Sodium in PDB 6s3b: Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate

The structure of Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate, PDB code: 6s3b was solved by J.A.Gavira, M.A.Mantilla, M.Fernandez, T.Krell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.390, 69.219, 92.333, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.6

The binding sites of Sodium atom in the Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate (pdb code 6s3b). 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 Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate, PDB code: 6s3b:

Sodium binding site 1 out of 1 in the Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Binding Domain of the P. Putida Receptor PCAY_PP in Complex with Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:50.1 occ:1.00 O A:ILE81 2.9 32.8 1.0 O B:LEU151 3.0 37.3 1.0 CA A:GLY85 3.3 37.8 1.0 CA A:GLU82 3.5 37.0 1.0 C B:LEU151 3.6 39.4 1.0 N A:GLY85 3.6 38.8 1.0 C A:ILE81 3.6 33.3 1.0 CD2 A:HIS87 3.7 38.6 1.0 CB B:LEU151 3.7 45.5 1.0 CB B:PHE155 3.7 35.8 1.0 O A:GLU82 3.8 33.7 1.0 N A:GLU82 3.9 31.3 1.0 C A:GLU82 4.0 35.2 1.0 CG2 A:ILE81 4.1 32.3 1.0 CA B:LEU151 4.1 40.7 1.0 C A:GLY85 4.2 39.6 1.0 N B:PHE155 4.4 33.0 1.0 NE2 A:HIS87 4.4 42.0 1.0 CD2 B:LEU151 4.4 44.3 1.0 N B:GLU152 4.4 40.1 1.0 CA B:PHE155 4.5 35.1 1.0 CB A:GLU82 4.6 37.7 1.0 O A:GLY85 4.6 43.0 1.0 CG B:LEU151 4.6 48.4 1.0 CA B:GLU152 4.7 41.0 1.0 CG B:PHE155 4.8 39.2 1.0 CG A:GLU82 4.8 37.7 1.0 CG A:HIS87 4.8 36.1 1.0 CA A:ILE81 4.8 30.7 1.0 C A:LEU84 4.9 39.2 1.0

J.A.Gavira, M.A.Matilla, M.Fernandez, T.Krell. The Structural Basis For Signal Promiscuity in A Bacterial Chemoreceptor. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 33021055
DOI: 10.1111/FEBS.15580