Sodium in PDB 8wtv: Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline

The structure of Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline (pdb code 8wtv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline, PDB code: 8wtv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:48.6 occ:1.00 OD1 A:ASN350 2.3 40.6 1.0 CG A:ASN350 3.2 34.2 1.0 O A:SER318 3.4 33.3 1.0 OD1 A:ASN78 3.4 35.3 1.0 CB A:ASN350 3.4 30.0 1.0 CD2 A:LEU319 4.0 35.7 1.0 C A:SER318 4.0 33.8 1.0 CA A:ASN350 4.2 27.9 1.0 CB A:ASP75 4.4 31.6 1.0 CG A:ASN78 4.4 35.0 1.0 ND2 A:ASN350 4.4 34.0 1.0 CA A:LEU319 4.4 32.1 1.0 CB A:SER318 4.5 30.4 1.0 N A:LEU319 4.5 40.0 1.0 ND2 A:ASN78 4.6 36.7 1.0 OD2 A:ASP75 4.6 44.1 1.0 OG A:SER318 4.6 39.9 1.0 CG2 A:THR346 4.8 32.9 1.0 CA A:SER318 4.8 31.8 1.0 CG A:LEU319 4.8 35.3 1.0 O A:THR346 4.9 41.0 1.0 N A:ASN350 4.9 24.8 1.0 CG A:ASP75 5.0 41.0 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Noradrenaline Transporter in Complex with Noradrenaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:55.7 occ:1.00 O A:VAL74 2.8 47.1 1.0 OD2 A:ASP418 3.3 40.9 1.0 CG2 A:THR266 3.6 49.2 1.0 CB A:ASP418 3.7 32.0 1.0 OG A:SER419 3.8 42.3 1.0 O A:LEU415 3.9 30.1 1.0 C A:VAL74 3.9 41.1 1.0 CG A:ASP418 4.0 44.1 1.0 CA A:ASP75 4.0 31.6 1.0 OD1 A:ASP75 4.1 44.7 1.0 CD2 A:LEU415 4.1 31.0 1.0 N A:ASP75 4.4 32.5 1.0 N A:SER419 4.4 35.7 1.0 N A:LEU76 4.4 30.3 1.0 CA A:LEU415 4.5 27.2 1.0 C A:ASP75 4.6 35.9 1.0 C A:LEU415 4.6 32.0 1.0 C A:ASP418 4.8 30.2 1.0 CB A:THR266 4.8 50.9 1.0 CA A:ASP418 4.8 26.9 1.0 OG1 A:THR266 4.9 54.3 1.0 CB A:LEU415 4.9 28.4 1.0 CG A:ASP75 4.9 41.0 1.0 CA A:SER419 4.9 29.2 1.0 CB A:SER419 5.0 34.1 1.0 CB A:ASP75 5.0 31.6 1.0

T.Hu, Z.Yu, J.Zhao, Y.Meng, K.Salomon, Q.Bai, Y.Wei, J.Zhang, S.Xu, Q.Dai, R.Yu, B.Yang, C.J.Loland, Y.Zhao. Transport and Inhibition Mechanisms of the Human Noradrenaline Transporter. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07638-Z