Sodium in PDB 5lq7: Salmonella Effector Spvd - G161 Variant

The structure of Salmonella Effector Spvd - G161 Variant, PDB code: 5lq7 was solved by M.Przydacz, G.J.Grabe, D.W.Holden, S.A.Hare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.98 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.000, 51.970, 47.220, 90.00, 107.70, 90.00
R / Rfree (%)	16.3 / 19.7

The structure of Salmonella Effector Spvd - G161 Variant also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Salmonella Effector Spvd - G161 Variant (pdb code 5lq7). 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 Effector Spvd - G161 Variant, PDB code: 5lq7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Salmonella Effector Spvd - G161 Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Effector Spvd - G161 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:22.2 occ:1.00 O A:TYR69 2.3 23.9 1.0 O A:HOH567 2.3 35.2 1.0 OG1 A:THR65 2.4 21.6 1.0 O A:HOH570 2.4 28.1 1.0 O A:TYR66 2.5 24.6 1.0 O A:HOH563 2.6 38.0 1.0 CB A:THR65 3.4 19.4 1.0 C A:TYR69 3.5 21.5 1.0 C A:TYR66 3.5 27.9 1.0 O A:THR65 3.7 22.7 1.0 C A:THR65 3.8 23.8 1.0 O A:HOH582 4.0 33.4 1.0 N A:TYR69 4.0 23.9 1.0 CA A:THR65 4.2 21.7 1.0 CA A:VAL67 4.2 31.8 1.0 N A:VAL67 4.2 29.5 1.0 N A:TYR66 4.2 22.8 1.0 O A:HOH492 4.3 35.3 1.0 CA A:TYR69 4.3 21.7 1.0 N A:HIS68 4.5 28.7 1.0 N A:SER70 4.5 19.3 1.0 CA A:TYR66 4.5 28.1 1.0 CA A:SER70 4.6 17.8 1.0 C A:VAL67 4.6 29.9 1.0 OD1 A:ASN63 4.6 18.5 1.0 CG2 A:THR65 4.6 19.8 1.0 CB A:TYR69 4.8 23.6 1.0 N A:THR65 4.8 19.8 1.0 O A:HOH440 4.8 15.9 1.0

Sodium binding site 2 out of 2 in the Salmonella Effector Spvd - G161 Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Salmonella Effector Spvd - G161 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:19.5 occ:1.00 NE2 A:HIS199 3.1 16.1 1.0 O A:HOH524 3.1 20.9 1.0 O A:HOH489 3.1 20.2 1.0 O A:HOH526 3.2 14.7 1.0 ND2 A:ASN188 3.2 13.6 1.0 CB A:ASN188 3.7 12.3 1.0 CG A:ASN188 3.9 13.6 1.0 CE1 A:HIS199 3.9 18.5 1.0 CD2 A:HIS199 4.1 16.8 1.0 CE A:LYS185 4.1 15.9 1.0 O A:HOH583 4.4 34.5 1.0 O A:GLU195 4.5 14.9 1.0 CG A:LYS185 4.5 13.0 1.0 CB A:GLU195 4.5 14.5 1.0 O A:HOH590 4.5 25.9 1.0 CB A:PRO191 4.6 12.2 1.0 O A:ASN188 4.8 10.8 1.0 O A:HOH455 4.8 13.9 1.0 C A:GLU195 4.8 13.0 1.0 CD A:LYS185 4.9 14.5 1.0

G.J.Grabe, Y.Zhang, M.Przydacz, N.Rolhion, Y.Yang, J.N.Pruneda, D.Komander, D.W.Holden, S.A.Hare. The Salmonella Effector Spvd Is A Cysteine Hydrolase with A Serovar-Specific Polymorphism Influencing Catalytic Activity, Suppression of Immune Responses, and Bacterial Virulence. J. Biol. Chem. V. 291 25853 2016.
ISSN: ESSN 1083-351X
PubMed: 27789710
DOI: 10.1074/JBC.M116.752782