Sodium in PDB 5j14: Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3

The structure of Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3, PDB code: 5j14 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 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.521, 49.053, 120.135, 90.00, 114.19, 90.00
R / Rfree (%)	16.7 / 20.4

The binding sites of Sodium atom in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3 (pdb code 5j14). 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 GM3, PDB code: 5j14:
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 GM3


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 GM3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:30.0 occ:1.00 O A:HOH840 2.4 23.8 1.0 O A:HOH906 2.4 23.0 1.0 O A:ASP62 2.4 10.7 1.0 O A:PRO64 2.5 10.1 1.0 O A:HOH746 2.5 17.4 1.0 OD1 A:ASP60 2.6 8.2 1.0 OD2 A:ASP60 2.6 7.2 1.0 CG A:ASP60 3.0 7.8 1.0 C A:PRO64 3.6 10.6 1.0 C A:ASP62 3.6 11.4 1.0 O A:HOH850 4.0 30.4 1.0 CD A:PRO67 4.2 8.8 1.0 CA A:TYR65 4.3 9.2 1.0 N A:PRO64 4.3 12.4 1.0 N A:TYR65 4.4 9.6 1.0 CA A:ASP62 4.4 12.1 1.0 C A:ALA63 4.4 12.1 1.0 N A:ASP62 4.4 10.8 1.0 CB A:ASP62 4.4 13.9 1.0 CB A:ASP60 4.5 7.8 1.0 O A:HOH824 4.5 14.4 1.0 CA A:PRO64 4.6 11.9 1.0 CG A:PRO67 4.6 8.9 1.0 N A:LEU66 4.6 8.4 1.0 N A:ALA63 4.6 11.2 1.0 O A:HOH688 4.7 28.8 1.0 O A:ALA63 4.7 12.0 1.0 CA A:ALA63 4.8 11.7 1.0 CD A:PRO64 4.8 12.7 1.0 OE1 A:GLU70 4.9 26.0 1.0 C A:TYR65 4.9 8.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Endoglycoceramidase I From Rhodococ-Cus Equi in Complex with GM3


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 GM3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:30.0 occ:1.00 O B:ASP62 2.3 10.4 1.0 O B:HOH879 2.3 17.1 1.0 O B:PRO64 2.4 8.6 1.0 O B:HOH898 2.4 13.9 1.0 O B:HOH873 2.6 13.7 1.0 OD1 B:ASP60 2.6 9.1 1.0 OD2 B:ASP60 2.7 8.8 1.0 CG B:ASP60 3.0 8.9 1.0 C B:ASP62 3.5 10.7 1.0 C B:PRO64 3.5 9.0 1.0 N B:PRO64 4.2 9.9 1.0 CA B:TYR65 4.2 8.3 1.0 C B:ALA63 4.3 9.9 1.0 CA B:ASP62 4.3 11.6 1.0 N B:TYR65 4.3 8.5 1.0 N B:ASP62 4.3 10.3 1.0 CB B:ASP62 4.4 13.4 1.0 N B:ALA63 4.4 10.1 1.0 CA B:PRO64 4.4 9.6 1.0 CB B:ASP60 4.5 8.7 1.0 O B:ALA63 4.5 9.4 1.0 CA B:ALA63 4.6 10.0 1.0 CD B:PRO67 4.6 11.1 1.0 O B:HOH906 4.6 14.5 1.0 N B:LEU66 4.7 8.9 1.0 CG B:PRO67 4.8 11.2 1.0 CD B:PRO64 4.8 10.1 1.0 C B:TYR65 4.9 8.4 1.0 CG B:PRO64 5.0 10.2 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