Sodium in PDB 7zhm: Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein

The structure of Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein, PDB code: 7zhm was solved by D.Jurenas, M.Rey, J.Chamot-Rooke, L.Terradot, E.Cascales, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.645, 94.036, 61.305, 90, 110.07, 90
R / Rfree (%)	21.4 / 25.7

The structure of Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein (pdb code 7zhm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein, PDB code: 7zhm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:9.9 occ:1.00 N B:ILE39 3.6 29.9 1.0 CA B:ASP38 3.6 28.2 1.0 O B:ALA37 3.8 37.0 1.0 OD1 B:ASP38 3.9 32.3 1.0 CG B:ASP38 4.1 32.6 1.0 C B:ASP38 4.1 27.9 1.0 CG2 B:ILE39 4.3 33.6 1.0 CB B:ASP38 4.3 29.8 1.0 N B:ASP38 4.5 27.4 1.0 C B:ALA37 4.5 29.2 1.0 CB B:ILE39 4.6 32.6 1.0 CA B:ILE39 4.7 30.3 1.0 O B:HOH320 4.7 21.5 1.0 OD2 B:ASP38 4.7 40.5 1.0

Sodium binding site 2 out of 2 in the Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Salmonella Enterica RHS1 C-Terminal Toxin Tretu Complex with Tritu Immunity Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:12.2 occ:1.00 N D:MET1 3.4 62.0 1.0 NZ D:LYS4 3.5 36.0 1.0 N D:LYS4 3.6 27.4 1.0 CA D:MET1 3.7 51.1 1.0 CB D:ASN3 3.8 31.4 1.0 C D:MET1 3.8 37.3 1.0 N D:ASN3 3.8 29.0 1.0 CG D:LYS4 3.8 29.8 1.0 O D:MET1 4.0 31.7 1.0 CA D:ASN3 4.1 29.4 1.0 CB D:LYS4 4.2 26.9 1.0 N D:LEU2 4.2 29.7 1.0 C D:ASN3 4.3 28.4 1.0 CE D:LYS4 4.4 31.7 1.0 CA D:LYS4 4.4 26.6 1.0 CD D:LYS4 4.6 31.0 1.0 CG D:ASN3 4.7 32.0 1.0 C D:LEU2 4.7 27.0 1.0 ND2 D:ASN3 4.8 34.9 1.0

D.Jurenas, M.Rey, D.Byrne, J.Chamot-Rooke, L.Terradot, E.Cascales. Salmonella Antibacterial Rhs Polymorphic Toxin Inhibits Translation Through Adp-Ribosylation of Ef-Tu P-Loop. Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
PubMed: 36484105
DOI: 10.1093/NAR/GKAC1162