Atomistry » Sodium » PDB 8xxi-8zj7 » 8y2d
Atomistry »
  Sodium »
    PDB 8xxi-8zj7 »
      8y2d »

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

Other elements in 8y2d:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

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 8y2d

Go back to Sodium Binding Sites List in 8y2d
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 8y2d

Go back to Sodium Binding Sites List in 8y2d
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

Reference:

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
Page generated: Mon Aug 18 16:26:38 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy