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

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

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Isofagomine Complex, PDB code: 2oyk 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)	53.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.545, 92.919, 94.489, 90.00, 98.32, 90.00
R / Rfree (%)	17.7 / 19.8

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Isofagomine Complex (pdb code 2oyk). 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 Isofagomine Complex, PDB code: 2oyk:
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 Isofagomine 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 Isofagomine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:13.1 occ:1.00 O A:VAL225 2.3 12.6 1.0 O A:HOH683 2.3 13.0 1.0 O A:HOH787 2.4 15.7 1.0 O A:HOH737 2.4 18.9 1.0 O A:ASN222 2.4 15.0 1.0 O A:HOH710 2.4 18.1 1.0 C A:VAL225 3.4 12.7 1.0 C A:ASN222 3.5 15.7 1.0 O A:HOH1058 3.6 26.0 1.0 N A:VAL225 4.0 13.4 1.0 O A:HOH969 4.1 25.8 1.0 CA A:VAL225 4.1 13.0 1.0 OG1 A:THR267 4.1 12.7 1.0 CA A:ASP223 4.2 16.0 1.0 CB A:VAL225 4.2 12.9 1.0 N A:ASP223 4.3 15.7 1.0 C A:ASP223 4.3 15.6 1.0 O A:ALA220 4.3 15.5 1.0 O A:PHE219 4.4 13.5 1.0 N A:ASN222 4.5 16.0 1.0 O A:HOH780 4.5 26.2 1.0 O A:HOH668 4.5 18.9 1.0 CA A:ASN222 4.5 15.5 1.0 N A:VAL226 4.5 12.2 1.0 O A:ASP223 4.6 16.1 1.0 O A:HOH740 4.7 30.3 1.0 O A:HOH1070 4.7 36.3 1.0 N A:ALA224 4.7 15.0 1.0 CA A:VAL226 4.8 12.1 0.5 CG1 A:VAL225 4.8 13.2 1.0 CA A:VAL226 4.9 12.4 0.5 C A:ALA224 4.9 14.2 1.0

Sodium binding site 2 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Isofagomine 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 Isofagomine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:27.3 occ:1.00 O A:HOH916 2.1 24.2 1.0 O A:HOH927 2.3 29.9 1.0 O A:HOH852 2.3 30.2 1.0 O A:THR165 2.4 15.5 1.0 O A:ALA162 2.5 15.1 1.0 C A:THR165 3.5 15.7 1.0 C A:ALA162 3.6 15.2 1.0 O A:HOH748 4.0 21.7 1.0 N A:THR165 4.1 15.0 1.0 CA A:THR165 4.1 15.2 1.0 CB A:THR165 4.1 15.0 1.0 O A:HOH1118 4.3 29.5 1.0 CA A:TRP163 4.4 15.0 1.0 N A:TRP163 4.4 15.2 1.0 C A:TRP163 4.5 15.0 1.0 CA A:ALA162 4.5 15.2 1.0 O A:TRP163 4.6 15.3 1.0 N A:TYR166 4.6 15.8 1.0 CB A:ALA162 4.8 15.4 1.0 CG2 A:THR165 4.9 14.7 1.0 CA A:TYR166 5.0 16.2 1.0

Sodium binding site 3 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Isofagomine 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 Isofagomine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:17.2 occ:1.00 O B:VAL225 2.3 15.3 1.0 O B:HOH770 2.4 19.5 1.0 O B:HOH811 2.4 23.4 1.0 O B:HOH802 2.4 22.7 1.0 O B:HOH740 2.4 17.6 1.0 O B:ASN222 2.4 19.2 1.0 C B:VAL225 3.5 15.2 1.0 C B:ASN222 3.5 19.9 1.0 N B:VAL225 4.0 15.9 1.0 CA B:ASP223 4.1 19.4 1.0 CA B:VAL225 4.1 15.3 1.0 O B:HOH1013 4.1 37.1 1.0 CB B:VAL225 4.2 15.3 1.0 OG1 B:THR267 4.2 16.0 1.0 O B:ALA220 4.2 20.0 1.0 C B:ASP223 4.2 18.9 1.0 N B:ASP223 4.2 19.5 1.0 O B:PHE219 4.4 19.6 1.0 O B:ASP223 4.4 19.4 1.0 O B:HOH805 4.4 23.2 1.0 O B:HOH693 4.5 24.0 1.0 N B:ASN222 4.5 20.2 1.0 CA B:ASN222 4.5 19.8 1.0 N B:VAL226 4.6 14.8 1.0 N B:ALA224 4.7 18.0 1.0 CG1 B:VAL225 4.8 14.6 1.0 CA B:VAL226 4.9 14.7 1.0 C B:ALA224 4.9 16.8 1.0 C B:ALA220 5.0 20.2 1.0

Sodium binding site 4 out of 4 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Cellobiose-Like Isofagomine 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 Isofagomine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:28.4 occ:1.00 O B:HOH977 2.4 30.3 1.0 O B:THR165 2.4 16.8 1.0 O B:ALA162 2.4 16.3 1.0 O B:HOH943 2.5 29.9 1.0 O B:HOH712 2.6 30.2 1.0 C B:ALA162 3.5 16.2 1.0 C B:THR165 3.5 16.5 1.0 O B:HOH702 4.0 20.6 1.0 N B:THR165 4.1 16.1 1.0 CA B:THR165 4.1 15.9 1.0 O B:HOH895 4.1 30.7 1.0 CB B:THR165 4.2 15.9 1.0 CA B:TRP163 4.3 16.0 1.0 N B:TRP163 4.3 16.1 1.0 CA B:ALA162 4.4 16.3 1.0 C B:TRP163 4.5 16.1 1.0 O B:TRP163 4.6 16.0 1.0 N B:TYR166 4.6 16.5 1.0 CB B:ALA162 4.7 16.4 1.0 CG2 B:THR165 5.0 15.7 1.0 O B:HOH1021 5.0 36.4 1.0 CA B:TYR166 5.0 16.8 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