Sodium in PDB 5lq6: Salmonella Effector Spvd - R161 Variant

The structure of Salmonella Effector Spvd - R161 Variant, PDB code: 5lq6 was solved by Y.Zhang, G.J.Grabe, N.Rolhion, Y.Yang, 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)	45.10 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.700, 51.810, 47.270, 90.00, 107.41, 90.00
R / Rfree (%)	17 / 20.1

The binding sites of Sodium atom in the Salmonella Effector Spvd - R161 Variant (pdb code 5lq6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Salmonella Effector Spvd - R161 Variant, PDB code: 5lq6:

Sodium binding site 1 out of 1 in the Salmonella Effector Spvd - R161 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 - R161 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:17.2 occ:1.00 NE2 A:HIS199 3.1 18.3 1.0 O A:HOH483 3.1 19.1 1.0 O A:HOH499 3.2 19.5 1.0 O A:HOH509 3.2 14.9 1.0 ND2 A:ASN188 3.3 13.8 1.0 CB A:ASN188 3.8 13.1 1.0 CE1 A:HIS199 3.9 18.4 1.0 CG A:ASN188 4.0 13.5 1.0 CE A:LYS185 4.1 16.8 1.0 CD2 A:HIS199 4.2 17.5 1.0 O A:HOH569 4.4 24.7 1.0 O A:GLU195 4.5 15.2 1.0 CB A:GLU195 4.5 13.6 1.0 CG A:LYS185 4.5 15.5 1.0 CB A:PRO191 4.6 12.3 1.0 O A:ASN188 4.8 13.2 1.0 O A:HOH431 4.8 16.2 1.0 C A:GLU195 4.8 16.3 1.0 CD A:LYS185 4.9 15.9 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