Sodium in PDB 8y2d: Cryo-Em Structure of Human Dopamine Transporter in Complex with Dopamine

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Cryo-Em Structure of Human Dopamine Transporter in Complex with Dopamine (pdb code 8y2d). 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 Human Dopamine Transporter in Complex with Dopamine, PDB code: 8y2d:
Jump to Sodium binding site number: 1; 2;

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


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 Human Dopamine Transporter in Complex with Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:33.7 occ:1.00 OD1 A:ASN82 2.3 21.7 1.0 O A:ALA77 2.3 33.1 1.0 OD1 A:ASP79 2.4 30.3 1.0 O A:SER321 2.5 23.0 1.0 OD1 A:ASN353 2.9 28.0 1.0 C A:SER321 3.2 24.3 1.0 CA A:SER321 3.3 12.6 1.0 CG A:ASN82 3.4 20.7 1.0 CB A:SER321 3.4 13.6 1.0 C A:ALA77 3.5 26.7 1.0 CG A:ASP79 3.6 28.0 1.0 OG A:SER321 3.7 35.8 1.0 ND2 A:ASN82 3.8 11.1 1.0 N A:ASP79 3.9 22.0 1.0 CA A:VAL78 3.9 24.9 1.0 CG A:ASN353 3.9 24.9 1.0 N A:VAL78 4.2 22.7 1.0 ND2 A:ASN353 4.3 25.4 1.0 C A:VAL78 4.3 24.3 1.0 O A:HOH801 4.4 17.1 1.0 OD2 A:ASP79 4.4 32.7 1.0 N A:LEU322 4.4 32.6 1.0 CB A:ASP79 4.6 18.8 1.0 CA A:ALA77 4.6 23.0 1.0 N A:ASN82 4.6 22.1 1.0 CB A:ASN82 4.7 22.1 1.0 CB A:ALA81 4.7 19.0 1.0 CA A:ASP79 4.7 21.7 1.0 N A:SER321 4.8 19.3 1.0 CA A:LEU322 5.0 21.2 1.0

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


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 Human Dopamine Transporter in Complex with Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:35.1 occ:1.00 O A:VAL78 2.2 30.6 1.0 O A:GLY75 2.4 33.1 1.0 O A:LEU418 2.7 28.3 1.0 OG A:SER422 3.3 25.6 1.0 C A:VAL78 3.4 24.3 1.0 C A:GLY75 3.6 23.2 1.0 C A:LEU418 3.6 21.1 1.0 CA A:ASP79 3.8 21.7 1.0 CB A:ASP421 3.8 31.7 1.0 N A:ASP79 4.0 22.0 1.0 N A:SER422 4.0 34.9 1.0 CB A:ASP79 4.1 18.8 1.0 CA A:LEU418 4.3 19.1 1.0 O A:PHE76 4.3 33.2 1.0 CB A:SER422 4.4 29.6 1.0 CA A:PHE76 4.4 18.4 1.0 N A:PHE76 4.5 17.8 1.0 C A:PHE76 4.5 28.5 1.0 N A:GLY419 4.5 26.3 1.0 CA A:GLY75 4.5 21.0 1.0 CA A:VAL78 4.6 24.9 1.0 CA A:ASP421 4.7 30.4 1.0 CD1 A:LEU418 4.7 31.9 1.0 C A:ASP421 4.7 36.8 1.0 O A:THR417 4.7 29.6 1.0 N A:VAL78 4.7 22.7 1.0 N A:ASP421 4.7 39.6 1.0 CA A:GLY419 4.8 24.7 1.0 CA A:SER422 4.8 30.2 1.0 OD2 A:ASP421 4.8 53.4 1.0 CG A:ASP421 4.9 49.3 1.0 CG A:LEU418 4.9 27.1 1.0

Y.Zhao, Y.Li. Dopamine Reuptake and Inhibitory Mechanisms in Human Dopamine Transporter Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07796-0