Sodium in PDB 6w3o: Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 4-Methylisoleucine

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 4-Methylisoleucine, PDB code: 6w3o 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)	40.45 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.420, 137.720, 48.790, 90.00, 94.04, 90.00
R / Rfree (%)	11.5 / 16.2

The structure of Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 4-Methylisoleucine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 4-Methylisoleucine (pdb code 6w3o). 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 4-Methylisoleucine, PDB code: 6w3o:
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 4-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 4-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:40.3 occ:1.00 O A:HOH653 2.8 26.6 1.0 OG A:SER74 2.8 11.7 0.8 OG A:SER74 3.0 14.0 0.2 O A:HOH432 3.4 28.6 1.0 CB A:SER74 3.5 8.5 0.8 CB A:SER74 3.5 11.7 0.2 O A:HOH447 3.5 30.4 1.0 O A:SER70 3.6 9.3 0.6 O A:SER70 3.6 9.3 0.1 O A:SER70 3.7 9.4 0.3 O A:HOH617 3.9 46.0 1.0 OG A:SER70 3.9 13.2 0.3 CA A:THR71 4.0 8.8 1.0 C A:SER70 4.0 9.2 0.6 C A:SER70 4.0 9.2 0.1 C A:SER70 4.0 9.0 0.3 N A:THR71 4.1 9.1 1.0 OG1 A:THR71 4.3 11.2 1.0 O B:HOH778 4.4 39.1 1.0 OG A:SER70 4.5 11.0 0.6 O A:HOH458 4.6 14.4 1.0 CB A:SER70 4.6 8.5 0.1 CB A:SER70 4.7 11.2 0.3 CB A:SER70 4.7 10.0 0.6 CB A:THR71 4.8 9.7 1.0 O A:HOH543 4.8 24.8 1.0 CA A:SER74 4.9 8.5 0.8 CA A:SER74 4.9 9.2 0.2 C A:THR71 4.9 7.7 1.0 O A:THR71 4.9 9.1 1.0 CA A:SER70 5.0 8.9 0.1 CA A:SER70 5.0 9.7 0.6 CA A:SER70 5.0 10.4 0.3

Sodium binding site 2 out of 3 in the Crystal Structure of Ligand-Binding Domain of Campylobacter Jejuni Chemoreceptor TLP3 in Complex with 4-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 4-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:22.3 occ:1.00 OG1 A:THR226 2.3 14.9 1.0 O A:GLY211 2.3 11.8 1.0 OG1 A:THR209 2.4 11.1 1.0 O A:THR209 2.4 11.9 1.0 OG1 A:THR213 2.4 11.1 1.0 O A:PRO210 2.5 11.7 1.0 C A:THR209 3.0 11.6 1.0 C A:PRO210 3.1 11.0 1.0 C A:GLY211 3.4 11.6 1.0 CB A:THR226 3.4 13.4 1.0 CB A:THR209 3.4 11.5 1.0 CB A:THR213 3.6 11.1 1.0 N A:GLY211 3.7 12.7 1.0 CA A:THR209 3.7 11.7 1.0 N A:PRO210 3.7 11.2 1.0 N A:THR213 3.7 12.6 1.0 CG2 A:THR226 3.8 16.3 1.0 CA A:PRO210 3.9 12.4 1.0 CA A:GLY211 3.9 13.4 1.0 O A:HOH503 3.9 11.4 1.0 CG2 A:THR213 3.9 11.8 1.0 O A:VAL206 4.0 11.3 1.0 N A:THR209 4.2 12.2 1.0 CA A:THR213 4.2 12.6 1.0 OG1 A:THR61 4.3 12.1 1.0 N A:ASN212 4.5 12.8 1.0 O A:THR213 4.5 12.8 1.0 CA A:THR226 4.6 13.5 1.0 O A:ALA207 4.7 16.2 1.0 O A:HOH567 4.7 22.5 1.0 C A:THR213 4.7 12.0 1.0 CG2 A:THR209 4.7 11.2 1.0 C A:ASN212 4.8 12.7 1.0 CA A:ASN212 4.9 12.4 1.0 CD A:PRO210 4.9 13.7 1.0 N A:THR226 4.9 12.6 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 4-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 4-Methylisoleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:47.7 occ:1.00 CG2 B:ILE112 2.8 15.8 0.4 CG2 A:ILE112 2.8 13.9 0.4 OG A:SER111 2.8 12.3 1.0 OG B:SER111 2.9 11.2 1.0 O B:HOH655 3.2 16.2 1.0 CB B:SER111 3.3 9.3 1.0 CB A:SER111 3.4 9.2 1.0 O A:HOH609 3.4 17.7 1.0 O B:SER111 3.6 11.6 1.0 C B:SER111 3.6 9.6 1.0 C A:SER111 3.7 9.4 1.0 O A:SER111 3.7 11.7 1.0 N B:ILE112 4.0 9.5 0.6 N B:ILE112 4.0 9.5 0.4 CD2 A:PHE75 4.0 8.7 1.0 N A:ILE112 4.0 10.0 0.4 N A:ILE112 4.0 10.2 0.6 CD1 B:PHE75 4.0 10.2 1.0 CB B:ILE112 4.0 11.9 0.6 CA B:SER111 4.1 9.3 1.0 CB B:ILE112 4.1 14.2 0.4 CB A:ILE112 4.1 13.8 0.6 CE2 A:PHE75 4.1 8.5 1.0 CA A:SER111 4.1 8.9 1.0 CE1 B:PHE75 4.2 10.0 1.0 CB A:ILE112 4.2 10.6 0.4 O A:HOH827 4.2 18.2 1.0 CA B:ILE112 4.3 11.2 0.6 CA B:ILE112 4.3 12.5 0.4 CA A:ILE112 4.3 11.1 0.6 CA A:ILE112 4.4 10.9 0.4 CG1 A:ILE112 4.5 12.4 0.6 CG1 B:ILE112 4.6 14.0 0.6 CG1 B:ILE112 4.9 11.8 0.4 CD1 A:ILE112 4.9 14.3 0.6 CD1 B:ILE112 4.9 13.8 0.6 CG1 A:ILE112 4.9 10.8 0.4

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