Sodium in PDB 7wlw: X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with SKF89976A

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with SKF89976A, PDB code: 7wlw was solved by A.Penmatsa, D.Joseph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.96 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.78, 141.755, 168.236, 90, 90, 90
R / Rfree (%)	23.5 / 26.4

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with SKF89976A 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 Complex with SKF89976A (pdb code 7wlw). 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 Complex with SKF89976A, PDB code: 7wlw:
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 Complex with SKF89976A


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 Complex with SKF89976A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:74.5 occ:1.00 OD1 A:ASN49 2.4 66.0 1.0 OG A:SER320 2.5 60.7 1.0 O A:SER320 2.7 63.1 1.0 O A:ALA44 2.8 57.4 1.0 CA A:SER320 3.2 70.8 1.0 CB A:SER320 3.2 65.2 1.0 CG A:ASN49 3.3 60.1 1.0 C A:SER320 3.3 65.3 1.0 OD1 A:ASN352 3.4 58.0 1.0 C6 A:1WR704 3.6 73.2 0.8 O1 A:1WR704 3.6 77.0 0.8 ND2 A:ASN49 3.7 62.1 1.0 C A:ALA44 4.0 60.5 1.0 N A:GLY46 4.2 58.4 1.0 N A:ASN49 4.3 64.1 1.0 C7 A:1WR704 4.3 72.0 0.8 CG A:ASN352 4.4 63.6 1.0 CB A:ASN49 4.5 60.8 1.0 N A:SER320 4.5 68.2 1.0 C11 A:1WR704 4.5 78.8 0.8 C4 A:1WR704 4.6 77.3 0.8 CA A:ASN49 4.6 60.9 1.0 ND2 A:ASN352 4.7 71.6 1.0 CA A:VAL45 4.7 61.9 1.0 N A:LEU321 4.7 64.9 1.0 C A:ALA48 4.8 64.2 1.0 N A:VAL45 4.8 54.5 1.0 O A:PHE319 4.8 66.2 1.0 CL A:CL701 4.8 67.3 1.0 CB A:ALA48 5.0 73.3 1.0 CA A:ALA44 5.0 61.3 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 Complex with SKF89976A


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 Complex with SKF89976A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:67.2 occ:1.00 O A:LEU417 2.4 62.1 1.0 O A:VAL45 2.4 61.9 1.0 O A:GLY42 2.4 68.5 1.0 CB A:ASP420 2.6 66.3 1.0 OG A:SER421 2.8 61.0 1.0 N A:SER421 3.3 63.2 1.0 OD2 A:ASP420 3.3 63.7 1.0 C A:VAL45 3.4 59.3 1.0 C A:LEU417 3.4 59.1 1.0 CG A:ASP420 3.5 68.9 1.0 C A:GLY42 3.5 68.1 1.0 CA A:ASP420 3.7 60.8 1.0 CA A:GLY46 3.8 62.4 1.0 C A:ASP420 3.9 62.8 1.0 CA A:LEU417 3.9 60.3 1.0 CB A:SER421 4.0 58.2 1.0 N A:GLY46 4.0 58.4 1.0 N A:ASP420 4.1 66.8 1.0 CA A:SER421 4.1 64.4 1.0 CA A:GLY42 4.2 62.6 1.0 O A:THR416 4.3 66.8 1.0 N A:GLY418 4.4 59.6 1.0 CA A:VAL45 4.5 61.9 1.0 N A:VAL45 4.5 54.5 1.0 N A:TYR43 4.6 62.2 1.0 OD1 A:ASP420 4.7 70.1 1.0 C A:TYR43 4.7 63.4 1.0 CA A:TYR43 4.7 62.9 1.0 CA A:GLY418 4.7 59.5 1.0 C A:GLY418 4.7 60.7 1.0 O A:TYR43 4.8 53.2 1.0 CB A:LEU417 4.8 58.5 1.0 O A:GLY418 4.8 62.5 1.0 CD2 A:LEU417 4.9 58.0 1.0 O A:ASP420 4.9 61.8 1.0 CB A:VAL45 5.0 64.9 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