Sodium in PDB 4xnu: X-Ray Structure of Drosophila Dopamine Transporter in Complex with Nisoxetine

The structure of X-Ray Structure of Drosophila Dopamine Transporter in Complex with Nisoxetine, PDB code: 4xnu 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)	47.10 / 2.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.901, 133.667, 161.682, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.1

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


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 Nisoxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:84.7 occ:1.00 O A:HOH708 2.4 1.0 1.0 O A:ALA44 2.5 72.1 1.0 OG A:SER320 2.5 71.9 1.0 O A:SER320 2.5 76.7 1.0 OD1 A:ASN49 2.8 73.4 1.0 OD1 A:ASN352 3.1 66.9 1.0 CA A:SER320 3.2 70.0 1.0 C A:SER320 3.2 73.2 1.0 CB A:SER320 3.3 69.5 1.0 OD1 A:ASP46 3.4 80.2 1.0 CG A:ASN49 3.4 74.1 1.0 ND2 A:ASN49 3.5 68.1 1.0 C A:ALA44 3.6 68.6 1.0 CA A:VAL45 4.0 73.5 1.0 CG A:ASN352 4.1 68.3 1.0 C16 A:41U605 4.1 89.5 1.0 N A:ASP46 4.2 71.5 1.0 N A:VAL45 4.3 62.2 1.0 N A:41U605 4.3 88.8 1.0 ND2 A:ASN352 4.4 73.2 1.0 CG A:ASP46 4.5 75.3 1.0 C A:VAL45 4.5 73.0 1.0 N A:LEU321 4.5 73.6 1.0 N A:ASN49 4.6 76.4 1.0 N A:SER320 4.6 81.0 1.0 CB A:ALA48 4.6 76.3 1.0 CA A:ALA44 4.8 73.1 1.0 CB A:ASN49 4.8 72.4 1.0 C15 A:41U605 4.8 96.8 1.0 O A:PHE319 4.8 76.3 1.0 CL A:CL603 4.8 74.6 1.0

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


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 Nisoxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:70.2 occ:1.00 O A:LEU417 2.3 77.5 1.0 O A:GLY42 2.3 75.4 1.0 O A:VAL45 2.3 73.8 1.0 OD1 A:ASP420 2.4 82.2 1.0 OG A:SER421 2.4 73.5 1.0 CB A:SER421 3.2 68.2 1.0 O A:HOH702 3.3 62.4 1.0 N A:SER421 3.3 72.9 1.0 C A:LEU417 3.3 75.5 1.0 CG A:ASP420 3.4 78.7 1.0 C A:VAL45 3.5 73.0 1.0 C A:GLY42 3.6 75.7 1.0 CA A:SER421 3.7 67.9 1.0 CB A:ASP46 3.7 68.0 1.0 CA A:ASP46 3.9 70.5 1.0 C A:ASP420 4.0 74.0 1.0 OD2 A:ASP420 4.1 72.2 1.0 N A:ASP46 4.1 71.5 1.0 O A:PHE43 4.2 71.8 1.0 N A:GLY418 4.2 76.1 1.0 CA A:LEU417 4.2 74.5 1.0 CA A:GLY418 4.3 61.2 1.0 C A:GLY418 4.4 73.6 1.0 CA A:PHE43 4.4 70.3 1.0 O A:THR416 4.4 75.1 1.0 N A:ASP420 4.4 76.0 1.0 C A:PHE43 4.4 74.1 1.0 N A:PHE43 4.4 79.5 1.0 CB A:ASP420 4.4 70.8 1.0 O A:GLY418 4.5 81.7 1.0 CA A:GLY42 4.5 70.7 1.0 CA A:ASP420 4.5 69.9 1.0 CA A:VAL45 4.7 73.5 1.0 N A:VAL45 4.7 62.2 1.0 CG2 A:VAL45 4.8 83.1 1.0 O A:ASP420 4.8 79.9 1.0 N A:LEU419 4.9 66.2 1.0 CD1 A:LEU417 5.0 72.4 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