Sodium in PDB 4xpb: X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine, PDB code: 4xpb was solved by P.Aravind, K.Wang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.33 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.498, 139.963, 166.959, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 26.9

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine (pdb code 4xpb). 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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine, PDB code: 4xpb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine


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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:89.8 occ:1.00 O A:ALA44 2.4 92.9 1.0 OG A:SER320 2.5 0.3 1.0 OD1 A:ASN49 2.5 98.3 1.0 O A:SER320 2.6 0.3 1.0 OD1 A:ASN352 2.6 96.7 1.0 O A:HOH801 2.6 0.0 1.0 C A:SER320 3.2 98.2 1.0 CG A:ASN49 3.2 95.8 1.0 ND2 A:ASN49 3.2 89.8 1.0 CA A:SER320 3.4 94.8 1.0 C A:ALA44 3.4 93.8 1.0 CG A:ASN352 3.5 92.9 1.0 CB A:SER320 3.5 91.4 1.0 ND2 A:ASN352 3.6 93.8 1.0 OD1 A:ASP46 4.0 0.8 1.0 C14 A:COC702 4.0 62.1 1.0 CA A:VAL45 4.1 96.6 1.0 N A:VAL45 4.2 91.3 1.0 N A:LEU321 4.3 0.1 1.0 CA A:ALA44 4.4 86.3 1.0 N A:ASP46 4.5 94.2 1.0 CB A:ALA44 4.7 81.9 1.0 CB A:ASN49 4.7 90.1 1.0 C21 A:COC702 4.7 65.2 1.0 N A:SER320 4.8 1.0 1.0 C A:VAL45 4.9 94.8 1.0 CB A:ASN352 4.9 92.6 1.0 CL A:CL707 4.9 0.3 1.0 C24 A:COC702 5.0 68.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine


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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Cocaine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:98.2 occ:1.00 O A:VAL45 2.2 0.0 1.0 O A:LEU417 2.3 0.2 1.0 OG A:SER421 2.3 94.8 1.0 OD1 A:ASP420 2.3 0.3 1.0 O A:GLY42 2.7 92.1 1.0 C A:VAL45 3.1 94.8 1.0 CA A:ASP46 3.3 93.2 1.0 CB A:SER421 3.3 88.5 1.0 CB A:ASP46 3.4 93.3 1.0 C A:LEU417 3.4 99.8 1.0 CG A:ASP420 3.4 0.9 1.0 N A:ASP46 3.6 94.2 1.0 N A:SER421 3.6 98.4 1.0 OD2 A:ASP420 3.8 94.1 1.0 C A:GLY42 3.9 92.5 1.0 CA A:SER421 4.0 96.0 1.0 CA A:LEU417 4.1 94.4 1.0 O A:PHE43 4.1 88.8 1.0 CA A:VAL45 4.3 96.6 1.0 N A:GLY418 4.4 99.8 1.0 N A:VAL45 4.4 91.3 1.0 C A:PHE43 4.5 88.0 1.0 C A:ASP420 4.6 97.1 1.0 CB A:ASP420 4.6 95.1 1.0 CA A:GLY418 4.6 89.8 1.0 OH A:TYR124 4.6 0.3 1.0 CA A:PHE43 4.7 85.6 1.0 C A:ASP46 4.7 91.8 1.0 N A:PHE43 4.7 90.5 1.0 CG A:ASP46 4.8 0.3 1.0 C A:GLY418 4.8 99.6 1.0 CB A:LEU417 4.8 96.8 1.0 O A:THR416 4.8 98.9 1.0 CA A:GLY42 4.9 91.2 1.0 N A:ASP420 4.9 98.6 1.0 CA A:ASP420 4.9 90.3 1.0 O A:GLY418 4.9 0.5 1.0 CD2 A:LEU417 4.9 87.5 1.0

K.H.Wang, A.Penmatsa, E.Gouaux. Neurotransmitter and Psychostimulant Recognition By the Dopamine Transporter. Nature 2015.
ISSN: ESSN 1476-4687
PubMed: 25970245
DOI: 10.1038/NATURE14431