Sodium in PDB 4mma: Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Clomipramine

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Clomipramine, PDB code: 4mma 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)	38.94 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.520, 88.811, 81.225, 90.00, 94.41, 90.00
R / Rfree (%)	24.6 / 26.1

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

Chlorine

(Cl)

1 atom

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


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 Clomipramine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:0.7 occ:1.00 O A:ALA351 2.0 0.5 1.0 O A:GLY20 2.2 0.8 1.0 OG1 A:THR354 2.3 97.8 1.0 OG A:SER355 2.4 91.6 1.0 O A:VAL23 2.4 0.2 1.0 C A:ALA351 3.0 99.9 1.0 CB A:THR354 3.3 99.0 1.0 C A:GLY20 3.4 0.5 1.0 C A:VAL23 3.5 0.9 1.0 CA A:ALA351 3.6 98.8 1.0 CB A:SER355 3.7 96.0 1.0 N A:SER355 3.7 0.3 1.0 O A:TYR21 3.8 0.3 1.0 C A:THR354 3.9 0.6 1.0 CA A:THR354 4.0 0.5 1.0 O A:PHE350 4.1 0.3 1.0 N A:THR354 4.1 96.7 1.0 CA A:SER355 4.1 0.6 1.0 N A:GLY352 4.2 97.0 1.0 O A:HOH703 4.2 0.5 1.0 C A:TYR21 4.3 0.3 1.0 CB A:VAL23 4.3 0.2 1.0 N A:TYR21 4.3 0.4 1.0 CA A:VAL23 4.3 0.1 1.0 CG1 A:VAL23 4.4 0.0 1.0 CA A:TYR21 4.4 0.7 1.0 CA A:GLY20 4.4 0.1 1.0 CG2 A:THR354 4.5 98.6 1.0 N A:VAL23 4.5 0.3 1.0 O A:THR354 4.5 0.8 1.0 CB A:ALA351 4.6 99.8 1.0 CA A:GLY352 4.6 92.5 1.0 N A:ASP24 4.6 0.4 1.0 C A:GLY352 4.7 96.4 1.0 C18 A:CXX603 4.7 0.7 1.0 N A:ALA351 4.7 99.2 1.0 CA A:ASP24 4.8 0.6 1.0 C A:PHE350 4.8 0.9 1.0 O A:GLY352 4.9 0.3 1.0

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


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 Clomipramine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:0.5 occ:1.00 OD1 A:ASP24 2.2 0.2 1.0 O A:SER254 2.3 0.4 1.0 OD1 A:ASN286 2.4 0.5 1.0 OD1 A:ASN27 2.4 0.6 1.0 OG A:SER254 2.5 0.5 1.0 O A:ALA22 2.7 0.1 1.0 CA A:SER254 2.9 0.6 1.0 C A:SER254 2.9 0.2 1.0 CG A:ASP24 3.0 0.4 1.0 OD2 A:ASP24 3.0 0.9 1.0 CB A:SER254 3.2 0.6 1.0 CG A:ASN286 3.4 0.8 1.0 CG A:ASN27 3.5 0.4 1.0 ND2 A:ASN286 3.7 0.2 1.0 C A:ALA22 3.7 0.4 1.0 ND2 A:ASN27 3.9 0.1 1.0 N A:ASP24 4.1 0.4 1.0 N A:LEU255 4.2 0.5 1.0 N A:SER254 4.2 0.7 1.0 CB A:ASP24 4.4 0.3 1.0 O A:PHE253 4.4 0.8 1.0 N A:VAL23 4.4 0.3 1.0 CA A:VAL23 4.4 0.1 1.0 CA A:ALA22 4.6 0.5 1.0 C A:VAL23 4.6 0.9 1.0 N A:ASN27 4.7 0.7 1.0 CB A:ASN286 4.7 0.7 1.0 OG A:SER290 4.8 0.4 1.0 C A:PHE253 4.8 0.6 1.0 CB A:ASN27 4.8 0.5 1.0 CA A:ASP24 4.9 0.6 1.0 CB A:ALA22 4.9 0.6 1.0 CA A:LEU255 4.9 0.7 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