Sodium in PDB 4mm8: Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine, PDB code: 4mm8 was solved by H.Wang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.55 / 3.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.613, 87.812, 80.770, 90.00, 94.50, 90.00
R / Rfree (%)	21.4 / 25

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine (pdb code 4mm8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine, PDB code: 4mm8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:23.0 occ:1.00 O A:ALA351 2.0 24.2 1.0 O A:GLY20 2.2 23.8 1.0 O A:VAL23 2.3 25.0 1.0 OG1 A:THR354 2.4 22.0 1.0 OG A:SER355 2.5 28.5 1.0 N A:SER355 3.1 26.0 1.0 C A:ALA351 3.2 23.9 1.0 C A:VAL23 3.3 24.4 1.0 C A:GLY20 3.4 26.7 1.0 CB A:SER355 3.4 24.1 1.0 CB A:THR354 3.4 21.1 1.0 C A:THR354 3.5 26.0 1.0 CA A:SER355 3.7 28.1 1.0 O A:TYR21 3.7 31.0 1.0 CA A:THR354 3.8 25.2 1.0 CA A:ASP24 3.9 25.1 1.0 CA A:ALA351 3.9 20.6 1.0 N A:ASP24 4.0 22.1 1.0 N A:THR354 4.1 23.3 1.0 C A:TYR21 4.1 27.3 1.0 O A:THR354 4.1 26.5 1.0 N A:GLY352 4.2 22.8 1.0 CA A:TYR21 4.2 25.7 1.0 N A:TYR21 4.2 27.8 1.0 CB A:ASP24 4.3 35.0 1.0 O A:PHE350 4.3 21.8 1.0 CA A:GLY20 4.4 24.7 1.0 CA A:VAL23 4.4 29.4 1.0 CA A:GLY352 4.4 22.7 1.0 N A:VAL23 4.4 28.2 1.0 C A:GLY352 4.6 23.1 1.0 CG2 A:THR354 4.7 19.3 1.0 O A:GLY352 4.7 25.9 1.0 CB A:ALA351 4.8 20.4 1.0 CB A:VAL23 4.9 27.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (R)- Fluoxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:41.5 occ:1.00 O A:SER254 2.4 42.0 1.0 OD1 A:ASN286 2.4 36.8 1.0 O A:ALA22 2.4 26.5 1.0 OD1 A:ASN27 2.5 32.2 1.0 OG A:SER254 2.6 47.0 1.0 C A:SER254 3.2 42.1 1.0 CG A:ASN27 3.2 28.4 1.0 CA A:SER254 3.2 44.0 1.0 O A:HOH701 3.3 24.4 1.0 CG A:ASN286 3.4 33.6 1.0 ND2 A:ASN27 3.4 33.4 1.0 CB A:SER254 3.4 50.2 1.0 C A:ALA22 3.5 29.0 1.0 ND2 A:ASN286 3.7 32.8 1.0 OD1 A:ASP24 3.7 42.8 1.0 N4 A:RFX603 4.2 42.1 1.0 CA A:VAL23 4.3 29.4 1.0 N A:VAL23 4.3 28.2 1.0 N A:LEU255 4.4 40.3 1.0 CA A:ALA22 4.4 30.3 1.0 N A:ASP24 4.5 22.1 1.0 C22 A:RFX603 4.5 36.4 1.0 CB A:ASN27 4.5 27.3 1.0 N A:ASN27 4.6 30.6 1.0 N A:SER254 4.6 45.0 1.0 CB A:ALA22 4.7 29.6 1.0 O A:PHE253 4.7 46.0 1.0 CB A:ASN286 4.7 31.5 1.0 CA A:ASN27 4.8 33.8 1.0 OG A:SER290 4.9 34.8 1.0 CG A:ASP24 4.9 41.8 1.0 C A:VAL23 4.9 24.4 1.0

H.Wang, A.Goehring, K.H.Wang, A.Penmatsa, R.Ressler, E.Gouaux. Structural Basis For Action By Diverse Antidepressants on Biogenic Amine Transporters. Nature V. 503 141 2013.
ISSN: ISSN 0028-0836
PubMed: 24121440
DOI: 10.1038/NATURE12648