Sodium in PDB 1uy0: Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Glc-1,3-Glc-1,4-Glc-1,3-Glc

The structure of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Glc-1,3-Glc-1,4-Glc-1,3-Glc, PDB code: 1uy0 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 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.550, 67.650, 85.290, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 17.7

The structure of Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Glc-1,3-Glc-1,4-Glc-1,3-Glc also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
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 Glc-1,3-Glc-1,4-Glc-1,3-Glc (pdb code 1uy0). 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 Glc-1,3-Glc-1,4-Glc-1,3-Glc, PDB code: 1uy0:
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 Glc-1,3-Glc-1,4-Glc-1,3-Glc


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 Glc-1,3-Glc-1,4-Glc-1,3-Glc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1138 b:20.7 occ:1.00 O A:HOH2100 2.7 32.1 1.0 N A:SER105 3.3 17.7 1.0 OG A:SER105 3.3 24.8 1.0 CE1 A:HIS109 3.4 18.7 1.0 NE2 A:HIS81 3.6 18.9 1.0 CB A:SER105 3.8 19.7 1.0 O A:HOH2125 3.9 20.1 1.0 CA A:LEU104 3.9 15.3 1.0 CD2 A:HIS81 4.0 11.3 1.0 C A:LEU104 4.1 16.6 1.0 CA A:SER105 4.2 18.7 1.0 NE2 A:HIS109 4.2 17.6 1.0 ND1 A:HIS109 4.3 15.8 1.0 CD2 A:LEU104 4.4 17.0 1.0 O A:ASN103 4.4 17.6 1.0 CG A:PRO79 4.5 23.8 1.0 CB A:LEU104 4.7 15.5 1.0 CE1 A:HIS81 4.7 14.7 1.0 N A:LEU104 4.9 15.3 1.0 O A:SER105 5.0 19.6 1.0

Sodium binding site 2 out of 3 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Glc-1,3-Glc-1,4-Glc-1,3-Glc


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 Glc-1,3-Glc-1,4-Glc-1,3-Glc within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1138 b:56.2 occ:1.00 NE1 B:TRP124 3.9 18.0 1.0 CE2 B:TRP124 3.9 17.9 1.0 NE2 B:GLN7 4.1 20.4 1.0 CD1 B:TRP124 4.1 17.4 1.0 CG2 B:THR5 4.1 19.1 1.0 CD2 B:TRP124 4.2 15.9 1.0 O B:HOH2011 4.3 33.3 1.0 CG B:TRP124 4.3 15.5 1.0 CZ2 B:TRP124 4.4 16.9 1.0 O B:HOH2006 4.5 27.2 1.0 NH2 B:ARG126 4.5 35.5 1.0 CE3 B:TRP124 4.9 17.8 1.0

Sodium binding site 3 out of 3 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Glc-1,3-Glc-1,4-Glc-1,3-Glc


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 Glc-1,3-Glc-1,4-Glc-1,3-Glc within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1140 b:28.6 occ:1.00 O B:HOH2151 2.5 29.7 1.0 O B:HOH2153 2.9 43.1 1.0 N B:ALA36 3.1 14.7 1.0 N B:GLY118 3.3 17.0 1.0 O B:HOH2034 3.4 30.3 1.0 CB B:ALA36 3.6 14.4 1.0 CA B:GLY118 3.8 17.6 1.0 CA B:ASP35 3.9 14.4 1.0 O B:HOH2074 3.9 24.3 1.0 C B:ASP35 3.9 14.2 1.0 CA B:ALA36 4.0 14.4 1.0 CB B:ASP35 4.2 15.3 1.0 C B:ALA117 4.3 16.7 1.0 CA B:ALA117 4.5 16.5 1.0 O A:HOH2007 4.6 42.1 1.0 C B:GLY118 4.7 17.9 1.0 OD1 B:ASP35 4.7 15.8 1.0 CG B:ASP35 4.9 16.7 1.0 O B:HOH2147 5.0 42.8 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