Sodium in PDB 5ccu: Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi

The structure of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi, PDB code: 5ccu was solved by L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.841, 48.980, 120.304, 90.00, 114.30, 90.00
R / Rfree (%)	18.4 / 21.8

The binding sites of Sodium atom in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi (pdb code 5ccu). 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 Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi, PDB code: 5ccu:

Sodium binding site 1 out of 1 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na612 b:25.4 occ:1.00 O A:ASP70 2.4 25.8 1.0 O A:PRO72 2.4 24.3 1.0 OD1 A:ASP68 2.7 19.8 1.0 OD2 A:ASP68 2.8 19.5 1.0 CG A:ASP68 3.1 19.7 1.0 C A:ASP70 3.5 26.1 1.0 C A:PRO72 3.5 24.2 1.0 CD A:PRO75 4.1 21.4 1.0 CG A:PRO75 4.2 21.4 1.0 N A:PRO72 4.2 25.5 1.0 CA A:ASP70 4.3 26.5 1.0 C A:ALA71 4.3 25.7 1.0 CA A:TYR73 4.3 22.3 1.0 CB A:ASP70 4.4 27.7 1.0 N A:TYR73 4.4 23.2 1.0 N A:ASP70 4.4 25.5 1.0 CA A:PRO72 4.5 25.2 1.0 N A:ALA71 4.5 25.9 1.0 N A:LEU74 4.6 21.2 1.0 CB A:ASP68 4.6 19.5 1.0 CA A:ALA71 4.6 25.7 1.0 O A:ALA71 4.7 26.2 1.0 CD A:PRO72 4.7 25.6 1.0 OE1 A:GLU78 4.9 34.1 1.0 C A:TYR73 4.9 21.8 1.0 CG A:PRO72 4.9 25.6 1.0

Y.B.Han, L.Q.Chen, Z.Li, Y.M.Tan, Y.Feng, G.Y.Yang. Structural Insights Into the Broad Substrate Specificity of A Novel Endoglycoceramidase I Belonging to A New Subfamily of GH5 Glycosidases J. Biol. Chem. V. 292 4789 2017.
ISSN: ESSN 1083-351X
PubMed: 28179425
DOI: 10.1074/JBC.M116.763821