Sodium in PDB 1odz: Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides

All present enzymatic activity of Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides:
3.2.1.78;

The structure of Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides, PDB code: 1odz was solved by M.Jahn, D.Stoll, R.A.J.Warren, L.Szabo, P.Singh, H.J.Gilbert, V.M.A.Ducros, G.J.Davies, S.G.Withers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.40
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	131.855, 131.855, 54.268, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.7

The structure of Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides (pdb code 1odz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides, PDB code: 1odz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1427 b:12.8 occ:1.00 O A:ARG352 2.2 12.4 1.0 O A:ARG69 2.2 12.8 1.0 O A:ILE354 2.3 10.8 1.0 O A:SER72 2.3 13.0 1.0 C A:ARG69 3.3 12.5 1.0 C A:SER72 3.3 13.1 1.0 CG1 A:ILE73 3.3 12.3 1.0 C A:ARG352 3.4 11.8 1.0 C A:ILE354 3.4 10.6 1.0 C A:GLU353 3.5 11.7 1.0 N A:ILE354 3.6 11.1 1.0 CA A:GLU353 3.7 11.5 1.0 CA A:ARG69 3.8 11.8 1.0 N A:GLU353 3.9 11.7 1.0 O A:GLU353 4.0 11.6 1.0 N A:ILE73 4.0 12.3 1.0 CE2 A:PHE404 4.0 14.1 1.0 CA A:ILE73 4.0 11.9 1.0 CA A:ILE354 4.1 10.6 1.0 CZ A:PHE404 4.2 15.7 1.0 CB A:ARG69 4.2 11.5 1.0 CB A:ILE73 4.3 11.9 1.0 N A:SER72 4.3 13.7 1.0 CD1 A:ILE73 4.4 12.2 1.0 N A:ARG70 4.4 13.1 1.0 CA A:SER72 4.4 13.4 1.0 N A:ALA355 4.4 10.3 1.0 CG1 A:ILE354 4.6 11.8 1.0 CA A:ARG352 4.6 12.4 1.0 CA A:ALA355 4.6 10.6 1.0 CA A:ARG70 4.7 13.3 1.0 NE2 A:GLN68 4.8 13.8 1.0 O A:GLN68 4.9 12.9 1.0 N A:HIS71 5.0 12.9 1.0 C A:ALA355 5.0 10.8 1.0 CB A:ILE354 5.0 11.2 1.0

Sodium binding site 2 out of 2 in the Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Expansion of the Glycosynthase Repertoire to Produce Defined Manno- Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1427 b:13.3 occ:1.00 O B:ARG69 2.2 13.2 1.0 O B:ILE354 2.3 11.4 1.0 O B:SER72 2.3 13.0 1.0 O B:ARG352 2.3 12.5 1.0 C B:ARG69 3.2 12.8 1.0 CG1 B:ILE73 3.3 13.3 1.0 C B:SER72 3.3 13.0 1.0 C B:ARG352 3.4 12.2 1.0 C B:ILE354 3.4 12.0 1.0 C B:GLU353 3.5 11.7 1.0 N B:ILE354 3.6 11.6 1.0 CA B:GLU353 3.7 11.4 1.0 CA B:ARG69 3.7 13.1 1.0 N B:GLU353 4.0 11.7 1.0 O B:GLU353 4.0 12.0 1.0 CE2 B:PHE404 4.0 14.9 1.0 N B:ILE73 4.0 13.2 1.0 CA B:ILE73 4.0 12.3 1.0 CA B:ILE354 4.1 11.5 1.0 CZ B:PHE404 4.1 15.9 1.0 CB B:ARG69 4.2 12.3 1.0 CB B:ILE73 4.3 12.4 1.0 N B:SER72 4.3 12.8 1.0 CD1 B:ILE73 4.4 14.4 1.0 N B:ARG70 4.4 12.7 1.0 N B:ALA355 4.4 11.5 1.0 CA B:SER72 4.4 13.6 1.0 CG1 B:ILE354 4.6 12.0 1.0 CA B:ALA355 4.6 11.9 1.0 CA B:ARG352 4.6 12.5 1.0 CA B:ARG70 4.7 13.4 1.0 NE2 B:GLN68 4.8 12.9 1.0 O B:GLN68 4.8 13.3 1.0 N B:HIS71 5.0 13.6 1.0 C B:ALA355 5.0 11.6 1.0

M.Jahn, D.Stoll, R.A.J.Warren, L.Szabo, P.Singh, H.J.Gilbert, V.M.A.Ducros, G.J.Davies, S.G.Withers. Expansion of the Glycosynthase Repertoire to Produce Defined Manno-Oligosaccharides Chem.Commun.(Camb.) V. 12 1327 2003.
ISSN: ISSN 1359-7345
PubMed: 12841226
DOI: 10.1039/B302380J