Sodium in PDB 4xp5: X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55, PDB code: 4xp5 was solved by E.Gouaux, A.Penmatsa, K.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.28 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.250, 137.980, 163.390, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 28.6

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55 also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55 (pdb code 4xp5). 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 Bound to Cocaine Analogue-RTI55, PDB code: 4xp5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55


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 Bound to Cocaine Analogue-RTI55 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:66.7 occ:1.00 OD1 A:ASN49 2.5 66.5 1.0 O A:SER320 2.6 66.9 1.0 OG A:SER320 2.7 67.9 1.0 O A:ALA44 2.8 62.2 1.0 CA A:SER320 3.1 62.5 1.0 C A:SER320 3.2 62.7 1.0 CG A:ASN49 3.3 65.9 1.0 OD1 A:ASN352 3.3 59.7 1.0 CB A:SER320 3.4 67.0 1.0 C A:42F602 3.4 66.6 1.0 ND2 A:ASN49 3.6 65.4 1.0 OD1 A:ASP46 3.8 71.2 1.0 C A:ALA44 4.0 59.2 1.0 CG A:ASN352 4.3 62.5 1.0 ND2 A:ASN352 4.4 67.5 1.0 N A:LEU321 4.4 61.0 1.0 N A:ASN49 4.5 64.5 1.0 N A:SER320 4.5 62.0 1.0 N A:ASP46 4.5 57.1 1.0 CL A:CL607 4.5 76.5 1.0 CB A:ASN49 4.5 60.3 1.0 O A:PHE319 4.6 69.3 1.0 CA A:VAL45 4.7 55.3 1.0 CB A:ALA48 4.7 65.1 1.0 CA A:ASN49 4.7 59.0 1.0 N A:42F602 4.7 63.6 1.0 N A:VAL45 4.8 58.0 1.0 CG A:ASP46 5.0 66.2 1.0 C1 A:42F602 5.0 64.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Cocaine Analogue-RTI55


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 Bound to Cocaine Analogue-RTI55 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:67.8 occ:1.00 OD1 A:ASP420 2.2 71.3 1.0 O A:VAL45 2.3 66.8 1.0 O A:GLY42 2.3 58.0 1.0 O A:LEU417 2.3 71.2 1.0 OG A:SER421 2.4 63.7 1.0 CG A:ASP420 3.0 62.5 1.0 C A:LEU417 3.3 61.8 1.0 C A:GLY42 3.4 56.2 1.0 N A:SER421 3.4 63.3 1.0 C A:VAL45 3.4 61.3 1.0 OD2 A:ASP420 3.5 58.5 1.0 CB A:SER421 3.6 65.1 1.0 CA A:LEU417 3.8 59.0 1.0 CA A:SER421 3.9 65.0 1.0 C A:ASP420 4.0 66.5 1.0 CB A:ASP420 4.1 60.7 1.0 CA A:GLY42 4.1 57.1 1.0 O A:THR416 4.1 63.2 1.0 CA A:ASP46 4.1 56.2 1.0 N A:ASP46 4.2 57.1 1.0 N A:GLY418 4.3 61.3 1.0 N A:ASP420 4.3 70.6 1.0 CB A:ASP46 4.3 54.9 1.0 N A:PHE43 4.3 59.2 1.0 CA A:ASP420 4.4 65.7 1.0 CA A:VAL45 4.4 55.3 1.0 N A:VAL45 4.5 58.0 1.0 CA A:PHE43 4.5 60.0 1.0 O A:PHE43 4.5 56.2 1.0 C A:PHE43 4.6 59.1 1.0 CA A:GLY418 4.6 63.0 1.0 C A:GLY418 4.7 63.2 1.0 CB A:VAL45 4.8 50.6 1.0 CB A:LEU417 4.8 54.2 1.0 O A:ASP420 4.9 66.9 1.0 N A:LEU417 4.9 60.8 1.0 C A:THR416 4.9 61.8 1.0 N A:LEU419 4.9 58.5 1.0 CD2 A:LEU417 4.9 61.9 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