Sodium in PDB 4xnx: X-Ray Structure of Drosophila Dopamine Transporter in Complex with Reboxetine

The structure of X-Ray Structure of Drosophila Dopamine Transporter in Complex with Reboxetine, PDB code: 4xnx 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)	48.42 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.673, 141.036, 167.247, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.8

The structure of X-Ray Structure of Drosophila Dopamine Transporter in Complex with Reboxetine 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 Reboxetine (pdb code 4xnx). 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 Reboxetine, PDB code: 4xnx:
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 Reboxetine


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 Reboxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:0.8 occ:1.00 OG A:SER320 2.3 97.1 1.0 O A:ALA44 2.5 99.6 1.0 O A:SER320 2.6 0.1 1.0 OD1 A:ASN49 2.6 93.8 1.0 O A:HOH801 2.7 91.0 1.0 OD1 A:ASN352 2.8 0.9 1.0 C A:SER320 3.2 0.9 1.0 CG A:ASN49 3.3 96.3 1.0 CA A:SER320 3.3 99.2 1.0 ND2 A:ASN49 3.3 92.6 1.0 CB A:SER320 3.3 97.2 1.0 C A:ALA44 3.6 97.3 1.0 CG A:ASN352 3.6 0.9 1.0 ND2 A:ASN352 3.7 99.1 1.0 C2 A:41X707 3.8 96.3 1.0 OD1 A:ASP46 3.8 0.1 1.0 CA A:VAL45 4.3 98.8 1.0 N A:VAL45 4.4 97.3 1.0 N A:LEU321 4.5 0.7 1.0 N A:ASP46 4.5 0.3 1.0 N A:41X707 4.5 97.7 1.0 CA A:ALA44 4.6 94.8 1.0 CB A:ASN49 4.7 96.0 1.0 N A:SER320 4.7 0.2 1.0 CG A:ASP46 4.8 0.0 1.0 C A:VAL45 4.9 0.7 1.0 N A:ASN49 4.9 0.7 1.0 CL A:CL706 4.9 0.7 1.0 C3 A:41X707 5.0 96.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter in Complex with Reboxetine


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 Reboxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:0.3 occ:1.00 O A:LEU417 2.4 98.6 1.0 O A:GLY42 2.4 0.6 1.0 O A:VAL45 2.5 0.4 1.0 CB A:ASP420 2.6 0.6 1.0 OG A:SER421 2.8 0.9 1.0 N A:SER421 3.1 0.8 1.0 OD2 A:ASP420 3.3 96.9 1.0 C A:GLY42 3.4 0.8 1.0 C A:LEU417 3.5 94.2 1.0 CA A:ASP420 3.5 98.4 1.0 CG A:ASP420 3.5 0.5 1.0 O A:HOH803 3.5 98.0 1.0 C A:ASP420 3.6 0.4 1.0 CB A:SER421 3.7 0.1 1.0 C A:VAL45 3.7 0.7 1.0 N A:ASP420 3.7 0.9 1.0 CA A:SER421 3.8 0.9 1.0 CB A:ASP46 4.1 94.0 1.0 O A:GLY418 4.2 87.9 1.0 CA A:ASP46 4.2 0.4 1.0 CA A:LEU417 4.2 98.8 1.0 CA A:GLY42 4.3 97.1 1.0 N A:PHE43 4.3 0.3 1.0 C A:GLY418 4.3 96.9 1.0 O A:THR416 4.3 0.7 1.0 O A:PHE43 4.4 0.2 1.0 N A:ASP46 4.4 0.3 1.0 CA A:PHE43 4.4 98.6 1.0 N A:GLY418 4.4 93.2 1.0 C A:PHE43 4.5 0.2 1.0 CA A:GLY418 4.6 94.5 1.0 O A:ASP420 4.6 95.5 1.0 OD1 A:ASP420 4.7 0.2 1.0 C A:LEU419 4.7 99.1 1.0 N A:VAL45 4.7 97.3 1.0 CA A:VAL45 4.8 98.8 1.0 N A:LEU419 4.9 95.6 1.0

A.Penmatsa, K.H.Wang, E.Gouaux. X-Ray Structures of Drosophila Dopamine Transporter in Complex with Nisoxetine and Reboxetine. Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
PubMed: 25961798
DOI: 10.1038/NSMB.3029