Sodium in PDB 8y95: Structure of Net-Ne in Occluded State

The structure of Structure of Net-Ne in Occluded State also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Net-Ne in Occluded State (pdb code 8y95). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Net-Ne in Occluded State, PDB code: 8y95:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Net-Ne in Occluded 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-Ne in Occluded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:30.0 occ:1.00 OD1 A:ASN78 1.4 93.2 1.0 OD1 A:ASN350 2.1 96.9 1.0 O A:ALA73 2.3 96.2 1.0 CG A:ASN78 2.4 93.2 1.0 ND2 A:ASN78 2.9 93.2 1.0 CB A:SER318 3.2 92.2 1.0 CG A:ASN350 3.2 96.9 1.0 C A:ALA73 3.4 96.2 1.0 O A:SER318 3.4 92.2 1.0 C A:SER318 3.8 92.2 1.0 CB A:ASN78 3.8 93.2 1.0 OG A:SER318 3.8 92.2 1.0 CA A:SER318 3.9 92.2 1.0 CB A:ASN350 3.9 96.9 1.0 OD1 A:ASP75 4.1 92.6 1.0 CA A:ALA73 4.1 96.2 1.0 ND2 A:ASN350 4.3 96.9 1.0 N A:VAL74 4.3 96.0 1.0 CA A:ASN350 4.5 96.9 1.0 N A:ASN78 4.5 93.2 1.0 CL A:CL702 4.5 30.0 1.0 CA A:VAL74 4.6 96.0 1.0 CA A:ASN78 4.6 93.2 1.0 N A:LEU319 4.7 93.7 1.0 CB A:ALA73 4.7 96.2 1.0 N A:ASP75 4.9 92.6 1.0

Sodium binding site 2 out of 2 in the Structure of Net-Ne in Occluded State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Net-Ne in Occluded State within 5.0Å range: probe atom residue distance (Å) B Occ D:Na703 b:30.0 occ:1.00 OD1 D:ASP75 2.4 92.6 1.0 OD1 D:ASN78 2.4 93.2 1.0 O D:SER318 2.5 92.2 1.0 O D:ALA73 2.6 96.2 1.0 CA D:SER318 2.9 92.2 1.0 CB D:SER318 3.0 92.2 1.0 C D:SER318 3.0 92.2 1.0 CB D:ALA77 3.2 89.0 1.0 CG D:ASP75 3.5 92.6 1.0 CG D:ASN78 3.5 93.2 1.0 C D:ALA73 3.6 96.2 1.0 O D:PHE72 3.8 96.5 1.0 N D:ASN78 3.8 93.2 1.0 OD1 D:ASN350 3.9 96.9 1.0 OD2 D:ASP75 4.0 92.6 1.0 CA D:ALA73 4.2 96.2 1.0 OG D:SER318 4.2 92.2 1.0 N D:SER318 4.2 92.2 1.0 CA D:ALA77 4.3 89.0 1.0 N D:LEU319 4.3 93.7 1.0 N D:ASP75 4.4 92.6 1.0 CB D:ASN78 4.4 93.2 1.0 C D:ALA77 4.4 89.0 1.0 ND2 D:ASN78 4.4 93.2 1.0 NAA D:E5E701 4.6 30.0 1.0 O D:PHE317 4.6 84.8 1.0 CA D:ASN78 4.6 93.2 1.0 N D:ALA77 4.7 89.0 1.0 N D:VAL74 4.8 96.0 1.0 CB D:ASP75 4.8 92.6 1.0 C D:PHE72 4.8 96.5 1.0 C D:PHE317 4.9 84.8 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