Calcium 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:

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 Xylotetraose (pdb code 1uyz). 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 Xylotetraose, PDB code: 1uyz:
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 Xylotetraose


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 Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1132 b:13.9 occ:1.00 OE1 A:GLN7 2.3 14.0 1.0 OD1 A:ASN123 2.3 12.9 1.0 O A:LYS29 2.3 14.1 1.0 O A:HOH2074 2.4 18.3 1.0 OE1 A:GLU9 2.4 13.4 1.0 O A:ASN123 2.5 11.9 1.0 OE2 A:GLU9 2.7 16.5 1.0 CD A:GLU9 2.9 13.0 1.0 CD A:GLN7 3.5 13.3 1.0 C A:ASN123 3.5 11.2 1.0 CG A:ASN123 3.5 12.4 1.0 C A:LYS29 3.5 14.6 1.0 CA A:ASN123 3.9 11.2 1.0 CB A:GLN7 4.1 11.4 1.0 N A:LYS29 4.1 16.6 1.0 CG A:GLN7 4.3 13.0 1.0 CB A:ASN123 4.3 11.8 1.0 CA A:LYS29 4.4 16.2 1.0 N A:ALA8 4.4 10.5 1.0 CG A:GLU9 4.4 13.5 1.0 N A:ASN30 4.5 14.2 1.0 NE2 A:GLN7 4.5 15.3 1.0 ND2 A:ASN123 4.5 13.7 1.0 CA A:GLN7 4.5 11.2 1.0 O A:HOH2020 4.5 32.4 1.0 CA A:ASN30 4.6 13.4 1.0 N A:TRP124 4.6 11.4 1.0 O A:HOH2019 4.8 26.8 1.0 CB A:TRP124 4.8 11.8 1.0 C A:GLN7 4.8 10.8 1.0 CD1 A:TRP124 4.9 12.7 1.0 CB A:LYS29 4.9 16.8 1.0 O A:GLY27 5.0 19.9 1.0 O A:HOH2068 5.0 17.9 1.0 O A:HOH2021 5.0 49.4 1.0

Calcium binding site 2 out of 4 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 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 Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1135 b:11.2 occ:1.00 O A:GLY16 2.3 12.0 1.0 OD2 A:ASP38 2.3 11.3 1.0 O A:TYR33 2.3 12.3 1.0 OD2 A:ASP35 2.3 14.8 1.0 O A:HOH2083 2.4 15.8 1.0 C A:GLY16 3.3 11.8 1.0 CG A:ASP38 3.4 11.6 1.0 C A:TYR33 3.4 12.8 1.0 CG A:ASP35 3.4 13.1 1.0 OD1 A:ASP38 3.7 12.2 1.0 N A:ASP35 3.9 12.4 1.0 CB A:ASP35 4.0 12.3 1.0 CA A:GLY16 4.1 12.0 1.0 N A:ILE34 4.2 12.9 1.0 CA A:ILE34 4.3 13.1 1.0 CB A:TYR33 4.3 13.5 1.0 C A:ILE34 4.3 13.2 1.0 N A:THR17 4.3 12.0 1.0 CA A:TYR33 4.4 13.0 1.0 OD1 A:ASP35 4.4 15.2 1.0 CA A:THR17 4.5 12.4 1.0 CA A:ASP35 4.6 12.4 1.0 CB A:ASP38 4.7 11.4 1.0

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


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 Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1132 b:14.5 occ:1.00 OE1 B:GLN7 2.3 14.6 1.0 OD1 B:ASN123 2.3 14.1 1.0 O B:LYS29 2.3 13.9 1.0 O B:HOH2062 2.4 16.9 1.0 OE1 B:GLU9 2.4 14.3 1.0 O B:ASN123 2.5 11.6 1.0 OE2 B:GLU9 2.8 16.1 1.0 CD B:GLU9 3.0 13.8 1.0 C B:ASN123 3.5 11.0 1.0 CG B:ASN123 3.5 12.1 1.0 CD B:GLN7 3.5 14.0 1.0 C B:LYS29 3.5 15.1 1.0 CA B:ASN123 3.9 11.0 1.0 N B:LYS29 4.1 17.1 1.0 CB B:GLN7 4.2 12.1 1.0 CG B:GLN7 4.3 13.5 1.0 CB B:ASN123 4.3 11.6 1.0 CA B:LYS29 4.3 16.3 1.0 N B:ALA8 4.4 11.6 1.0 NE2 B:GLN7 4.5 15.1 1.0 CG B:GLU9 4.5 13.1 1.0 ND2 B:ASN123 4.5 13.6 1.0 N B:ASN30 4.5 14.0 1.0 CA B:GLN7 4.5 11.9 1.0 O B:HOH2007 4.5 30.1 1.0 N B:TRP124 4.6 11.2 1.0 CA B:ASN30 4.6 13.7 1.0 O B:HOH2011 4.7 28.2 1.0 CD1 B:TRP124 4.8 13.6 1.0 CB B:TRP124 4.8 12.2 1.0 C B:GLN7 4.9 11.8 1.0 O B:GLY27 4.9 20.9 1.0 O B:HOH2014 4.9 38.7 1.0 O B:HOH2061 4.9 22.8 1.0 CB B:LYS29 5.0 16.8 1.0

Calcium binding site 4 out of 4 in the Carbohydrate Binding Module (CBM6CM-2) From Cellvibrio Mixtus Lichenase 5A in Complex with Xylotetraose


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 Xylotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1134 b:11.6 occ:1.00 O B:GLY16 2.3 11.3 1.0 O B:HOH2070 2.3 12.1 1.0 O B:TYR33 2.3 11.4 1.0 OD2 B:ASP35 2.3 14.0 1.0 OD2 B:ASP38 2.3 10.7 1.0 O A:HOH2015 2.4 13.9 1.0 C B:GLY16 3.3 11.2 1.0 CG B:ASP35 3.4 12.8 1.0 CG B:ASP38 3.4 11.9 1.0 C B:TYR33 3.4 11.9 1.0 OD1 B:ASP38 3.7 11.8 1.0 N B:ASP35 3.8 12.0 1.0 CB B:ASP35 4.0 12.2 1.0 CA B:GLY16 4.0 11.0 1.0 O B:HOH2071 4.2 17.3 1.0 CA B:ILE34 4.2 11.5 1.0 N B:ILE34 4.2 11.6 1.0 C B:ILE34 4.3 12.1 1.0 O A:HOH2023 4.3 13.5 1.0 CB B:TYR33 4.4 12.9 1.0 N B:THR17 4.4 11.6 1.0 OD1 B:ASP35 4.4 13.2 1.0 O A:THR5 4.5 12.7 1.0 CA B:TYR33 4.5 12.7 1.0 CA B:ASP35 4.5 12.1 1.0 CA B:THR17 4.6 12.0 1.0 CG2 A:THR45 4.7 11.9 1.0 CB B:ASP38 4.7 11.3 1.0 O A:HOH2096 4.8 13.6 1.0 CB A:THR45 5.0 11.3 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