Sodium in PDB 2oyl: Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex

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

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex, PDB code: 2oyl 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)	53.15 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.752, 93.246, 94.432, 90.00, 98.35, 90.00
R / Rfree (%)	17.4 / 20.5

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex (pdb code 2oyl). 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.: Cellobiose-Like Imidazole Complex, PDB code: 2oyl:
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.: Cellobiose-Like Imidazole Complex


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.: Cellobiose-Like Imidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:16.7 occ:1.00 O A:HOH812 2.3 21.2 1.0 O A:VAL225 2.3 14.4 1.0 O A:HOH771 2.4 15.9 1.0 O A:ASN222 2.4 17.5 1.0 O A:HOH707 2.4 17.6 1.0 O A:HOH763 2.5 18.6 1.0 C A:VAL225 3.5 14.4 1.0 C A:ASN222 3.5 18.5 1.0 O A:HOH1074 3.7 33.1 1.0 N A:VAL225 4.0 15.4 1.0 CA A:VAL225 4.1 15.0 1.0 OG1 A:THR267 4.1 15.7 1.0 CB A:VAL225 4.2 15.1 1.0 O A:ALA220 4.3 18.8 1.0 CA A:ASP223 4.3 18.8 1.0 N A:ASP223 4.3 18.3 1.0 O A:PHE219 4.4 16.8 1.0 O A:HOH747 4.4 27.1 1.0 C A:ASP223 4.4 18.3 1.0 O A:HOH659 4.4 20.3 1.0 N A:ASN222 4.5 19.1 1.0 CA A:ASN222 4.5 18.6 1.0 N A:VAL226 4.6 13.8 1.0 O A:ASP223 4.6 18.8 1.0 O A:HOH881 4.6 34.2 1.0 O A:HOH760 4.7 38.7 1.0 N A:ALA224 4.8 17.6 1.0 CA A:VAL226 4.9 13.7 0.5 CG1 A:VAL225 4.9 14.8 1.0 CA A:VAL226 4.9 13.5 0.5 C A:ALA220 5.0 18.8 1.0 C A:ALA224 5.0 16.5 1.0

Sodium binding site 2 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex


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.: Cellobiose-Like Imidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:32.5 occ:1.00 O A:HOH1035 2.1 23.5 1.0 O A:HOH1034 2.3 35.7 1.0 O A:HOH927 2.3 34.2 1.0 O A:THR165 2.3 17.6 1.0 O A:ALA162 2.5 17.4 1.0 C A:THR165 3.4 17.9 1.0 C A:ALA162 3.6 17.8 1.0 N A:THR165 4.0 17.4 1.0 CA A:THR165 4.1 17.1 1.0 O A:HOH781 4.1 22.7 1.0 CB A:THR165 4.1 16.9 1.0 CA A:TRP163 4.4 17.7 1.0 C A:TRP163 4.4 17.6 1.0 N A:TRP163 4.4 17.8 1.0 O A:TRP163 4.4 17.5 1.0 N A:TYR166 4.5 18.5 1.0 CA A:ALA162 4.6 17.7 1.0 CA A:TYR166 4.8 19.2 1.0 CD1 A:TYR166 4.9 22.1 1.0 CG2 A:THR165 4.9 16.1 1.0 N A:ALA164 4.9 17.2 1.0 CB A:ALA162 5.0 18.0 1.0

Sodium binding site 3 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex


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.: Cellobiose-Like Imidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:19.6 occ:1.00 O B:VAL225 2.3 17.6 1.0 O B:HOH726 2.4 22.1 1.0 O B:HOH795 2.4 22.9 1.0 O B:ASN222 2.4 20.7 1.0 O B:HOH781 2.4 22.0 1.0 O B:HOH802 2.5 28.3 1.0 C B:ASN222 3.5 20.7 1.0 C B:VAL225 3.5 16.9 1.0 N B:VAL225 4.0 17.5 1.0 CA B:ASP223 4.0 20.6 1.0 CA B:VAL225 4.1 17.2 1.0 CB B:VAL225 4.2 17.0 1.0 N B:ASP223 4.2 20.5 1.0 O B:ALA220 4.2 21.1 1.0 C B:ASP223 4.2 20.3 1.0 O B:HOH834 4.2 26.7 1.0 OG1 B:THR267 4.2 18.3 1.0 O B:HOH968 4.3 36.0 1.0 O B:ASP223 4.4 21.2 1.0 O B:PHE219 4.4 19.8 1.0 N B:ASN222 4.4 21.1 1.0 O B:HOH738 4.5 26.9 1.0 CA B:ASN222 4.5 20.8 1.0 N B:VAL226 4.6 16.3 1.0 N B:ALA224 4.7 19.4 1.0 CG1 B:VAL225 4.8 16.9 1.0 CA B:VAL226 4.9 16.2 1.0 C B:ALA224 4.9 18.1 1.0 C B:ALA220 4.9 20.9 1.0

Sodium binding site 4 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Imidazole Complex


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.: Cellobiose-Like Imidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:41.5 occ:1.00 O B:HOH736 2.3 29.7 1.0 O B:HOH924 2.3 30.0 1.0 O B:THR165 2.4 18.2 1.0 O B:ALA162 2.5 18.7 1.0 C B:THR165 3.5 18.5 1.0 C B:ALA162 3.6 18.3 1.0 O B:HOH702 4.0 19.1 1.0 N B:THR165 4.1 18.1 1.0 O B:HOH893 4.1 36.0 1.0 CA B:THR165 4.1 17.8 1.0 CB B:THR165 4.2 17.8 1.0 CA B:TRP163 4.3 17.7 1.0 N B:TRP163 4.4 18.1 1.0 C B:TRP163 4.4 17.7 1.0 O B:TRP163 4.5 17.0 1.0 CA B:ALA162 4.5 18.3 1.0 N B:TYR166 4.6 18.5 1.0 CB B:ALA162 4.9 18.5 1.0 CG2 B:THR165 5.0 16.9 1.0 N B:ALA164 5.0 17.7 1.0 CA B:TYR166 5.0 19.0 1.0

M.E.Caines, S.M.Hancock, C.A.Tarling, T.M.Wrodnigg, R.V.Stick, A.E.Stutz, A.Vasella, S.G.Withers, N.C.Strynadka. The Structural Basis of Glycosidase Inhibition By Five-Membered Iminocyclitols: the Clan A Glycoside Hydrolase Endoglycoceramidase As A Model System. Angew.Chem.Int.Ed.Engl. V. 46 4474 2007.
ISSN: ISSN 1433-7851
PubMed: 17487923
DOI: 10.1002/ANIE.200700268