Sodium in PDB 2oym: Endo-Glycoceramidase II From Rhodococcus Sp.: Five-Membered Iminocyclitol Complex

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

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Five-Membered Iminocyclitol Complex, PDB code: 2oym 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)	18.30 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.786, 93.282, 94.471, 90.00, 98.30, 90.00
R / Rfree (%)	18 / 21.2

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

Sodium binding site 1 out of 2 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Five-Membered Iminocyclitol 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.: Five-Membered Iminocyclitol Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:19.8 occ:1.00 O A:VAL225 2.3 17.0 1.0 O A:HOH733 2.3 17.5 1.0 O A:HOH775 2.4 18.2 1.0 O A:ASN222 2.4 21.6 1.0 O A:HOH788 2.4 20.4 1.0 O A:HOH705 2.4 18.2 1.0 C A:VAL225 3.4 17.5 1.0 C A:ASN222 3.5 23.0 1.0 O A:HOH923 3.6 26.5 1.0 N A:VAL225 4.0 18.6 1.0 O A:HOH956 4.0 31.6 1.0 CA A:VAL225 4.0 17.9 1.0 OG1 A:THR267 4.1 17.4 1.0 O A:ALA220 4.2 23.1 1.0 CB A:VAL225 4.2 17.9 1.0 CA A:ASP223 4.2 23.3 1.0 N A:ASP223 4.3 22.8 1.0 O A:PHE219 4.4 21.4 1.0 C A:ASP223 4.4 22.3 1.0 N A:ASN222 4.4 23.8 1.0 O A:HOH628 4.5 21.0 1.0 CA A:ASN222 4.5 23.2 1.0 O A:HOH801 4.5 30.0 1.0 N A:VAL226 4.6 16.6 1.0 O A:HOH951 4.6 36.7 1.0 O A:ASP223 4.7 22.8 1.0 N A:ALA224 4.8 21.2 1.0 CG1 A:VAL225 4.8 17.5 1.0 CA A:VAL226 4.9 16.9 1.0 C A:ALA220 5.0 23.1 1.0 C A:ALA224 5.0 19.5 1.0 CB A:ASN222 5.0 23.2 1.0

Sodium binding site 2 out of 2 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Five-Membered Iminocyclitol 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.: Five-Membered Iminocyclitol Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:22.9 occ:1.00 O B:VAL225 2.3 19.4 1.0 O B:HOH707 2.3 22.6 1.0 O B:HOH718 2.4 26.1 1.0 O B:HOH798 2.4 25.1 1.0 O B:HOH766 2.4 27.7 1.0 O B:ASN222 2.5 25.5 1.0 C B:VAL225 3.4 19.4 1.0 C B:ASN222 3.5 25.7 1.0 N B:VAL225 4.0 20.7 1.0 CA B:VAL225 4.1 19.7 1.0 CA B:ASP223 4.1 26.0 1.0 OG1 B:THR267 4.1 20.8 1.0 CB B:VAL225 4.2 19.6 1.0 O B:ALA220 4.2 25.5 1.0 N B:ASP223 4.2 25.8 1.0 O B:HOH682 4.3 25.9 1.0 C B:ASP223 4.3 25.2 1.0 O B:HOH892 4.4 34.9 1.0 O B:PHE219 4.5 23.9 1.0 N B:ASN222 4.5 25.8 1.0 N B:VAL226 4.6 18.6 1.0 CA B:ASN222 4.6 25.7 1.0 O B:ASP223 4.6 26.0 1.0 CA B:VAL226 4.8 18.2 1.0 N B:ALA224 4.9 24.1 1.0 CG1 B:VAL225 4.9 19.2 1.0 C B:ALA220 4.9 25.3 1.0 OD1 B:ASP223 4.9 33.3 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: ESSN 0570-0833
PubMed: 17487923
DOI: 10.1002/ANIE.200700268