Sodium in PDB 2qb4: Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine

The structure of Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine, PDB code: 2qb4 was solved by S.K.Singh, A.Yamashita, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.73 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.290, 86.770, 81.250, 90.00, 96.02, 90.00
R / Rfree (%)	20.1 / 21.7

The binding sites of Sodium atom in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine (pdb code 2qb4). 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 Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine, PDB code: 2qb4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:26.5 occ:1.00 O A:VAL23 2.2 27.6 1.0 O A:GLY20 2.2 29.2 1.0 OG1 A:THR354 2.2 26.9 1.0 O A:ALA351 2.3 24.7 1.0 OG A:SER355 2.4 24.6 1.0 N A:SER355 3.0 26.7 1.0 C A:VAL23 3.2 26.9 1.0 CB A:THR354 3.3 26.9 1.0 CB A:SER355 3.3 24.5 1.0 C A:THR354 3.3 27.5 1.0 C A:GLY20 3.4 29.6 1.0 C A:ALA351 3.4 25.2 1.0 CA A:SER355 3.5 25.7 1.0 CA A:GLY24 3.7 25.6 1.0 CA A:THR354 3.7 27.5 1.0 N A:GLY24 3.8 26.3 1.0 CA A:ALA351 4.0 25.9 1.0 O A:THR354 4.0 27.8 1.0 CA A:GLY20 4.0 30.0 1.0 N A:THR354 4.0 24.5 1.0 CA A:VAL23 4.3 25.6 1.0 O A:ASN21 4.4 29.9 1.0 O A:PHE350 4.4 26.6 1.0 N A:VAL23 4.4 25.8 1.0 N A:ASN21 4.5 28.5 1.0 N A:GLY352 4.5 23.8 1.0 CG2 A:THR354 4.6 26.9 1.0 C A:ASN21 4.6 30.8 1.0 O A:GLY352 4.6 24.4 1.0 C A:GLY352 4.7 24.5 1.0 CA A:GLY352 4.8 24.9 1.0 CA A:ASN21 4.8 29.3 1.0 CB A:ALA351 4.8 25.0 1.0 CB A:VAL23 4.8 27.8 1.0 C A:ALA22 4.9 26.3 1.0 C A:SER355 5.0 25.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium and Desipramine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:28.3 occ:1.00 O A:ALA22 2.2 24.9 1.0 O A:THR254 2.3 25.3 1.0 OD1 A:ASN27 2.3 27.1 1.0 OG1 A:THR254 2.5 29.7 1.0 OD1 A:ASN286 2.5 28.5 1.0 OXT A:LEU601 2.5 26.2 1.0 C A:THR254 3.1 26.8 1.0 C A:ALA22 3.1 26.3 1.0 CA A:THR254 3.2 28.1 1.0 CG A:ASN27 3.3 28.5 1.0 CB A:THR254 3.4 28.2 1.0 CG A:ASN286 3.4 30.4 1.0 N A:LEU601 3.5 23.6 1.0 C A:LEU601 3.6 24.6 1.0 ND2 A:ASN27 3.6 29.5 1.0 ND2 A:ASN286 3.7 30.9 1.0 N A:VAL23 3.8 25.8 1.0 CA A:VAL23 3.8 25.6 1.0 N A:GLY24 3.9 26.3 1.0 CA A:ALA22 4.1 27.7 1.0 CA A:LEU601 4.1 25.6 1.0 OE2 A:GLU290 4.3 32.3 1.0 N A:LEU255 4.3 27.6 1.0 N A:ASN27 4.4 26.7 1.0 C A:VAL23 4.4 26.9 1.0 CB A:ALA22 4.4 26.6 1.0 CG2 A:THR254 4.5 28.6 1.0 O A:LEU601 4.5 26.3 1.0 N A:THR254 4.6 27.9 1.0 CB A:ASN27 4.6 27.2 1.0 O A:PHE253 4.7 26.2 1.0 CB A:ASN286 4.8 29.9 1.0 C A:GLY26 4.9 28.1 1.0 CA A:ASN27 4.9 28.5 1.0 CA A:GLY26 4.9 27.3 1.0 CA A:LEU255 5.0 28.4 1.0

S.K.Singh, A.Yamashita, E.Gouaux. Antidepressant Binding Site in A Bacterial Homologue of Neurotransmitter Transporters. Nature V. 448 952 2007.
ISSN: ISSN 0028-0836
PubMed: 17687333
DOI: 10.1038/NATURE06038