Sodium in PDB 4mm6: Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (S)- Duloxetine

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (S)- Duloxetine, PDB code: 4mm6 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)	38.80 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.897, 88.383, 81.311, 90.00, 94.84, 90.00
R / Rfree (%)	21.4 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with (S)- Duloxetine (pdb code 4mm6). 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 (S)- Duloxetine, PDB code: 4mm6:
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 (S)- Duloxetine


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 (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:41.2 occ:1.00 O A:ALA351 1.9 37.4 1.0 OG1 A:THR354 2.2 31.2 1.0 O A:GLY20 2.4 38.5 1.0 O A:VAL23 2.5 39.7 1.0 OG A:SER355 2.6 32.7 1.0 N A:SER355 2.9 36.8 1.0 C A:ALA351 3.0 39.6 1.0 CB A:THR354 3.2 33.1 1.0 C A:THR354 3.2 37.5 1.0 CB A:SER355 3.4 30.6 1.0 CA A:THR354 3.5 35.5 1.0 C A:GLY20 3.6 40.6 1.0 CA A:SER355 3.6 33.4 1.0 CA A:ALA351 3.7 39.1 1.0 N A:THR354 3.7 38.5 1.0 C A:VAL23 3.8 38.6 1.0 O A:THR354 4.0 34.6 1.0 N A:GLY352 4.0 39.5 1.0 O A:PHE350 4.1 41.6 1.0 O A:TYR21 4.2 40.5 1.0 O A:GLY352 4.2 37.8 1.0 C A:GLY352 4.2 35.0 1.0 CA A:GLY352 4.3 35.7 1.0 CA A:ASP24 4.3 39.2 1.0 N A:TYR21 4.4 42.4 1.0 CB A:ASP24 4.5 42.6 1.0 CA A:TYR21 4.5 37.1 1.0 CG2 A:THR354 4.5 35.9 1.0 CA A:GLY20 4.5 37.1 1.0 C A:TYR21 4.5 39.1 1.0 N A:ASP24 4.5 37.1 1.0 CB A:ALA351 4.6 35.8 1.0 N A:ALA351 4.8 35.7 1.0 CA A:VAL23 4.8 42.7 1.0 N A:LEU353 4.8 32.6 1.0 C A:LEU353 4.8 36.4 1.0 C A:PHE350 4.9 38.2 1.0 N A:VAL23 5.0 41.1 1.0

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


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 (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:44.7 occ:1.00 O A:ALA22 2.3 44.2 1.0 OD1 A:ASN286 2.4 45.1 1.0 OD1 A:ASN27 2.5 48.1 1.0 O A:SER254 2.5 43.8 1.0 OG A:SER254 2.5 58.0 1.0 O A:HOH701 3.0 49.9 1.0 C A:SER254 3.2 46.6 1.0 OD1 A:ASP24 3.3 46.3 1.0 CA A:SER254 3.3 47.2 1.0 C A:ALA22 3.4 43.8 1.0 CG A:ASN27 3.4 45.1 1.0 CG A:ASN286 3.4 46.4 1.0 CB A:SER254 3.4 54.3 1.0 ND2 A:ASN27 3.8 45.6 1.0 ND2 A:ASN286 3.8 46.4 1.0 C A:29E603 4.1 46.7 1.0 N A:VAL23 4.2 41.1 1.0 CA A:VAL23 4.2 42.7 1.0 CA A:ALA22 4.3 43.9 1.0 N A:ASP24 4.4 37.1 1.0 N A:LEU255 4.5 48.8 1.0 CG A:ASP24 4.5 44.9 1.0 CB A:ALA22 4.5 42.0 1.0 N A:ASN27 4.6 39.4 1.0 CB A:ASN27 4.7 39.9 1.0 OG A:SER290 4.7 53.8 1.0 C A:VAL23 4.7 38.6 1.0 N A:SER254 4.7 50.3 1.0 N A:29E603 4.7 50.0 1.0 CB A:ASN286 4.8 43.1 1.0 CA A:ASN27 4.9 40.4 1.0 O A:PHE253 4.9 46.2 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