Sodium in PDB 7wgd: X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form.

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form., PDB code: 7wgd was solved by D.Joseph, A.Penmatsa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.388, 140.709, 168.021, 90, 90, 90
R / Rfree (%)	24.4 / 28.6

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form. (pdb code 7wgd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form., PDB code: 7wgd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:86.8 occ:1.00 O A:SER320 2.6 90.0 1.0 OD1 A:ASN49 2.8 82.8 1.0 O A:ALA44 2.9 79.6 1.0 OG A:SER320 2.9 78.0 1.0 CA A:SER320 3.2 82.2 1.0 C A:SER320 3.3 85.7 1.0 CB A:SER320 3.6 82.0 1.0 CG A:ASN49 3.8 79.7 1.0 OD1 A:ASN352 3.9 76.9 1.0 N A:GLY46 4.0 77.6 1.0 C A:ALA44 4.1 75.9 1.0 CB A:ALA48 4.2 75.2 1.0 ND2 A:ASN49 4.3 83.1 1.0 O A:PHE319 4.4 83.0 1.0 N A:SER320 4.4 83.3 1.0 CA A:VAL45 4.5 82.8 1.0 N A:ASN49 4.6 80.7 1.0 N A:LEU321 4.6 78.4 1.0 C A:VAL45 4.7 80.6 1.0 C A:ALA48 4.7 83.8 1.0 CA A:GLY46 4.8 71.8 1.0 N A:VAL45 4.8 76.7 1.0 CG A:ASN352 4.9 85.0 1.0 C A:PHE319 4.9 82.6 1.0 CA A:ALA48 4.9 77.9 1.0 CB A:ASN49 5.0 77.0 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Substrate-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:94.5 occ:1.00 O A:VAL45 2.1 77.0 1.0 O A:LEU417 2.1 89.0 1.0 OG A:SER421 2.1 81.4 1.0 OD1 A:ASP420 2.2 92.4 1.0 O A:GLY42 2.9 86.7 1.0 CB A:SER421 3.1 80.2 1.0 C A:VAL45 3.1 80.6 1.0 CA A:GLY46 3.3 71.8 1.0 C A:LEU417 3.3 84.8 1.0 CG A:ASP420 3.4 87.7 1.0 N A:SER421 3.5 75.7 1.0 N A:GLY46 3.6 77.6 1.0 CA A:SER421 3.8 79.5 1.0 OD2 A:ASP420 3.9 79.3 1.0 CA A:LEU417 4.1 81.5 1.0 C A:GLY42 4.1 76.9 1.0 O A:TYR43 4.2 76.8 1.0 CA A:VAL45 4.3 82.8 1.0 N A:VAL45 4.3 76.7 1.0 N A:GLY418 4.3 79.3 1.0 C A:ASP420 4.4 77.2 1.0 C A:TYR43 4.4 77.4 1.0 CA A:GLY418 4.5 75.1 1.0 CB A:ASP420 4.6 78.7 1.0 CA A:TYR43 4.7 76.3 1.0 CB A:LEU417 4.7 76.2 1.0 C A:GLY46 4.7 78.2 1.0 C A:GLY418 4.7 80.8 1.0 O A:GLY418 4.7 80.1 1.0 CG2 A:VAL45 4.8 91.3 1.0 CD2 A:LEU417 4.8 75.7 1.0 N A:TYR43 4.8 78.2 1.0 CA A:ASP420 4.9 79.5 1.0 N A:ASP420 4.9 83.7 1.0 C A:ALA44 4.9 75.9 1.0

D.Joseph, S.R.Nayak, A.Penmatsa. Structural Insights Into Gaba Transport Inhibition Using An Engineered Neurotransmitter Transporter. Embo J. V. 41 10735 2022.
ISSN: ESSN 1460-2075
PubMed: 35796008
DOI: 10.15252/EMBJ.2022110735