Sodium in PDB 5eld: Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y

The structure of Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y, PDB code: 5eld was solved by J.E.Heggelund, D.Burschowsky, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.700, 69.806, 134.735, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.3

The binding sites of Sodium atom in the Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y (pdb code 5eld). 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 Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y, PDB code: 5eld:

Sodium binding site 1 out of 1 in the Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cholera Toxin Classical B-Pentamer in Complex with A Lewis-Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:12.0 occ:0.80 OG1 B:THR15 2.3 10.2 1.0 O B:TYR12 2.3 11.3 1.0 O B:HOH366 2.4 16.4 1.0 O B:CYS9 2.5 11.3 1.0 C B:TYR12 3.5 10.0 1.0 C B:CYS9 3.5 11.1 1.0 CB B:THR15 3.6 9.0 1.0 O B:THR15 3.8 9.7 1.0 CA B:ALA10 3.8 11.4 1.0 N B:THR15 4.0 8.2 1.0 N B:ALA10 4.0 10.3 1.0 SG B:CYS9 4.1 18.6 0.5 C B:THR15 4.1 8.5 1.0 N B:TYR12 4.1 10.0 1.0 CA B:THR15 4.1 8.5 1.0 C B:ALA10 4.2 11.6 1.0 CA B:TYR12 4.3 9.8 1.0 O B:HOH392 4.4 23.6 1.0 O B:ALA10 4.5 13.1 1.0 CG2 B:THR15 4.5 9.2 1.0 N B:HIS13 4.5 9.9 1.0 CA B:HIS13 4.6 9.2 1.0 CB B:TYR12 4.6 10.3 1.0 CA B:CYS9 4.7 11.4 0.5 CA B:CYS9 4.7 9.2 0.5 C B:HIS13 4.7 8.9 1.0 SG B:CYS9 4.8 6.7 0.5 N B:GLU11 4.8 10.9 1.0 CB B:CYS9 4.9 13.1 0.5 N B:ASN14 4.9 8.2 1.0 N B:GLN16 5.0 7.2 1.0 CB B:CYS9 5.0 8.3 0.5

J.E.Heggelund, D.Burschowsky, V.A.Bjrnestad, V.Hodnik, G.Anderluh, U.Krengel. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Plos Pathog. V. 12 05567 2016.
ISSN: ESSN 1553-7374
PubMed: 27082955
DOI: 10.1371/JOURNAL.PPAT.1005567