Sodium in PDB 6s5x: Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae

The structure of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae, PDB code: 6s5x was solved by F.Whelan, J.P.Turkenburg, S.C.Griffiths, A.Bateman, J.R.Potts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.31 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.880, 48.880, 144.573, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.2

The binding sites of Sodium atom in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae (pdb code 6s5x). 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 Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae, PDB code: 6s5x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:16.7 occ:1.00 O A:ASN234 2.3 12.0 1.0 O A:HOH551 2.3 19.2 1.0 OD2 A:ASP295 2.3 13.0 1.0 O A:HOH578 2.3 22.6 1.0 O A:ALA231 2.4 11.9 1.0 OD1 A:ASP295 2.7 17.2 1.0 CG A:ASP295 2.9 16.7 1.0 O A:HOH586 3.4 26.5 1.0 C A:ALA231 3.4 12.5 1.0 HA A:ASP235 3.5 9.6 1.0 C A:ASN234 3.5 13.1 1.0 H A:ASN234 3.7 8.7 1.0 HB1 A:ALA231 3.7 14.0 1.0 HD2 A:PRO236 3.7 15.2 1.0 HA A:ALA231 3.7 10.3 1.0 HH A:TYR289 4.0 12.2 1.0 CA A:ALA231 4.0 8.6 1.0 HD3 A:PRO236 4.1 15.2 1.0 O A:HOH613 4.2 31.3 1.0 CA A:ASP235 4.3 8.0 1.0 N A:ASP235 4.3 10.3 1.0 CB A:ASP295 4.3 12.6 1.0 CB A:ALA231 4.4 11.7 1.0 N A:ASN234 4.4 7.2 1.0 CD A:PRO236 4.4 12.7 1.0 HA A:ASP232 4.5 14.5 1.0 CA A:ASN234 4.5 9.2 1.0 OH A:TYR289 4.5 10.2 1.0 N A:ASP232 4.5 9.7 1.0 HB2 A:ASN234 4.5 13.2 1.0 HB3 A:ASP295 4.6 15.1 1.0 O A:HOH504 4.6 43.1 1.0 HE2 A:TYR289 4.7 11.1 1.0 HB2 A:ASP295 4.7 15.1 1.0 OD1 A:ASP235 4.7 17.6 1.0 HB2 A:ASP235 4.7 12.2 1.0 CA A:ASP232 4.8 12.1 1.0 C A:ASP232 4.9 16.4 1.0 HB3 A:ALA231 4.9 14.0 1.0 CB A:ASN234 5.0 11.0 1.0

Sodium binding site 2 out of 2 in the Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ribr, the Most N-Terminal Rib Domain From Group B Streptococcus Species Streptococcus Agalactiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:12.4 occ:1.00 O B:ASN234 2.3 12.9 1.0 O B:ALA231 2.3 11.6 1.0 OD2 B:ASP295 2.3 11.7 1.0 O B:HOH600 2.4 27.3 1.0 O B:HOH627 2.4 15.3 1.0 O B:HOH520 2.8 28.6 1.0 OD1 B:ASP295 2.8 16.6 1.0 CG B:ASP295 2.9 11.6 1.0 C B:ALA231 3.4 8.4 1.0 HD2 B:PRO236 3.4 13.2 1.0 C B:ASN234 3.5 12.9 1.0 HA B:ASP235 3.5 14.5 1.0 HA B:ALA231 3.7 9.6 1.0 H B:ASN234 3.7 10.9 1.0 HH B:TYR289 3.7 11.4 1.0 HB1 B:ALA231 3.7 9.9 1.0 HD3 B:PRO236 3.9 13.2 1.0 CA B:ALA231 4.0 8.0 1.0 CD B:PRO236 4.1 11.0 1.0 OD1 B:ASP235 4.1 29.9 1.0 HA B:ASP232 4.2 16.1 1.0 O B:HOH515 4.3 42.0 1.0 N B:ASP235 4.3 8.5 1.0 CA B:ASP235 4.3 12.1 1.0 CB B:ASP295 4.3 7.2 1.0 OH B:TYR289 4.3 9.5 1.0 N B:ASN234 4.4 9.1 1.0 CB B:ALA231 4.4 8.3 1.0 N B:ASP232 4.4 8.7 1.0 CA B:ASN234 4.4 7.8 1.0 HB2 B:ASN234 4.4 8.5 1.0 HE2 B:TYR289 4.5 9.3 1.0 HB3 B:ASP295 4.5 8.6 1.0 HB2 B:ASP295 4.6 8.6 1.0 CA B:ASP232 4.7 13.4 1.0 O B:HOH563 4.7 28.2 1.0 CG B:ASP235 4.8 97.2 1.0 C B:ASP232 4.8 11.1 1.0 O B:HOH637 4.9 24.6 1.0 HB3 B:ALA231 4.9 9.9 1.0 CB B:ASN234 4.9 7.1 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