Sodium in PDB 2osy: Endo-Glycoceramidase II From Rhodococcus Sp.: Lactosyl-Enzyme Intermediate

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

The structure of Endo-Glycoceramidase II From Rhodococcus Sp.: Lactosyl-Enzyme Intermediate, PDB code: 2osy 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)	18.73 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.947, 93.687, 94.460, 90.00, 98.12, 90.00
R / Rfree (%)	20.5 / 25.1

The binding sites of Sodium atom in the Endo-Glycoceramidase II From Rhodococcus Sp.: Lactosyl-Enzyme Intermediate (pdb code 2osy). 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.: Lactosyl-Enzyme Intermediate, PDB code: 2osy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Lactosyl-Enzyme Intermediate


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.: Lactosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:23.6 occ:1.00 O A:HOH756 2.2 24.8 1.0 O A:HOH757 2.3 26.4 1.0 O A:HOH755 2.3 20.9 1.0 O A:HOH758 2.3 22.2 1.0 O A:VAL225 2.4 22.6 1.0 O A:ASN222 2.4 27.8 1.0 C A:ASN222 3.5 28.0 1.0 C A:VAL225 3.5 23.1 1.0 N A:VAL225 4.0 24.6 1.0 CA A:ASP223 4.0 28.1 1.0 CA A:VAL225 4.1 23.4 1.0 OG1 A:THR267 4.1 19.7 1.0 N A:ASP223 4.2 28.1 1.0 O A:ALA220 4.3 26.7 1.0 C A:ASP223 4.3 27.6 1.0 CB A:VAL225 4.3 23.5 1.0 O A:HOH687 4.3 22.5 1.0 O A:PHE219 4.4 25.1 1.0 N A:ASN222 4.5 28.4 1.0 O A:ASP223 4.5 28.2 1.0 CA A:ASN222 4.5 27.8 1.0 O A:HOH764 4.6 32.4 1.0 N A:VAL226 4.6 22.1 1.0 O A:HOH680 4.8 31.9 1.0 N A:ALA224 4.8 26.9 1.0 C A:ALA224 4.9 24.9 1.0 CA A:VAL226 4.9 22.0 1.0 CG1 A:VAL225 4.9 22.0 1.0

Sodium binding site 2 out of 2 in the Endo-Glycoceramidase II From Rhodococcus Sp.: Lactosyl-Enzyme Intermediate


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.: Lactosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:27.6 occ:1.00 O B:HOH676 2.3 24.7 1.0 O B:VAL225 2.3 22.9 1.0 O B:HOH705 2.3 27.4 1.0 O B:ASN222 2.4 29.2 1.0 C B:VAL225 3.4 23.3 1.0 C B:ASN222 3.4 29.3 1.0 N B:VAL225 4.0 24.7 1.0 CA B:VAL225 4.0 23.5 1.0 CA B:ASP223 4.1 29.7 1.0 CB B:VAL225 4.1 23.6 1.0 N B:ASP223 4.2 29.2 1.0 OG1 B:THR267 4.2 22.8 1.0 C B:ASP223 4.2 28.5 1.0 O B:ALA220 4.3 27.1 1.0 O B:PHE219 4.4 26.0 1.0 N B:ASN222 4.4 29.6 1.0 CA B:ASN222 4.5 29.4 1.0 O B:HOH679 4.5 30.8 1.0 O B:ASP223 4.5 28.7 1.0 N B:VAL226 4.5 22.9 1.0 N B:ALA224 4.7 27.0 1.0 CG1 B:VAL225 4.8 21.5 1.0 CA B:VAL226 4.8 23.1 1.0 C B:ALA224 4.9 25.6 1.0 C B:ALA220 5.0 27.9 1.0 CB B:ASN222 5.0 29.1 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