Sodium in PDB 4xp9: X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant D-Amphetamine

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant D-Amphetamine, PDB code: 4xp9 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)	46.72 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.348, 140.748, 166.760, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.2

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant D-Amphetamine 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 Bound to Psychostimulant D-Amphetamine (pdb code 4xp9). 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 Psychostimulant D-Amphetamine, PDB code: 4xp9:
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 Psychostimulant D-Amphetamine


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 Psychostimulant D-Amphetamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na609 b:72.7 occ:1.00 OG C:SER279 2.3 76.5 1.0 OD1 C:ASN49 2.4 75.9 1.0 O C:ALA44 2.4 74.0 1.0 O C:HOH705 2.7 76.9 1.0 OD1 C:ASN311 2.8 73.9 1.0 O C:SER279 2.8 74.3 1.0 CG C:ASN49 3.2 68.2 1.0 C C:SER279 3.3 71.6 1.0 CA C:SER279 3.3 75.5 1.0 CB C:SER279 3.3 71.3 1.0 ND2 C:ASN49 3.4 66.0 1.0 C C:ALA44 3.6 75.0 1.0 CG C:ASN311 3.6 73.9 1.0 ND2 C:ASN311 3.7 71.5 1.0 N C:1WE606 3.9 77.3 1.0 OD1 C:ASP46 4.0 74.3 1.0 CA C:VAL45 4.2 72.8 1.0 N C:VAL45 4.3 71.8 1.0 N C:ASP46 4.4 72.0 1.0 N C:LEU280 4.4 71.5 1.0 CA C:ALA44 4.5 68.8 1.0 CB C:ASN49 4.6 64.9 1.0 N C:SER279 4.7 80.1 1.0 N C:ASN49 4.8 78.8 1.0 C C:VAL45 4.8 73.7 1.0 CL C:CL611 4.8 77.4 1.0 CB C:ALA44 4.8 70.6 1.0 CG C:ASP46 4.9 78.5 1.0 CA C:ASN49 4.9 68.8 1.0 O C:PHE278 5.0 68.4 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant D-Amphetamine


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 Psychostimulant D-Amphetamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na610 b:70.2 occ:1.00 O C:GLY42 2.3 77.2 1.0 O C:LEU376 2.3 74.3 1.0 O C:VAL45 2.5 72.7 1.0 OG C:SER380 2.6 73.2 1.0 OD2 C:ASP379 2.9 75.0 1.0 N C:SER380 3.2 76.1 1.0 CB C:ASP379 3.3 75.1 1.0 C C:LEU376 3.4 70.3 1.0 C C:GLY42 3.5 72.2 1.0 CB C:SER380 3.5 74.7 1.0 CG C:ASP379 3.5 80.5 1.0 O C:HOH701 3.6 74.5 1.0 C C:VAL45 3.6 73.7 1.0 N C:ASP379 3.8 80.8 1.0 C C:ASP379 3.8 76.6 1.0 CA C:ASP379 3.8 70.7 1.0 CA C:SER380 3.8 73.4 1.0 CB C:ASP46 4.0 70.6 1.0 CA C:ASP46 4.0 73.3 1.0 CA C:LEU376 4.2 66.7 1.0 O C:THR375 4.2 75.5 1.0 O C:PHE43 4.2 73.9 1.0 N C:GLY377 4.2 75.1 1.0 CA C:GLY42 4.3 71.3 1.0 N C:ASP46 4.3 72.0 1.0 C C:GLY377 4.3 74.2 1.0 CA C:GLY377 4.4 71.9 1.0 O C:GLY377 4.4 77.8 1.0 N C:PHE43 4.4 71.0 1.0 C C:PHE43 4.5 73.8 1.0 CA C:PHE43 4.5 71.9 1.0 N C:LEU378 4.7 75.1 1.0 C C:LEU378 4.8 76.6 1.0 OD1 C:ASP379 4.8 79.3 1.0 CA C:VAL45 4.8 72.8 1.0 O C:ASP379 4.8 80.1 1.0 N C:VAL45 4.8 71.8 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