Calcium 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
Sodium	(Na)	3 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca1131 b:13.3 occ:1.00 O A:GLY16 2.3 14.3 1.0 O A:TYR33 2.3 14.0 1.0 OD2 A:ASP35 2.3 15.8 1.0 OD2 A:ASP38 2.3 14.0 1.0 O A:HOH2054 2.4 21.3 1.0 C A:GLY16 3.3 13.6 1.0 CG A:ASP38 3.4 14.0 1.0 C A:TYR33 3.4 14.7 1.0 CG A:ASP35 3.4 14.6 1.0 OD1 A:ASP38 3.7 14.1 1.0 N A:ASP35 3.9 13.8 1.0 CB A:ASP35 4.0 12.2 1.0 CA A:GLY16 4.0 12.7 1.0 CA A:ILE34 4.2 14.3 1.0 N A:ILE34 4.2 14.1 1.0 C A:ILE34 4.2 14.1 1.0 N A:THR17 4.3 13.9 1.0 O A:HOH2055 4.4 29.0 1.0 CB A:TYR33 4.4 14.9 1.0 OD1 A:ASP35 4.4 16.6 1.0 CA A:TYR33 4.4 14.6 1.0 CA A:THR17 4.5 14.6 1.0 CA A:ASP35 4.6 13.4 1.0 CB A:ASP38 4.7 13.8 1.0

Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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 A:Ca1136 b:26.1 occ:1.00 OD1 A:ASN123 2.3 16.3 1.0 OE1 A:GLN7 2.3 17.2 1.0 O A:LYS29 2.3 18.5 1.0 O A:ASN123 2.5 15.2 1.0 OE1 A:GLU9 2.5 18.4 1.0 O A:HOH2050 2.5 26.5 1.0 OE2 A:GLU9 3.2 23.3 1.0 CD A:GLU9 3.2 20.2 1.0 C A:ASN123 3.4 14.3 1.0 CG A:ASN123 3.5 14.7 1.0 CD A:GLN7 3.5 16.9 1.0 C A:LYS29 3.5 18.1 1.0 CA A:ASN123 3.9 14.3 1.0 CB A:GLN7 4.0 15.3 1.0 N A:LYS29 4.2 19.6 1.0 CG A:GLN7 4.2 16.6 1.0 O A:HOH2006 4.2 30.8 1.0 CB A:ASN123 4.3 14.3 1.0 N A:ALA8 4.3 14.4 1.0 CA A:GLN7 4.4 15.2 1.0 CA A:LYS29 4.4 19.4 1.0 ND2 A:ASN123 4.5 16.2 1.0 N A:ASN30 4.5 16.1 1.0 CA A:ASN30 4.5 14.9 1.0 N A:TRP124 4.5 14.8 1.0 NE2 A:GLN7 4.6 19.7 1.0 CG A:GLU9 4.7 18.3 1.0 C A:GLN7 4.7 14.9 1.0 CB A:TRP124 4.8 14.1 1.0 CD1 A:TRP124 4.9 17.4 1.0 N A:GLU9 5.0 15.2 1.0 CA A:TRP124 5.0 14.4 1.0

Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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:Ca1131 b:16.8 occ:1.00 OD2 B:ASP35 2.3 17.4 1.0 O B:GLY16 2.3 13.6 1.0 O B:TYR33 2.3 14.7 1.0 OD2 B:ASP38 2.4 12.7 1.0 O B:HOH2075 2.4 19.1 1.0 O A:HOH2003 2.4 17.3 1.0 CG B:ASP35 3.3 16.7 1.0 C B:GLY16 3.4 12.8 1.0 CG B:ASP38 3.4 13.4 1.0 C B:TYR33 3.5 14.3 1.0 OD1 B:ASP38 3.7 13.2 1.0 N B:ASP35 3.7 14.6 1.0 CB B:ASP35 3.9 15.3 1.0 CA B:GLY16 4.0 13.6 1.0 CA B:ILE34 4.2 13.9 1.0 N B:ILE34 4.2 14.4 1.0 C B:ILE34 4.2 14.3 1.0 O B:HOH2076 4.3 28.5 1.0 O A:HOH2010 4.3 19.8 1.0 N B:THR17 4.4 14.2 1.0 OD1 B:ASP35 4.4 15.8 1.0 CB B:TYR33 4.4 14.7 1.0 O A:THR5 4.4 15.4 1.0 CA B:ASP35 4.4 14.4 1.0 CA B:TYR33 4.5 14.8 1.0 CA B:THR17 4.6 13.7 1.0 CB B:ASP38 4.8 13.2 1.0 O A:HOH2066 4.8 19.4 1.0 CG2 A:THR45 4.9 13.8 1.0

Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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:Ca1137 b:25.4 occ:1.00 OD1 B:ASN123 2.2 18.0 1.0 O B:LYS29 2.3 17.8 1.0 OE1 B:GLN7 2.4 19.8 1.0 O B:HOH2015 2.4 26.4 1.0 OE1 B:GLU9 2.5 20.2 1.0 O B:ASN123 2.5 15.3 1.0 CD B:GLU9 3.2 21.2 1.0 OE2 B:GLU9 3.3 25.5 1.0 CG B:ASN123 3.4 15.3 1.0 C B:ASN123 3.4 14.1 1.0 C B:LYS29 3.5 18.6 1.0 CD B:GLN7 3.6 18.4 1.0 CA B:ASN123 3.9 14.8 1.0 CB B:GLN7 4.1 16.4 1.0 N B:LYS29 4.2 21.2 1.0 CB B:ASN123 4.2 14.7 1.0 N B:ALA8 4.3 14.2 1.0 CG B:GLN7 4.3 17.8 1.0 O B:HOH2011 4.3 33.3 1.0 CA B:LYS29 4.4 19.8 1.0 ND2 B:ASN123 4.4 17.3 1.0 CA B:GLN7 4.4 15.1 1.0 N B:ASN30 4.5 17.3 1.0 O B:HOH2010 4.5 40.0 1.0 CA B:ASN30 4.5 17.0 1.0 N B:TRP124 4.5 14.3 1.0 NE2 B:GLN7 4.6 20.4 1.0 CG B:GLU9 4.7 19.5 1.0 C B:GLN7 4.7 15.3 1.0 CB B:TRP124 4.8 14.3 1.0 CD1 B:TRP124 4.9 17.4 1.0 N B:GLU9 5.0 14.9 1.0 CA B:TRP124 5.0 14.5 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