Sodium in PDB 2osw: Endo-Glycoceramidase II From Rhodococcus Sp.

All present enzymatic activity of Endo-Glycoceramidase II From Rhodococcus Sp.:
3.2.1.123;

The structure of Endo-Glycoceramidase II From Rhodococcus Sp., PDB code: 2osw was solved by M.E.C.Caines, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.750, 92.941, 94.545, 90.00, 98.55, 90.00
R / Rfree (%)	18.1 / 20.4

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp. (pdb code 2osw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Endo-Glycoceramidase II From Rhodococcus Sp., PDB code: 2osw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endo-Glycoceramidase II From Rhodococcus Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:15.8 occ:1.00 O A:VAL225 2.3 14.4 1.0 O A:HOH691 2.4 15.8 1.0 O A:HOH808 2.4 19.3 1.0 O A:HOH715 2.4 18.3 1.0 O A:ASN222 2.4 17.6 1.0 O A:HOH687 2.4 19.1 1.0 C A:VAL225 3.5 14.3 1.0 O A:HOH943 3.5 27.1 1.0 C A:ASN222 3.5 18.3 1.0 N A:VAL225 4.0 15.1 1.0 CA A:VAL225 4.1 14.8 1.0 O A:HOH921 4.1 28.2 1.0 OG1 A:THR267 4.2 14.8 1.0 CB A:VAL225 4.2 14.7 1.0 CA A:ASP223 4.2 18.5 1.0 N A:ASP223 4.3 18.3 1.0 C A:ASP223 4.3 17.8 1.0 O A:ALA220 4.3 17.6 1.0 O A:PHE219 4.4 16.4 1.0 N A:ASN222 4.5 18.9 1.0 O A:ASP223 4.5 18.3 1.0 O A:HOH620 4.5 21.9 1.0 CA A:ASN222 4.5 18.5 1.0 O A:HOH740 4.5 25.6 1.0 N A:VAL226 4.6 13.7 1.0 O A:HOH804 4.7 34.9 1.0 CG1 A:VAL225 4.8 15.3 1.0 N A:ALA224 4.8 17.0 1.0 CA A:VAL226 4.8 13.7 0.5 CA A:VAL226 4.8 13.4 0.5 C A:ALA224 5.0 15.8 1.0

Sodium binding site 2 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Endo-Glycoceramidase II From Rhodococcus Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:33.0 occ:1.00 O A:HOH1063 2.2 25.8 1.0 O A:HOH1062 2.3 33.2 1.0 O A:HOH900 2.3 30.8 1.0 O A:THR165 2.4 17.3 1.0 O A:ALA162 2.6 16.9 1.0 C A:THR165 3.5 17.5 1.0 C A:ALA162 3.7 16.9 1.0 N A:THR165 4.1 16.8 1.0 O A:HOH767 4.1 24.8 1.0 CA A:THR165 4.1 17.0 1.0 CB A:THR165 4.1 17.0 1.0 CA A:TRP163 4.4 16.9 1.0 C A:TRP163 4.5 16.9 1.0 O A:TRP163 4.5 17.0 1.0 N A:TRP163 4.5 17.0 1.0 N A:TYR166 4.6 17.7 1.0 CA A:ALA162 4.7 17.0 1.0 CA A:TYR166 4.9 18.1 1.0 CG2 A:THR165 4.9 16.9 1.0

Sodium binding site 3 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Endo-Glycoceramidase II From Rhodococcus Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:20.3 occ:1.00 O B:HOH845 2.3 25.1 1.0 O B:HOH766 2.3 24.8 1.0 O B:VAL225 2.3 16.9 1.0 O B:HOH763 2.3 23.1 1.0 O B:HOH779 2.4 26.4 1.0 O B:ASN222 2.5 19.1 1.0 C B:VAL225 3.5 16.9 1.0 C B:ASN222 3.5 19.9 1.0 N B:VAL225 4.1 17.4 1.0 CA B:ASP223 4.1 20.0 1.0 CA B:VAL225 4.1 17.1 1.0 OG1 B:THR267 4.2 17.4 1.0 O B:ALA220 4.2 20.3 1.0 CB B:VAL225 4.2 17.2 1.0 O B:HOH851 4.2 27.1 1.0 N B:ASP223 4.2 19.8 1.0 C B:ASP223 4.3 19.7 1.0 O B:HOH937 4.3 37.3 1.0 O B:PHE219 4.4 19.4 1.0 N B:ASN222 4.5 20.5 1.0 O B:ASP223 4.5 20.1 1.0 O B:HOH683 4.5 26.1 1.0 CA B:ASN222 4.5 20.0 1.0 N B:VAL226 4.6 16.4 1.0 O B:HOH969 4.7 39.7 1.0 N B:ALA224 4.7 18.8 1.0 CG1 B:VAL225 4.9 16.8 1.0 CA B:VAL226 4.9 16.5 1.0 C B:ALA220 4.9 20.4 1.0 C B:ALA224 5.0 18.0 1.0

Sodium binding site 4 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Endo-Glycoceramidase II From Rhodococcus Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:30.7 occ:1.00 O B:HOH889 2.3 29.4 1.0 O B:THR165 2.5 18.7 1.0 O B:ALA162 2.5 18.7 1.0 O B:HOH684 2.7 32.7 1.0 C B:THR165 3.6 18.8 1.0 C B:ALA162 3.6 18.4 1.0 O B:HOH781 4.0 23.0 1.0 N B:THR165 4.1 18.4 1.0 CA B:THR165 4.2 18.0 1.0 CB B:THR165 4.2 18.3 1.0 CA B:TRP163 4.4 18.3 1.0 N B:TRP163 4.4 18.4 1.0 CA B:ALA162 4.5 18.5 1.0 C B:TRP163 4.5 18.5 1.0 O B:TRP163 4.6 18.5 1.0 N B:TYR166 4.7 18.6 1.0 CB B:ALA162 4.8 18.6 1.0 CG2 B:THR165 5.0 17.4 1.0

M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, N.C.Strynadka. Structural and Mechanistic Analyses of Endo-Glycoceramidase II, A Membrane-Associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-Bound Forms. J.Biol.Chem. V. 282 14300 2007.
ISSN: ISSN 0021-9258
PubMed: 17329247
DOI: 10.1074/JBC.M611455200