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Sodium in PDB 2q6h: Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine

Protein crystallography data

The structure of Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine, PDB code: 2q6h 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) 50.00 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.080, 86.360, 80.770, 90.00, 95.71, 90.00
R / Rfree (%) 19.8 / 21.8

Other elements in 2q6h:

The structure of Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine (pdb code 2q6h). 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 Clomipramine, PDB code: 2q6h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2q6h

Go back to Sodium Binding Sites List in 2q6h
Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and 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 Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:23.0
occ:1.00
O A:VAL23 2.1 24.8 1.0
O A:GLY20 2.2 25.9 1.0
O A:ALA351 2.3 21.7 1.0
OG1 A:THR354 2.3 23.5 1.0
OG A:SER355 2.4 23.3 1.0
N A:SER355 3.0 22.6 1.0
C A:VAL23 3.1 24.1 1.0
CB A:SER355 3.2 19.9 1.0
C A:GLY20 3.3 27.5 1.0
CB A:THR354 3.3 24.4 1.0
C A:THR354 3.4 24.4 1.0
C A:ALA351 3.4 23.0 1.0
CA A:SER355 3.5 23.3 1.0
CA A:GLY24 3.6 25.5 1.0
CA A:THR354 3.8 23.5 1.0
N A:GLY24 3.8 24.6 1.0
CA A:ALA351 3.9 23.4 1.0
CA A:GLY20 4.0 26.4 1.0
O A:THR354 4.0 24.0 1.0
N A:THR354 4.1 23.3 1.0
O A:ASN21 4.2 25.6 1.0
CA A:VAL23 4.2 24.0 1.0
N A:VAL23 4.4 24.1 1.0
O A:PHE350 4.4 25.0 1.0
N A:ASN21 4.4 25.9 1.0
N A:GLY352 4.5 21.9 1.0
C A:ASN21 4.5 27.2 1.0
O A:GLY352 4.6 24.0 1.0
CG2 A:THR354 4.7 24.1 1.0
C A:GLY352 4.7 22.7 1.0
CB A:VAL23 4.8 26.2 1.0
CA A:ASN21 4.8 26.4 1.0
CB A:ALA351 4.8 23.2 1.0
C A:ALA22 4.8 24.8 1.0
CA A:GLY352 4.8 21.5 1.0
C A:SER355 5.0 22.7 1.0

Sodium binding site 2 out of 2 in 2q6h

Go back to Sodium Binding Sites List in 2q6h
Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Leut Complexed with L-Leucine, Sodium, and 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 Analysis of Leut Complexed with L-Leucine, Sodium, and Clomipramine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:25.4
occ:1.00
O A:ALA22 2.2 23.4 1.0
O A:THR254 2.2 22.9 1.0
OD1 A:ASN27 2.4 25.3 1.0
OG1 A:THR254 2.5 26.0 1.0
OXT A:LEU601 2.5 22.7 1.0
OD1 A:ASN286 2.6 23.6 1.0
C A:THR254 3.0 24.1 1.0
C A:ALA22 3.1 24.8 1.0
CA A:THR254 3.1 24.8 1.0
CG A:ASN27 3.3 26.2 1.0
CB A:THR254 3.4 25.2 1.0
CG A:ASN286 3.4 27.2 1.0
N A:LEU601 3.5 21.2 1.0
C A:LEU601 3.5 23.3 1.0
ND2 A:ASN286 3.6 26.1 1.0
ND2 A:ASN27 3.7 26.3 1.0
N A:VAL23 3.8 24.1 1.0
CA A:VAL23 3.8 24.0 1.0
N A:GLY24 3.9 24.6 1.0
CA A:ALA22 4.1 24.9 1.0
CA A:LEU601 4.1 22.9 1.0
OE2 A:GLU290 4.3 27.5 1.0
N A:LEU255 4.3 24.9 1.0
C A:VAL23 4.4 24.1 1.0
N A:ASN27 4.4 24.7 1.0
CB A:ALA22 4.4 24.4 1.0
CG2 A:THR254 4.4 23.9 1.0
N A:THR254 4.5 23.5 1.0
O A:LEU601 4.5 23.4 1.0
CB A:ASN27 4.6 25.8 1.0
O A:PHE253 4.6 23.5 1.0
CB A:ASN286 4.8 26.5 1.0
C A:GLY26 4.8 25.1 1.0
CA A:ASN27 4.9 26.9 1.0
CA A:GLY26 4.9 25.3 1.0
CA A:LEU255 5.0 25.7 1.0
CA A:GLY24 5.0 25.5 1.0

Reference:

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
Page generated: Tue Dec 15 05:54:25 2020

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