Sodium in PDB 8yk7: Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri

The structure of Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri, PDB code: 8yk7 was solved by Y.Xue, X.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 1.35
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	76.274, 76.274, 23.326, 90, 90, 120
R / Rfree (%)	12.7 / 16.7

The structure of Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri (pdb code 8yk7). 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 Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri, PDB code: 8yk7:

Sodium binding site 1 out of 1 in the Structure of Rib Domain From Surface Adhesin of Limosilactobacillus Reuteri


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 Domain From Surface Adhesin of Limosilactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1303 b:9.3 occ:1.00 O A:ALA1194 2.2 12.3 1.0 O A:TYR1197 2.3 14.0 1.0 OD2 A:ASP1258 2.4 10.0 1.0 O A:HOH1506 2.4 14.7 1.0 O A:HOH1467 2.5 22.4 1.0 OD1 A:ASP1258 2.8 10.2 1.0 CG A:ASP1258 2.9 8.6 1.0 C A:ALA1194 3.4 10.6 1.0 C A:TYR1197 3.5 10.7 1.0 CA A:ALA1194 4.1 9.0 1.0 CD A:PRO1199 4.1 10.3 1.0 CA A:THR1198 4.2 10.8 1.0 N A:THR1198 4.3 10.7 1.0 CB A:ASP1258 4.3 8.0 1.0 N A:ASP1195 4.4 11.7 1.0 OH A:TYR1252 4.5 9.8 1.0 N A:TYR1197 4.5 11.4 1.0 CA A:TYR1197 4.6 11.6 1.0 CA A:ASP1195 4.6 14.3 1.0 C A:ASP1195 4.6 15.5 1.0 CB A:ALA1194 4.6 10.4 1.0 OG1 A:THR1198 4.7 15.4 1.0 O A:ASP1195 4.7 21.9 1.0 O A:HOH1404 4.7 29.2 1.0 O A:ASP1193 5.0 11.0 1.0

Y.Xue, Z.Wu, X.Kang. Crystal Structure of the Rib Domain of the Cell-Wall-Anchored Surface Protein From Limosilactobacillus Reuteri. Acta Crystallogr.,Sect.F 2024.
ISSN: ESSN 2053-230X
PubMed: 39196706
DOI: 10.1107/S2053230X24007970