Sodium in PDB 4xp6: X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant Methamphetamine

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant Methamphetamine, PDB code: 4xp6 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)	45.45 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.040, 141.370, 165.680, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 25.9

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Psychostimulant Methamphetamine 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 Methamphetamine (pdb code 4xp6). 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 Methamphetamine, PDB code: 4xp6:
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 Methamphetamine


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 Methamphetamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:76.6 occ:1.00 OD1 A:ASN49 2.4 72.1 1.0 OG A:SER320 2.4 81.5 1.0 O A:ALA44 2.4 82.9 1.0 O A:SER320 2.7 85.4 1.0 OD1 A:ASN352 2.7 86.3 1.0 O A:HOH703 2.9 80.9 1.0 CG A:ASN49 3.1 78.8 1.0 ND2 A:ASN49 3.1 74.2 1.0 C A:SER320 3.3 82.9 1.0 ND2 A:ASN352 3.3 85.6 1.0 CA A:SER320 3.4 84.1 1.0 CG A:ASN352 3.4 82.5 1.0 CB A:SER320 3.4 84.1 1.0 C A:ALA44 3.6 77.4 1.0 OD1 A:ASP46 3.8 88.2 1.0 CA A:VAL45 4.2 77.2 1.0 N A:VAL45 4.4 76.7 1.0 N A:LEU321 4.4 79.4 1.0 N A:ASP46 4.4 77.1 1.0 CB A:ASN49 4.5 71.9 1.0 CG A:ASP46 4.6 90.0 1.0 CA A:ALA44 4.6 69.0 1.0 N A:SER320 4.8 87.4 1.0 N A:ASN49 4.8 78.4 1.0 C A:VAL45 4.8 76.3 1.0 CL A:CL605 4.9 83.0 1.0 CB A:ASN352 4.9 80.4 1.0 CA A:ASN49 5.0 72.3 1.0 CB A:ALA44 5.0 77.9 1.0

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


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 Methamphetamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:80.3 occ:1.00 O A:LEU417 2.3 79.7 1.0 O A:GLY42 2.3 77.7 1.0 OD1 A:ASP420 2.4 89.8 1.0 OG A:SER421 2.4 79.8 1.0 O A:VAL45 2.4 80.8 1.0 N A:SER421 3.1 82.8 1.0 CG A:ASP420 3.1 81.1 1.0 O A:HOH705 3.2 70.8 1.0 CB A:SER421 3.3 78.3 1.0 C A:LEU417 3.3 76.4 1.0 C A:GLY42 3.5 77.7 1.0 C A:VAL45 3.6 76.3 1.0 CA A:SER421 3.6 82.0 1.0 OD2 A:ASP420 3.7 77.5 1.0 C A:ASP420 3.8 82.9 1.0 CB A:ASP420 4.0 78.3 1.0 CA A:LEU417 4.1 73.5 1.0 N A:ASP420 4.1 81.0 1.0 CA A:ASP420 4.1 80.0 1.0 N A:GLY418 4.2 77.3 1.0 O A:THR416 4.3 75.2 1.0 CA A:ASP46 4.3 74.0 1.0 CA A:GLY42 4.3 82.6 1.0 N A:PHE43 4.4 79.0 1.0 N A:ASP46 4.4 77.1 1.0 O A:PHE43 4.4 81.4 1.0 CA A:PHE43 4.4 76.8 1.0 CA A:GLY418 4.4 75.0 1.0 C A:GLY418 4.5 76.0 1.0 CB A:ASP46 4.5 76.5 1.0 C A:PHE43 4.5 82.3 1.0 CA A:VAL45 4.6 77.2 1.0 N A:VAL45 4.6 76.7 1.0 O A:ASP420 4.6 85.5 1.0 O A:GLY418 4.7 74.7 1.0 N A:LEU419 4.7 75.6 1.0 C A:LEU419 4.9 80.6 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