Sodium in PDB 8py0: Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate.

The structure of Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate., PDB code: 8py0 was solved by J.A.Gavira, T.Krell, E.Monteagudo-Cascales, F.Velando, M.A.Matilla, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.56 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.379, 58.379, 156.462, 90, 90, 120
R / Rfree (%)	18.8 / 21.7

The binding sites of Sodium atom in the Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate. (pdb code 8py0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate., PDB code: 8py0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:39.8 occ:1.00 O B:HOH334 2.6 47.8 1.0 O A:HOH416 2.6 31.9 1.0 O A:HOH398 2.9 26.2 1.0 OG A:SER132 2.9 23.8 1.0 OD2 A:ASP130 3.1 27.1 1.0 CA A:GLY133 3.6 14.8 1.0 N A:GLY133 3.7 20.1 1.0 O A:HOH304 3.7 25.6 1.0 C A:SER132 3.8 25.2 1.0 CG A:ASP130 3.8 30.6 1.0 O A:SER132 3.9 25.6 1.0 O B:HOH386 4.0 39.4 1.0 O B:HOH393 4.0 52.6 1.0 O B:HOH319 4.0 45.9 1.0 CB A:SER132 4.1 22.9 1.0 OD1 A:ASP130 4.2 20.6 1.0 O A:HOH375 4.2 43.4 1.0 CA A:SER132 4.5 22.4 1.0 O A:HOH366 4.6 32.7 1.0 CB A:ASP130 4.7 15.2 1.0

Sodium binding site 2 out of 2 in the Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sensor Domain of Oscillibacter Ruminantium Chemoreceptor in Complex with Formate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:17.2 occ:1.00 O B:HOH377 3.0 19.1 1.0 O B:HOH338 3.1 30.6 1.0 N B:LEU152 3.1 14.2 1.0 O B:HOH352 3.2 28.4 1.0 O B:HOH307 3.3 39.7 1.0 CG2 A:THR127 3.9 18.6 1.0 CA B:LEU152 3.9 20.0 1.0 CA B:ILE151 4.0 14.6 1.0 CB B:ASP130 4.0 16.8 1.0 C B:ILE151 4.0 14.5 1.0 CD2 B:LEU152 4.1 34.2 1.0 O B:THR150 4.1 16.9 1.0 N B:ASP130 4.6 14.3 1.0 CG B:LEU152 4.6 25.1 1.0 C B:THR150 4.6 15.2 1.0 O A:HOH302 4.6 28.9 1.0 N B:ILE151 4.7 16.6 1.0 OD2 B:ASP130 4.7 23.3 1.0 CA B:ASP130 4.7 12.2 1.0 O B:ALA128 4.8 20.0 1.0 CG B:ASP130 4.8 20.7 1.0 NH2 B:ARG111 4.8 18.7 1.0 CD2 A:LEU152 4.9 27.7 1.0 CB B:LEU152 4.9 22.8 1.0 CB A:THR127 4.9 17.8 1.0 N B:GLY153 4.9 17.5 1.0 CG2 B:ILE151 5.0 15.0 1.0

E.Monteagudo-Cascales, J.A.Gavira, J.Xing, F.Velando, M.A.Matilla, I.B.Zhulin, T.Krell. Bacterial Sensor Evolved By Decreasing Complexity. Proc.Natl.Acad.Sci.Usa V. 122 81122 2025.
ISSN: ESSN 1091-6490
PubMed: 39879239
DOI: 10.1073/PNAS.2409881122