Sodium in PDB 6w3r: Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine, PDB code: 6w3r 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)	35.99 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.260, 138.080, 48.830, 90.00, 93.82, 90.00
R / Rfree (%)	12.1 / 18

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine (pdb code 6w3r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine, PDB code: 6w3r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine


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 3-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:45.0 occ:1.00 O A:HOH642 2.9 24.2 1.0 N A:ASP150 3.1 21.1 1.0 CA A:LYS149 3.7 21.3 1.0 C A:LYS149 3.9 18.1 1.0 CB A:ASP150 3.9 22.3 1.0 CD A:LYS149 4.0 28.3 1.0 CG A:ASP150 4.0 34.9 1.0 CB A:LYS149 4.1 22.0 1.0 CA A:ASP150 4.1 18.4 1.0 O A:HOH708 4.1 36.9 1.0 OD2 A:ASP150 4.2 54.0 1.0 O A:THR148 4.4 26.5 1.0 OD1 A:ASP150 4.5 39.7 1.0 CG A:LYS149 4.7 25.4 1.0 O A:HOH409 4.7 57.5 1.0 N A:LYS149 4.8 21.3 1.0 N A:TRP151 4.9 17.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine


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 3-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:15.2 occ:1.00 OG1 A:THR226 2.3 19.3 1.0 O A:GLY211 2.4 16.4 1.0 OG1 A:THR209 2.4 15.1 1.0 O A:THR209 2.4 16.2 1.0 OG1 A:THR213 2.4 13.8 1.0 O A:PRO210 2.5 15.8 1.0 C A:THR209 3.0 15.6 1.0 C A:PRO210 3.1 14.9 1.0 CB A:THR226 3.4 15.2 1.0 C A:GLY211 3.4 16.2 1.0 CB A:THR209 3.5 16.4 1.0 CB A:THR213 3.6 14.5 1.0 N A:PRO210 3.7 16.7 1.0 N A:GLY211 3.7 16.0 1.0 N A:THR213 3.7 16.1 1.0 CA A:THR209 3.8 15.3 1.0 CG2 A:THR226 3.8 20.3 1.0 CA A:PRO210 3.9 15.5 1.0 CA A:GLY211 3.9 16.9 1.0 O A:HOH512 4.0 16.0 1.0 CG2 A:THR213 4.0 15.2 1.0 O A:VAL206 4.1 14.2 1.0 CA A:THR213 4.2 15.4 1.0 N A:THR209 4.2 16.9 1.0 OG1 A:THR61 4.4 15.1 1.0 O A:THR213 4.5 16.6 1.0 N A:ASN212 4.5 15.8 1.0 CA A:THR226 4.6 15.4 1.0 O A:ALA207 4.6 20.7 1.0 O A:HOH514 4.7 24.5 1.0 C A:THR213 4.7 14.7 1.0 C A:ASN212 4.8 15.6 1.0 CG2 A:THR209 4.8 17.0 1.0 CA A:ASN212 4.9 15.1 1.0 CD A:PRO210 4.9 17.2 1.0 N A:THR226 4.9 16.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine


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 Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 3-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:40.6 occ:1.00 O B:HOH742 2.6 56.0 1.0 OE2 B:GLU200 2.7 25.0 1.0 ND2 B:ASN204 2.9 20.9 1.0 CD B:GLU200 3.5 18.9 1.0 CG B:ASN204 3.8 20.4 1.0 CG B:GLU200 3.9 18.2 1.0 OD1 B:ASN204 4.0 24.3 1.0 O B:HOH507 4.3 35.3 1.0 OE1 B:GLU200 4.3 22.5 1.0 O B:HOH728 4.9 58.9 1.0 O B:HOH445 4.9 44.9 1.0 O B:HOH661 4.9 26.6 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