Sodium in PDB 4m48: X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism

The structure of X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism, PDB code: 4m48 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)	47.38 / 2.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.839, 133.684, 162.443, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.6

The structure of X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism (pdb code 4m48). 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 Dopamine Transporter Elucidates Antidepressant Mechanism, PDB code: 4m48:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism


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 Dopamine Transporter Elucidates Antidepressant Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:71.2 occ:1.00 O A:ALA44 2.3 73.7 1.0 O A:SER320 2.4 73.1 1.0 OG A:SER320 2.4 71.4 1.0 OD1 A:ASN49 2.7 74.2 1.0 O A:HOH809 2.9 69.6 1.0 OD1 A:ASN352 3.0 79.5 1.0 C A:SER320 3.2 73.4 1.0 CA A:SER320 3.2 68.6 1.0 CB A:SER320 3.3 70.5 1.0 CG A:ASN49 3.4 71.5 1.0 C A:ALA44 3.4 72.5 1.0 ND2 A:ASN49 3.5 72.2 1.0 OD1 A:ASP46 3.6 81.0 1.0 CG A:ASN352 4.0 76.9 1.0 CA A:VAL45 4.1 69.7 1.0 N A:ASP46 4.2 71.0 1.0 N A:VAL45 4.2 68.3 1.0 ND2 A:ASN352 4.3 80.2 1.0 N A:LEU321 4.5 77.5 1.0 CA A:ALA44 4.5 76.1 1.0 C16 A:21B704 4.6 72.1 1.0 N A:SER320 4.6 74.5 1.0 C A:VAL45 4.6 68.5 1.0 CG A:ASP46 4.7 76.2 1.0 N A:ASN49 4.7 75.0 1.0 CB A:ASN49 4.8 67.5 1.0 CB A:ALA48 4.8 80.4 1.0 CB A:ALA44 4.9 73.5 1.0 O A:PHE319 4.9 72.8 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism


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 Dopamine Transporter Elucidates Antidepressant Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:67.1 occ:1.00 O A:GLY42 2.3 75.2 1.0 O A:VAL45 2.3 72.4 1.0 O A:LEU417 2.3 79.6 1.0 OG A:SER421 2.4 77.0 1.0 OD1 A:ASP420 2.6 79.8 1.0 C A:VAL45 3.2 68.5 1.0 O A:HOH806 3.3 67.9 1.0 CB A:SER421 3.3 69.0 1.0 N A:SER421 3.3 71.9 1.0 C A:LEU417 3.4 74.6 1.0 C A:GLY42 3.5 76.1 1.0 CG A:ASP420 3.5 76.0 1.0 CA A:ASP46 3.6 73.0 1.0 CB A:ASP46 3.6 67.5 1.0 CA A:SER421 3.8 69.8 1.0 N A:ASP46 3.8 71.0 1.0 OD2 A:ASP420 4.2 68.6 1.0 C A:ASP420 4.2 75.6 1.0 CA A:LEU417 4.2 76.9 1.0 O A:PHE43 4.2 73.4 1.0 CA A:GLY42 4.4 72.9 1.0 CA A:VAL45 4.4 69.7 1.0 N A:GLY418 4.4 70.3 1.0 C A:PHE43 4.4 74.4 1.0 N A:PHE43 4.4 76.3 1.0 N A:VAL45 4.4 68.3 1.0 CB A:ASP420 4.4 66.9 1.0 CA A:PHE43 4.5 70.7 1.0 CA A:GLY418 4.5 66.6 1.0 O A:GLY418 4.6 78.4 1.0 C A:GLY418 4.6 71.7 1.0 N A:ASP420 4.6 79.0 1.0 CA A:ASP420 4.6 73.1 1.0 O A:THR416 4.6 77.7 1.0 CG A:ASP46 5.0 76.2 1.0

A.Penmatsa, K.H.Wang, E.Gouaux. X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism. Nature V. 503 85 2013.
ISSN: ISSN 0028-0836
PubMed: 24037379
DOI: 10.1038/NATURE12533