Sodium in PDB 6s5z: Structure of Rib R28N From Streptococcus Pyogenes

The structure of Structure of Rib R28N From Streptococcus Pyogenes, PDB code: 6s5z was solved by F.Whelan, S.C.Griffiths, J.L.Whittingham, A.Bateman, J.R.Potts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.94 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.423, 43.560, 47.615, 90.00, 118.27, 90.00
R / Rfree (%)	17 / 22.4

The binding sites of Sodium atom in the Structure of Rib R28N From Streptococcus Pyogenes (pdb code 6s5z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Rib R28N From Streptococcus Pyogenes, PDB code: 6s5z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Rib R28N From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rib R28N From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.7 occ:1.00 O A:LYS231 2.4 23.5 1.0 OD2 A:ASP297 2.5 20.6 1.0 O A:TYR234 2.5 17.3 1.0 O A:HOH627 2.6 46.2 1.0 O A:HOH580 2.6 29.1 1.0 O A:HOH524 2.7 39.8 1.0 OD1 A:ASP297 3.2 23.3 1.0 CG A:ASP297 3.2 21.9 1.0 C A:LYS231 3.5 22.7 1.0 C A:TYR234 3.7 20.3 1.0 CD A:PRO236 4.0 18.2 1.0 CA A:LYS231 4.3 18.1 1.0 CA A:SER235 4.3 16.1 1.0 N A:SER235 4.5 16.2 1.0 O A:HOH556 4.5 32.9 1.0 OH A:TYR291 4.5 21.2 1.0 O A:HOH607 4.5 33.0 1.0 N A:ILE232 4.5 23.2 1.0 CB A:ASP297 4.6 16.0 1.0 CA A:ILE232 4.7 23.8 1.0 CB A:LYS231 4.7 16.3 1.0 O A:ILE232 4.7 26.1 1.0 N A:TYR234 4.8 18.2 1.0 CA A:TYR234 4.8 16.2 1.0 C A:ILE232 4.8 22.2 1.0 OG A:SER235 4.9 21.9 1.0 CG A:PRO236 4.9 16.1 1.0

Sodium binding site 2 out of 2 in the Structure of Rib R28N From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rib R28N From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:31.7 occ:1.00 O B:LYS231 2.5 55.0 1.0 O B:TYR234 2.8 20.9 1.0 OD2 B:ASP297 2.9 24.2 1.0 O B:HOH614 2.9 47.5 1.0 OD1 B:ASP297 3.3 34.4 1.0 CG B:ASP297 3.4 26.0 1.0 C B:LYS231 3.7 51.7 1.0 C B:TYR234 4.0 22.2 1.0 O B:HOH551 4.4 46.4 1.0 CD B:PRO236 4.4 13.8 1.0 CA B:SER235 4.5 17.7 1.0 CA B:LYS231 4.5 47.4 1.0 N B:ILE232 4.6 49.6 1.0 CG B:LYS231 4.7 46.2 1.0 N B:SER235 4.7 14.6 1.0 CA B:ILE232 4.7 47.4 1.0 O B:ILE232 4.8 44.1 1.0 CB B:ASP297 4.8 21.1 1.0 OG B:SER235 4.9 23.6 1.0 C B:ILE232 4.9 43.8 1.0 OH B:TYR291 4.9 21.1 1.0 N B:TYR234 5.0 18.5 1.0

F.Whelan, A.Lafita, S.C.Griffiths, R.E.M.Cooper, J.L.Whittingham, J.P.Turkenburg, I.W.Manfield, A.N.St John, E.Paci, A.Bateman, J.R.Potts. Defining the Remarkable Structural Malleability of A Bacterial Surface Protein Rib Domain Implicated in Infection. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31818940
DOI: 10.1073/PNAS.1911776116