Sodium in PDB 4mmd: Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine

The structure of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine, PDB code: 4mmd 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)	35.98 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.409, 92.207, 88.308, 90.00, 94.09, 90.00
R / Rfree (%)	21.3 / 24.4

The binding sites of Sodium atom in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine (pdb code 4mmd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine, PDB code: 4mmd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Leubat (DELTA6 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 (DELTA6 Mutant) in Complex with (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:39.2 occ:1.00 O A:ALA351 2.2 35.6 1.0 O A:GLY20 2.2 35.6 1.0 O A:VAL23 2.2 39.4 1.0 OG1 A:THR354 2.3 44.6 1.0 OG A:SER355 2.5 38.5 1.0 N A:SER355 3.1 38.1 1.0 C A:ALA351 3.3 43.2 1.0 CB A:THR354 3.4 41.3 1.0 C A:VAL23 3.4 39.8 1.0 C A:GLY20 3.4 42.2 1.0 CB A:SER355 3.4 33.1 1.0 C A:THR354 3.5 40.0 1.0 CA A:SER355 3.6 42.2 1.0 CA A:ALA351 3.8 46.3 1.0 CA A:THR354 3.8 44.8 1.0 O A:TYR21 4.0 40.6 1.0 N A:THR354 4.1 32.5 1.0 CA A:ASP24 4.2 43.8 1.0 O A:THR354 4.2 40.6 1.0 N A:ASP24 4.2 46.0 1.0 O A:PHE350 4.3 39.7 1.0 C A:TYR21 4.3 45.3 1.0 CA A:GLY20 4.3 40.1 1.0 N A:TYR21 4.3 40.9 1.0 N A:GLY352 4.4 36.4 1.0 CA A:TYR21 4.4 44.4 1.0 CA A:VAL23 4.4 37.1 1.0 N A:VAL23 4.5 44.4 1.0 CB A:ASP24 4.5 50.5 1.0 O A:GLY352 4.6 41.8 1.0 CG2 A:THR354 4.6 44.3 1.0 C A:GLY352 4.7 38.7 1.0 CB A:ALA351 4.7 39.1 1.0 CA A:GLY352 4.7 41.7 1.0 CB A:VAL23 4.8 48.7 1.0 N A:ALA351 4.9 36.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Leubat (DELTA6 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 (DELTA6 Mutant) in Complex with (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:48.6 occ:1.00 O A:SER254 2.3 42.0 1.0 OD1 A:ASN27 2.3 50.4 1.0 O A:ALA22 2.5 46.3 1.0 OD1 A:ASN286 2.6 49.3 1.0 O A:HOH714 2.6 48.9 1.0 OG A:SER254 2.7 53.5 1.0 C A:SER254 3.1 39.7 1.0 CG A:ASN27 3.2 55.6 1.0 CA A:SER254 3.2 43.9 1.0 C A:ALA22 3.5 41.8 1.0 ND2 A:ASN27 3.5 46.0 1.0 CB A:SER254 3.5 40.0 1.0 CG A:ASN286 3.5 49.8 1.0 OE1 A:GLU290 3.6 66.7 1.0 ND2 A:ASN286 3.8 49.5 1.0 C A:29E603 3.9 42.4 1.0 OD2 A:ASP24 4.0 53.6 1.0 N A:VAL23 4.2 44.4 1.0 CA A:VAL23 4.3 37.1 1.0 CA A:ALA22 4.3 41.1 1.0 N A:LEU255 4.4 38.3 1.0 CG A:ASP24 4.4 54.8 1.0 N A:ASP24 4.4 46.0 1.0 OD1 A:ASP24 4.5 51.2 1.0 CB A:ALA22 4.5 36.6 1.0 CB A:ASN27 4.6 48.9 1.0 N A:SER254 4.6 44.3 1.0 N A:29E603 4.6 50.5 1.0 O A:PHE253 4.8 44.1 1.0 N A:ASN27 4.8 52.4 1.0 CD A:GLU290 4.8 70.6 1.0 C A:VAL23 4.8 39.8 1.0 CB A:ASN286 4.9 43.7 1.0 CA A:ASN27 5.0 51.