 1.0 O A:THR266 4.7 96.6 1.0 N A:GLY71 4.8 96.8 1.0 N A:GLY416 4.8 95.9 1.0 CA A:ASP75 4.9 92.6 1.0 N A:ASP75 5.0 92.6 1.0 CA A:PHE72 5.0 96.5 1.0

H.Zhang, Y.L.Yin, A.Dai, T.Zhang, C.Zhang, C.Wu, W.Hu, X.He, B.Pan, S.Jin, Q.Yuan, M.W.Wang, D.Yang, H.E.Xu, Y.Jiang. Dimerization and Antidepressant Recognition at Noradrenaline Transporter Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07437-6