Sodium in PDB 7wgt: X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with NO711.

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with NO711., PDB code: 7wgt 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)	47.42 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.007, 135.025, 162.559, 90, 90, 90
R / Rfree (%)	24.8 / 29.6

The structure of X-Ray Structure of Thermostabilized Drosophila Dopamine Transporter with Gaba TRANSPORTER1-Like Substitutions in the Binding Site, in Complex with NO711. 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 NO711. (pdb code 7wgt). 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 NO711., PDB code: 7wgt:
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 NO711.


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 NO711. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:88.4 occ:1.00 O A:ALA44 2.4 81.0 1.0 O A:SER320 2.4 79.4 1.0 OG A:SER320 2.4 80.7 1.0 OD1 A:ASN49 2.6 87.1 1.0 OD1 A:ASN352 3.0 80.3 1.0 O08 A:9BC701 3.1 89.9 0.8 C A:SER320 3.2 82.9 1.0 CB A:SER320 3.4 79.2 1.0 CA A:SER320 3.4 82.4 1.0 C A:ALA44 3.5 85.5 1.0 CG A:ASN49 3.5 85.4 1.0 C6 A:9BC701 3.7 87.4 0.8 ND2 A:ASN49 3.9 83.7 1.0 N A:GLY46 3.9 82.8 1.0 CA A:VAL45 3.9 83.7 1.0 C7 A:9BC701 4.0 90.7 0.8 CG A:ASN352 4.1 81.1 1.0 N A:VAL45 4.2 79.4 1.0 C A:VAL45 4.4 83.2 1.0 C5 A:9BC701 4.4 93.3 0.8 N A:LEU321 4.5 81.7 1.0 ND2 A:ASN352 4.6 78.1 1.0 CA A:ALA44 4.6 82.2 1.0 N A:ASN49 4.7 83.8 1.0 CB A:ASN49 4.8 84.7 1.0 C1 A:9BC701 4.8 89.6 0.8 CA A:GLY46 4.9 79.2 1.0 N A:SER320 4.9 84.6 1.0 CB A:ALA48 4.9 80.3 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 NO711.


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 NO711. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:78.9 occ:1.00 O A:GLY42 2.3 90.8 1.0 O A:LEU417 2.6 81.2 1.0 OG A:SER421 2.6 83.6 1.0 O A:VAL45 2.8 82.3 1.0 N A:SER421 3.0 84.4 1.0 OD2 A:ASP420 3.0 89.6 1.0 CB A:ASP420 3.2 88.3 1.0 C A:LEU417 3.4 86.5 1.0 C A:GLY42 3.4 88.5 1.0 CB A:SER421 3.5 82.9 1.0 CG A:ASP420 3.6 94.2 1.0 C A:ASP420 3.6 87.3 1.0 CA A:ASP420 3.7 85.0 1.0 N A:ASP420 3.7 88.4 1.0 CA A:SER421 3.7 84.3 1.0 CA A:LEU417 4.0 84.9 1.0 C A:VAL45 4.0 83.2 1.0 O A:THR416 4.0 86.0 1.0 CA A:GLY42 4.2 82.4 1.0 N A:GLY418 4.3 84.5 1.0 CA A:GLY46 4.3 79.2 1.0 N A:TYR43 4.4 87.7 1.0 CA A:TYR43 4.5 83.9 1.0 C A:GLY418 4.5 85.0 1.0 O A:TYR43 4.6 80.6 1.0 CA A:GLY418 4.6 79.7 1.0 O A:ASP420 4.6 92.9 1.0 C A:LEU419 4.7 86.9 1.0 N A:GLY46 4.7 82.8 1.0 C A:TYR43 4.7 82.2 1.0 N A:LEU419 4.7 83.0 1.0 O A:GLY418 4.8 91.8 1.0 OD1 A:ASP420 4.8 98.6 1.0 C A:THR416 4.9 85.0 1.0 CG2 A:VAL45 4.9 88.4 1.0 N A:LEU417 5.0 86.5 1.0 CB A:LEU417 5.0 78.0 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