Sodium in PDB 8bby: Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain)

The structure of Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain), PDB code: 8bby was solved by A.Barwinska-Sendra, P.S.Salgado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.23 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.926, 131.291, 138.269, 90, 108.78, 90
R / Rfree (%)	24.4 / 28.7

The binding sites of Sodium atom in the Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain) (pdb code 8bby). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain), PDB code: 8bby:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:46.0 occ:1.00 OE2 B:GLU98 2.2 33.9 1.0 O B:VAL180 2.2 40.9 1.0 OD2 B:ASP183 2.2 50.6 1.0 OD1 B:ASP221 2.4 54.8 1.0 CD B:GLU98 2.8 51.0 1.0 OE1 B:GLU98 2.9 72.8 1.0 CG B:ASP221 3.2 36.1 1.0 OD2 B:ASP221 3.3 29.5 1.0 C B:VAL180 3.3 47.7 1.0 CG B:ASP183 3.4 42.7 1.0 O B:GLY181 3.7 56.6 1.0 CA B:GLY181 3.8 36.3 1.0 N B:GLY181 4.0 47.6 1.0 C B:GLY181 4.0 30.8 1.0 CG B:GLU98 4.2 38.9 1.0 CB B:ASP183 4.2 40.1 1.0 OD1 B:ASP183 4.2 54.3 1.0 CG1 B:VAL180 4.3 25.9 1.0 CA B:VAL180 4.4 38.2 1.0 O B:ALA222 4.5 41.8 1.0 CB B:ASP221 4.6 36.2 1.0 N B:ALA222 4.7 33.1 1.0 O B:HOH607 4.7 41.1 1.0 N B:ASP183 4.9 32.7 1.0 CB B:VAL180 5.0 40.1 1.0

Sodium binding site 2 out of 2 in the Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Varb H/L (Slpl/Slph) Complex From C. Difficile Slpa (R20291 Strain) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:33.7 occ:1.00 O D:VAL180 2.2 22.2 1.0 OD2 D:ASP221 2.2 48.5 1.0 OD1 D:ASP183 2.4 60.6 1.0 OE2 D:GLU98 2.5 43.0 1.0 CG D:ASP221 3.0 41.5 1.0 CB D:ASP221 3.2 39.2 1.0 C D:VAL180 3.4 32.5 1.0 CD D:GLU98 3.4 52.5 1.0 CG D:ASP183 3.6 57.4 1.0 OE1 D:GLU98 3.6 68.3 1.0 CA D:GLY181 3.7 37.6 1.0 O D:GLY181 3.8 60.3 1.0 N D:GLY181 4.0 37.0 1.0 C D:GLY181 4.0 54.9 1.0 OD1 D:ASP221 4.2 42.1 1.0 CA D:ASP221 4.3 42.9 1.0 CB D:ASP183 4.4 55.1 1.0 OD2 D:ASP183 4.5 71.7 1.0 CA D:VAL180 4.6 30.0 1.0 CG1 D:VAL180 4.7 28.8 1.0 CG D:GLU98 4.8 36.1 1.0 N D:ALA222 4.8 29.4 1.0 O D:ALA222 5.0 47.7 1.0 C D:ASP221 5.0 29.8 1.0

M.J.Ormsby, F.Vaz, J.A.Kirk, A.Barwinska-Sendra, J.C.Hallam, P.Lanzoni-Mangutchi, J.Cole, R.R.Chaudhuri, P.S.Salgado, R.P.Fagan, G.R.Douce. An Intact S-Layer Is Advantageous to Clostridioides Difficile Within the Host. Plos Pathog. V. 19 11015 2023.
ISSN: ESSN 1553-7374
PubMed: 37384772
DOI: 10.1371/JOURNAL.PPAT.1011015