Sodium in PDB 4xp4: X-Ray Structure of Drosophila Dopamine Transporter in Complex with Cocaine

The structure of X-Ray Structure of Drosophila Dopamine Transporter in Complex with Cocaine, PDB code: 4xp4 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)	45.88 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.063, 140.727, 166.688, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.6

The structure of X-Ray Structure of Drosophila Dopamine Transporter in Complex with 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 in Complex with Cocaine (pdb code 4xp4). 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 in Complex with Cocaine, PDB code: 4xp4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter in Complex with 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 in Complex with Cocaine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:62.3 occ:1.00 OD1 A:ASN49 2.6 63.8 1.0 O A:ALA44 2.6 57.2 1.0 OG A:SER320 2.6 58.4 1.0 O A:SER320 2.9 57.1 1.0 OD1 A:ASN352 3.1 62.8 1.0 CG A:ASN49 3.3 60.0 1.0 CA A:SER320 3.4 57.1 1.0 ND2 A:ASN49 3.4 56.1 1.0 C A:SER320 3.5 56.8 1.0 CB A:SER320 3.5 61.1 1.0 C14 A:COC706 3.6 62.1 1.0 OD1 A:ASP46 3.7 65.4 1.0 C A:ALA44 3.8 63.2 1.0 CG A:ASN352 4.0 54.8 1.0 ND2 A:ASN352 4.1 57.9 1.0 CB A:ALA48 4.4 66.7 1.0 N A:ASP46 4.5 53.3 1.0 CA A:VAL45 4.5 59.1 1.0 N A:ASN49 4.5 66.8 1.0 N A:VAL45 4.6 53.3 1.0 CB A:ASN49 4.6 63.0 1.0 N A:LEU321 4.7 60.6 1.0 C A:ALA48 4.7 66.5 1.0 CL A:CL709 4.8 79.5 1.0 CA A:ALA44 4.8 57.7 1.0 N A:SER320 4.8 63.5 1.0 C21 A:COC706 4.8 65.2 1.0 CG A:ASP46 4.8 63.3 1.0 N12 A:COC706 4.8 66.2 1.0 C24 A:COC706 4.8 68.1 1.0 CA A:ASN49 4.9 63.8 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter in Complex with 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 in Complex with Cocaine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na708 b:56.8 occ:1.00 O A:GLY42 2.3 59.9 1.0 O A:LEU417 2.3 63.3 1.0 OG A:SER421 2.4 58.9 1.0 O A:VAL45 2.5 56.1 1.0 OD1 A:ASP420 2.5 66.8 1.0 CB A:SER421 3.0 58.4 1.0 N A:SER421 3.1 59.7 1.0 C A:VAL45 3.4 56.1 1.0 CA A:SER421 3.5 58.1 1.0 C A:GLY42 3.5 60.0 1.0 C A:LEU417 3.5 65.0 1.0 CB A:ASP46 3.5 52.4 1.0 CG A:ASP420 3.6 64.2 1.0 O A:PHE43 3.6 58.9 1.0 O A:HOH802 3.7 57.3 1.0 CA A:ASP46 3.7 63.1 1.0 C A:ASP420 3.9 62.8 1.0 N A:ASP46 3.9 53.3 1.0 C A:PHE43 4.1 59.1 1.0 CA A:PHE43 4.3 54.5 1.0 N A:PHE43 4.3 59.4 1.0 N A:GLY418 4.4 67.5 1.0 CA A:GLY418 4.4 58.1 1.0 O A:GLY418 4.4 62.8 1.0 C A:GLY418 4.4 62.5 1.0 CB A:ASP420 4.4 54.6 1.0 CA A:LEU417 4.4 56.1 1.0 OD2 A:ASP420 4.4 59.7 1.0 N A:ASP420 4.5 62.1 1.0 CA A:ASP420 4.5 59.2 1.0 N A:VAL45 4.5 53.3 1.0 CA A:GLY42 4.5 59.0 1.0 CA A:VAL45 4.5 59.1 1.0 O A:ASP420 4.6 62.2 1.0 O A:THR416 4.8 62.7 1.0 OH A:TYR124 4.8 58.7 1.0 CG A:ASP46 4.9 63.3 1.0 C A:SER421 4.9 63.5 1.0 N A:LEU419 5.0 59.9 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