Sodium in PDB 6awo: X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site

The structure of X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site, PDB code: 6awo was solved by J.A.Coleman, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.86 / 3.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	128.980, 161.960, 140.820, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 28.3

The structure of X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site (pdb code 6awo). 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 the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site, PDB code: 6awo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site


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 the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:0.0 occ:0.50 O A:ALA96 1.8 0.9 1.0 OD1 A:ASN101 2.1 0.7 1.0 O A:SER336 2.4 0.8 1.0 OG A:SER336 2.8 0.7 1.0 CA A:SER336 2.9 0.7 1.0 C A:SER336 3.0 0.5 1.0 C A:ALA96 3.0 1.0 1.0 CG A:ASN101 3.2 0.9 1.0 CB A:SER336 3.3 0.6 1.0 OD1 A:ASN368 3.5 0.9 1.0 ND2 A:ASN101 3.8 0.9 1.0 N A:VAL97 4.0 0.4 1.0 CA A:ALA96 4.0 0.2 1.0 OD1 A:ASP98 4.0 0.8 1.0 CA A:VAL97 4.1 0.3 1.0 N A:SER336 4.2 0.9 1.0 CG A:ASP98 4.3 0.5 1.0 N A:LEU337 4.3 0.8 1.0 CG A:ASN368 4.3 0.8 1.0 N A:ASP98 4.4 0.0 1.0 CB A:ASN101 4.4 0.2 1.0 ND2 A:ASN368 4.5 0.9 1.0 OD2 A:ASP98 4.5 0.4 1.0 O A:PHE335 4.5 0.8 1.0 CB A:ALA96 4.5 0.7 1.0 C A:VAL97 4.6 0.3 1.0 N11 A:SRE701 4.6 0.4 1.0 C1 A:SRE701 4.6 0.7 1.0 C A:PHE335 4.8 0.2 1.0 O A:TYR95 5.0 0.9 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site


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 the TS3 Human Serotonin Transporter Complexed with Sertraline at the Central Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:0.8 occ:1.00 O A:VAL97 2.2 0.1 1.0 O A:LEU434 2.4 0.5 1.0 O A:GLY94 2.5 0.9 1.0 OG A:SER438 2.5 0.9 1.0 OD1 A:ASP437 2.6 0.9 1.0 O A:HOH801 2.9 1.0 1.0 CG A:ASP437 3.0 0.9 1.0 N A:SER438 3.2 0.8 1.0 CB A:SER438 3.4 0.4 1.0 C A:VAL97 3.4 0.3 1.0 C A:LEU434 3.5 1.0 1.0 OD2 A:ASP437 3.5 0.6 1.0 CB A:ASP437 3.6 0.9 1.0 C A:GLY94 3.7 0.8 1.0 CA A:SER438 3.9 0.6 1.0 CA A:ASP98 3.9 0.9 1.0 C A:ASP437 4.0 0.6 1.0 N A:ASP437 4.1 0.6 1.0 CA A:ASP437 4.1 0.4 1.0 N A:ASP98 4.1 0.0 1.0 CB A:ASP98 4.2 0.1 1.0 CA A:LEU434 4.4 0.0 1.0 O A:TYR95 4.4 0.9 1.0 N A:GLY435 4.5 0.9 1.0 CA A:TYR95 4.5 0.2 1.0 N A:TYR95 4.5 0.1 1.0 C A:GLY435 4.6 0.7 1.0 CA A:VAL97 4.6 0.3 1.0 O A:GLY435 4.6 0.8 1.0 CA A:GLY94 4.6 0.3 1.0 C A:TYR95 4.6 0.9 1.0 O A:THR433 4.6 0.3 1.0 CA A:GLY435 4.7 0.9 1.0 N A:VAL97 4.7 0.4 1.0 OH A:TYR176 5.0 0.2 1.0 CB A:VAL97 5.0 0.8 1.0

J.A.Coleman, E.Gouaux. Structural Basis For Recognition of Diverse Antidepressants By the Human Serotonin Transporter. Nat. Struct. Mol. Biol. V. 25 170 2018.
ISSN: ESSN 1545-9985
PubMed: 29379174
DOI: 10.1038/S41594-018-0026-8