Sodium in PDB 9eup: Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter

The structure of Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter (pdb code 9eup). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter, PDB code: 9eup:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:26.9 occ:1.00 O A:SER320 2.2 32.7 1.0 O A:ALA44 2.3 22.7 1.0 HG A:SER320 2.5 26.1 1.0 OD1 A:ASN49 2.6 29.7 1.0 OG A:SER320 2.7 27.6 1.0 OD1 A:ASN352 2.8 24.1 1.0 HD22 A:ASN49 3.0 24.1 1.0 HA A:SER320 3.0 27.2 1.0 C A:SER320 3.1 25.6 1.0 H A:ASP46 3.1 28.3 1.0 HA A:VAL45 3.3 24.2 1.0 CA A:SER320 3.4 27.5 1.0 CG A:ASN49 3.4 24.0 1.0 C A:ALA44 3.4 18.1 1.0 ND2 A:ASN49 3.5 18.1 1.0 CB A:SER320 3.5 26.2 1.0 O4 A:144702 3.6 36.6 1.0 H41 A:144702 3.7 32.5 1.0 HB2 A:ASN352 3.8 22.9 1.0 HO4 A:144702 3.9 30.7 1.0 CG A:ASN352 3.9 22.9 1.0 N A:ASP46 3.9 28.8 1.0 C4 A:144702 4.0 40.6 1.0 HB2 A:ASP46 4.1 27.8 1.0 CA A:VAL45 4.1 21.5 1.0 HB2 A:SER320 4.1 26.8 1.0 HB3 A:ALA44 4.1 23.8 1.0 N A:VAL45 4.1 23.9 1.0 H42 A:144702 4.2 31.1 1.0 HB3 A:SER320 4.2 25.4 1.0 N A:LEU321 4.2 25.7 1.0 HA A:ALA44 4.3 23.2 1.0 HA A:LEU321 4.3 26.2 1.0 HD21 A:ASN49 4.3 24.8 1.0 HB3 A:ASP46 4.3 27.8 1.0 CA A:ALA44 4.4 17.0 1.0 CB A:ASN352 4.4 19.1 1.0 HB3 A:ALA48 4.4 27.2 1.0 H A:ASN49 4.5 26.5 1.0 C A:VAL45 4.5 26.3 1.0 CB A:ASP46 4.6 28.6 1.0 HG A:SER356 4.7 25.2 1.0 CL A:CL706 4.7 43.0 1.0 HG22 A:VAL45 4.7 23.3 1.0 CB A:ALA44 4.8 22.1 1.0 N A:SER320 4.8 23.0 1.0 CA A:LEU321 4.8 25.3 1.0 CB A:ASN49 4.8 21.7 1.0 CA A:ASP46 4.9 22.3 1.0 H A:LEU321 4.9 26.3 1.0 H A:VAL45 4.9 25.2 1.0 N A:ASN49 5.0 26.9 1.0 ND2 A:ASN352 5.0 30.0 1.0

Sodium binding site 2 out of 2 in the Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inhibitor-Free Outward-Open Structure of Drosophila Dopamine Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:23.2 occ:1.00 HG A:SER421 1.7 28.3 1.0 O A:LEU417 2.2 37.6 1.0 O A:VAL45 2.3 24.9 1.0 OD1 A:ASP420 2.3 40.0 1.0 OG A:SER421 2.4 21.2 1.0 O A:GLY42 2.5 25.8 1.0 H A:SER421 2.9 28.4 1.0 HA A:ASP46 3.2 26.6 1.0 HA A:LEU417 3.2 25.8 1.0 CG A:ASP420 3.3 29.7 1.0 C A:LEU417 3.3 27.5 1.0 C A:VAL45 3.4 26.3 1.0 N A:SER421 3.5 24.8 1.0 CB A:SER421 3.6 24.7 1.0 C A:GLY42 3.6 23.6 1.0 OD2 A:ASP420 3.7 32.3 1.0 CA A:LEU417 3.8 26.7 1.0 HB2 A:SER421 3.8 28.1 1.0 HA2 A:GLY42 3.9 22.4 1.0 CA A:SER421 4.0 25.7 1.0 CA A:ASP46 4.0 22.3 1.0 N A:ASP46 4.1 28.8 1.0 HA A:SER421 4.1 27.9 1.0 HB3 A:LEU417 4.2 24.9 1.0 H A:ASP420 4.3 26.5 1.0 HB A:VAL45 4.3 24.0 1.0 HA A:PHE43 4.3 26.4 1.0 O A:THR416 4.3 23.2 1.0 HB3 A:SER421 4.3 28.1 1.0 CA A:GLY42 4.3 15.7 1.0 HD21 A:LEU417 4.3 27.2 1.0 C A:ASP420 4.4 24.7 1.0 N A:GLY418 4.4 20.2 1.0 CB A:ASP420 4.4 19.4 1.0 O A:PHE43 4.4 30.3 1.0 CA A:VAL45 4.5 21.5 1.0 HA2 A:GLY418 4.5 25.7 1.0 H A:VAL45 4.5 25.2 1.0 N A:PHE43 4.6 26.5 1.0 HB2 A:ASP420 4.6 25.9 1.0 CB A:LEU417 4.6 19.0 1.0 HG11 A:VAL45 4.6 25.5 1.0 N A:VAL45 4.6 23.9 1.0 HA3 A:GLY42 4.6 22.2 1.0 N A:ASP420 4.6 21.8 1.0 C A:PHE43 4.7 22.4 1.0 CA A:ASP420 4.7 20.2 1.0 CA A:PHE43 4.7 24.6 1.0 CA A:GLY418 4.8 20.1 1.0 HD23 A:LEU417 4.8 25.8 1.0 CB A:VAL45 4.8 19.6 1.0 C A:GLY418 4.8 27.7 1.0 N A:LEU417 4.9 29.1 1.0 H A:ASP46 4.9 28.3 1.0 C A:ASP46 4.9 20.4 1.0 CD2 A:LEU417 5.0 24.8 1.0 HB2 A:ASP46 5.0 27.8 1.0 CB A:ASP46 5.0 28.6 1.0

C.N.Pedersen, F.Yang, S.Ita, Y.Xu, R.Akunuri, S.Trampari, C.M.T.Neumann, L.M.Desdorf, B.Schiott, J.M.Salvino, O.V.Mortensen, P.Nissen, A.Shahsavar. Cryo-Em Structure of the Dopamine Transporter with A Novel Atypical Non-Competitive Inhibitor Bound to the Orthosteric Site. J.Neurochem. 2024.
ISSN: ESSN 1471-4159
PubMed: 39010681
DOI: 10.1111/JNC.16179