Sodium in PDB 5j7z: Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1

The structure of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1, PDB code: 5j7z 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 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.283, 48.921, 120.227, 90.00, 113.95, 90.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Sodium atom in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1 (pdb code 5j7z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1, PDB code: 5j7z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1


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 in Complex with GM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:30.0 occ:1.00 O A:ASP62 2.1 23.8 1.0 O A:PRO64 2.2 23.1 1.0 OD2 A:ASP60 2.3 22.7 1.0 OD1 A:ASP60 2.3 22.3 1.0 O A:HOH862 2.4 29.1 1.0 CG A:ASP60 2.7 23.3 1.0 C A:ASP62 3.3 24.0 1.0 C A:PRO64 3.3 23.1 1.0 CA A:TYR65 3.8 21.2 1.0 N A:TYR65 4.0 21.4 1.0 CD A:PRO67 4.1 23.6 1.0 CA A:ASP62 4.1 24.0 1.0 N A:LEU66 4.2 20.1 1.0 N A:ASP62 4.2 23.0 1.0 CB A:ASP60 4.2 22.1 1.0 C A:ALA63 4.3 26.3 1.0 CB A:ASP62 4.3 24.9 1.0 N A:ALA63 4.3 24.5 1.0 N A:PRO64 4.3 27.6 1.0 C A:TYR65 4.5 20.5 1.0 CA A:PRO64 4.5 25.9 1.0 O A:HOH848 4.5 29.5 1.0 CA A:ALA63 4.5 25.1 1.0 CD1 A:TYR65 4.6 21.0 1.0 O A:ALA63 4.6 28.3 1.0 CG A:PRO67 4.6 23.8 1.0 CB A:TYR65 4.9 20.8 1.0 CD A:PRO64 5.0 27.7 1.0 CG A:TYR65 5.0 20.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:30.0 occ:1.00 O B:ASP62 1.9 26.3 1.0 O B:PRO64 2.1 22.1 1.0 OD1 B:ASP60 2.5 24.8 1.0 OD2 B:ASP60 2.6 21.4 1.0 CG B:ASP60 2.9 24.2 1.0 C B:PRO64 3.2 22.0 1.0 C B:ASP62 3.2 28.3 1.0 CA B:TYR65 3.8 20.4 1.0 N B:TYR65 3.9 20.3 1.0 N B:PRO64 4.0 24.6 1.0 C B:ALA63 4.0 25.7 1.0 CA B:ASP62 4.1 30.6 1.0 N B:ALA63 4.1 26.8 1.0 CA B:PRO64 4.2 23.4 1.0 CA B:ALA63 4.2 26.0 1.0 N B:ASP62 4.2 28.6 1.0 CB B:ASP62 4.3 32.9 1.0 N B:LEU66 4.3 20.1 1.0 CB B:ASP60 4.4 24.1 1.0 CD1 B:TYR65 4.5 19.0 1.0 O B:ALA63 4.5 24.3 1.0 C B:TYR65 4.5 20.1 1.0 CD B:PRO67 4.6 24.6 1.0 CD B:PRO64 4.6 24.1 1.0 CG B:PRO67 4.7 24.7 1.0 CG B:TYR65 4.9 19.0 1.0 CB B:TYR65 4.9 19.2 1.0 CG B:PRO64 4.9 24.2 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