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Leubat (DELTA6 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 3 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:38.0 occ:1.00 O B:VAL23 2.2 43.8 1.0 O B:ALA351 2.2 32.1 1.0 O B:GLY20 2.2 36.0 1.0 OG B:SER355 2.3 32.9 1.0 OG1 B:THR354 2.4 38.5 1.0 N B:SER355 3.1 33.5 1.0 C B:VAL23 3.3 42.2 1.0 CB B:SER355 3.3 32.2 1.0 C B:ALA351 3.3 34.8 1.0 C B:GLY20 3.4 44.3 1.0 CB B:THR354 3.5 35.6 1.0 C B:THR354 3.6 36.5 1.0 CA B:SER355 3.6 32.1 1.0 CA B:ALA351 3.9 33.4 1.0 CA B:THR354 4.0 36.9 1.0 CA B:ASP24 4.0 45.4 1.0 O B:TYR21 4.0 38.4 1.0 N B:ASP24 4.1 41.5 1.0 N B:THR354 4.2 34.4 1.0 CB B:ASP24 4.3 47.0 1.0 CA B:VAL23 4.3 42.4 1.0 C B:TYR21 4.3 38.5 1.0 O B:THR354 4.3 34.6 1.0 CA B:GLY20 4.3 30.9 1.0 N B:VAL23 4.4 36.0 1.0 N B:TYR21 4.4 38.1 1.0 O B:PHE350 4.4 34.1 1.0 CA B:TYR21 4.4 35.4 1.0 N B:GLY352 4.4 31.6 1.0 O B:GLY352 4.7 37.1 1.0 CB B:VAL23 4.7 43.8 1.0 CB B:ALA351 4.7 30.9 1.0 C B:GLY352 4.7 31.1 1.0 CA B:GLY352 4.8 31.9 1.0 CG2 B:THR354 4.8 37.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Leubat (DELTA6 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 4 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with (S)- Duloxetine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:49.2 occ:1.00 OD1 B:ASN27 2.3 50.5 1.0 O B:SER254 2.4 39.0 1.0 O B:HOH726 2.4 47.2 1.0 O B:ALA22 2.5 41.0 1.0 OD1 B:ASN286 2.5 40.1 1.0 OG B:SER254 2.6 62.4 1.0 C B:SER254 3.1 43.7 1.0 CG B:ASN27 3.1 48.7 1.0 CA B:SER254 3.2 44.6 1.0 ND2 B:ASN27 3.4 47.2 1.0 CB B:SER254 3.5 44.3 1.0 CG B:ASN286 3.5 43.7 1.0 C B:ALA22 3.5 41.8 1.0 OE1 B:GLU290 3.6 64.7 1.0 OD1 B:ASP24 3.8 57.7 1.0 ND2 B:ASN286 3.8 44.2 1.0 O B:HOH758 4.0 61.9 1.0 C B:29E603 4.2 40.6 1.0 CA B:VAL23 4.2 42.4 1.0 N B:VAL23 4.3 36.0 1.0 N B:ASP24 4.4 41.5 1.0 N B:LEU255 4.4 45.0 1.0 CB B:ASN27 4.5 44.3 1.0 CA B:ALA22 4.5 40.5 1.0 N B:SER254 4.6 44.4 1.0 CG B:ASP24 4.6 55.0 1.0 N B:ASN27 4.7 46.1 1.0 CB B:ALA22 4.7 40.3 1.0 O B:PHE253 4.8 49.1 1.0 CA B:ASN27 4.8 45.6 1.0 C B:VAL23 4.8 42.2 1.0 CD B:GLU290 4.8 62.1 1.0 CB B:ASN286 4.9 39.2 1.0 N B:29E603 5.0 57.8 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