Sodium in PDB 6w3p: Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine, PDB code: 6w3p was solved by M.F.Khan, M.A.Machuca, M.M.Rahman, A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.43 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.110, 138.110, 48.790, 90.00, 94.72, 90.00
R / Rfree (%)	13.8 / 18.7

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine (pdb code 6w3p). 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 Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine, PDB code: 6w3p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine


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 Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:18.9 occ:1.00 O A:HOH733 2.7 17.0 1.0 OG1 A:THR71 2.7 13.0 1.0 O A:HOH725 2.7 16.0 1.0 O A:HOH752 2.7 24.5 1.0 CB A:THR71 3.5 12.4 1.0 O A:ASP67 3.6 11.8 1.0 CG2 A:THR71 4.0 13.6 1.0 C A:ASP67 4.1 11.8 1.0 O A:HOH500 4.1 36.7 1.0 O A:HOH786 4.1 17.1 1.0 O B:HOH793 4.2 17.4 1.0 O B:HOH489 4.2 15.3 1.0 O A:HOH585 4.2 27.1 1.0 O A:HOH739 4.3 31.5 1.0 O B:HOH761 4.3 19.6 1.0 CB A:ASP67 4.3 10.9 1.0 O A:HOH514 4.4 22.0 1.0 O A:HOH574 4.6 16.9 1.0 N A:PHE68 4.6 11.3 1.0 O A:HOH544 4.7 16.7 1.0 CA A:ASP67 4.8 11.9 1.0 O A:HOH763 4.8 18.8 1.0 O B:HOH755 4.8 27.7 1.0 O A:HOH796 4.9 25.7 1.0 CA A:THR71 4.9 10.2 1.0 CA A:PHE68 4.9 10.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine


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 Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with Beta-Methylnorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:24.7 occ:1.00 O A:HOH652 3.0 21.5 1.0 N A:GLN218 3.1 21.4 1.0 O A:HOH738 3.1 30.0 1.0 CB A:GLN218 3.4 37.6 1.0 CB A:ASP217 3.7 15.9 1.0 CA A:GLN218 3.8 24.9 1.0 CA A:ASP217 4.0 17.8 1.0 C A:ASP217 4.0 21.6 1.0 OE1 A:GLN218 4.0 62.8 1.0 CB A:PRO165 4.0 22.7 1.0 CA A:PRO165 4.4 16.5 1.0 CG A:GLN218 4.5 45.9 1.0 CG A:ASP217 4.6 18.9 1.0 CB A:ALA271 4.6 21.8 1.0 O A:HOH668 4.6 50.0 1.0 CD A:GLN218 4.6 58.6 1.0 CG A:PRO165 4.7 29.2 1.0 O A:HOH571 4.7 24.1 1.0 O A:HOH420 4.7 26.5 1.0 CE1 A:TYR272 4.7 21.1 1.0 O A:HOH592 4.8 47.8 1.0 O A:HOH509 4.9 22.0 1.0 CD1 A:TYR272 5.0 19.4 1.0

M.F.Khan, M.A.Machuca, M.M.Rahman, C.Koc, R.S.Norton, B.J.Smith, A.Roujeinikova. Structure-Activity Relationship Study Reveals the Molecular Basis For Specific Sensing of Hydrophobic Amino Acids By the Campylobacter Jejuni Chemoreceptor TLP3 Biomolecules 2020.
ISSN: ESSN 2218-273X
DOI: 10.3390/BIOM10050744