Sodium in PDB 1uyz: Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose

The structure of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose, PDB code: 1uyz was solved by M.Czjzek, V.M.R.Pires, J.Henshaw, J.A.M.Prates, D.Bolam, B.Henrissat, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.70 / 1.6
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.010, 67.394, 85.240, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 17.8

The structure of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose (pdb code 1uyz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose, PDB code: 1uyz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1133 b:13.3 occ:1.00 O A:HOH2082 3.0 20.6 1.0 N A:GLY118 3.2 17.0 1.0 N A:ALA36 3.2 12.8 1.0 CB A:ALA36 3.7 13.5 1.0 CA A:GLY118 3.8 17.1 1.0 CA A:ASP35 4.0 12.4 1.0 C A:ASP35 4.1 12.4 1.0 CA A:ALA36 4.1 13.1 1.0 CB A:ASP35 4.1 12.3 1.0 C A:ALA117 4.2 17.6 1.0 CA A:ALA117 4.3 17.2 1.0 OD1 A:ASP35 4.6 15.2 1.0 C A:GLY118 4.7 16.6 1.0 CG A:ASP35 4.9 13.1 1.0 O A:HOH2177 5.0 34.4 1.0

Sodium binding site 2 out of 3 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1134 b:20.7 occ:1.00 OG1 A:THR94 3.1 19.8 1.0 N A:GLN93 3.3 17.9 1.0 C A:GLN93 3.6 17.9 1.0 N A:THR94 3.6 17.9 1.0 CA A:GLN93 3.8 17.9 1.0 CA A:GLY91 3.8 21.8 1.0 C A:GLY91 3.8 21.0 1.0 N A:TRP92 3.8 19.5 1.0 CB A:GLN93 4.0 17.8 1.0 O A:GLN93 4.1 18.9 1.0 CB A:THR94 4.2 18.3 1.0 O A:HOH2119 4.2 27.3 1.0 O A:GLY91 4.4 19.8 1.0 CA A:THR94 4.4 17.9 1.0 C A:TRP92 4.4 18.4 1.0 O A:HOH2144 4.6 42.0 1.0 CA A:TRP92 4.6 18.7 1.0 N A:GLY91 4.7 23.2 1.0 O A:GLY90 4.9 25.2 1.0

Sodium binding site 3 out of 3 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1133 b:19.5 occ:1.00 OG1 B:THR94 3.2 20.6 1.0 N B:GLN93 3.3 19.1 1.0 C B:GLN93 3.6 19.1 1.0 N B:THR94 3.6 18.9 1.0 CA B:GLN93 3.7 18.9 1.0 CA B:GLY91 3.7 22.3 1.0 N B:TRP92 3.8 20.5 1.0 C B:GLY91 3.8 21.3 1.0 CB B:GLN93 3.9 18.8 1.0 O B:GLN93 4.1 19.8 1.0 O B:HOH2108 4.2 24.7 1.0 CB B:THR94 4.2 19.4 1.0 C B:TRP92 4.4 19.4 1.0 CA B:THR94 4.4 18.8 1.0 O B:GLY91 4.5 21.2 1.0 CA B:TRP92 4.6 19.8 1.0 N B:GLY91 4.7 23.0 1.0 CG B:GLN93 4.9 17.6 1.0

V.M.R.Pires, J.Henshaw, J.A.M.Prates, D.Bolam, L.M.A.Ferreira, C.M.G.A.Fontes, B.Henrissat, A.Planas, H.J.Gilbert, M.Czjzek. The Crystal Structure of the Family 6 Carbohydrate Binding Module From Cellvibrio Mixtus Endoglucanase 5A in Complex with Oligosaccharides Reveals Two Distinct Binding Sites with Different Ligand Specificities J.Biol.Chem. V. 279 21560 2004.
ISSN: ISSN 0021-9258
PubMed: 15010454
DOI: 10.1074/JBC.M401599200