Calcium in PDB 2yb7: CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose

The structure of CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose, PDB code: 2yb7 was solved by C.Y.Montanier, M.A.S.Correia, J.E.Flint, Y.Zhu, L.S.Mckee, J.A.M.Prates, S.J.Polizzi, P.M.Coutinho, B.Henrissat, C.M.G.A.Fontes, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	110.43 / 1.70
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	191.352, 191.352, 191.352, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.6

The binding sites of Calcium atom in the CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose (pdb code 2yb7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose, PDB code: 2yb7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1880 b:12.8 occ:1.00 OE1 A:GLU869 2.3 14.1 1.0 O A:LYS763 2.3 13.5 1.0 O A:ASP768 2.3 12.9 1.0 O A:ALA868 2.4 10.9 1.0 OG1 A:THR771 2.5 12.2 1.0 OD1 A:ASP766 2.5 13.9 1.0 O A:THR771 2.5 12.1 1.0 C A:THR771 3.5 12.6 1.0 C A:ASP768 3.5 12.1 1.0 C A:LYS763 3.5 12.9 1.0 CG A:ASP766 3.5 13.3 1.0 CD A:GLU869 3.5 9.8 1.0 C A:ALA868 3.6 9.6 1.0 CB A:THR771 3.7 11.7 1.0 OD2 A:ASP766 3.8 14.0 1.0 CA A:THR771 3.9 11.8 1.0 N A:ASP768 4.0 12.1 1.0 N A:THR771 4.0 11.8 1.0 CA A:ASP768 4.2 12.7 1.0 CA A:ALA764 4.2 10.9 1.0 CB A:ASP768 4.3 10.4 1.0 OE2 A:GLU869 4.3 14.0 1.0 N A:ALA764 4.3 11.8 1.0 N A:PHE772 4.4 13.2 1.0 CA A:ALA868 4.4 11.7 1.0 CA A:GLU869 4.4 9.8 1.0 N A:LEU769 4.4 11.3 1.0 CB A:GLU869 4.5 10.8 1.0 CA A:LYS763 4.5 10.8 1.0 C A:ALA764 4.5 10.4 1.0 N A:GLU869 4.5 10.1 1.0 N A:ASP766 4.6 11.4 1.0 CA A:LEU769 4.6 11.3 1.0 CG A:GLU869 4.6 12.4 1.0 CB A:LYS763 4.7 10.5 1.0 CB A:ALA868 4.7 11.5 1.0 CA A:PHE772 4.8 12.2 1.0 N A:GLY767 4.8 11.7 1.0 N A:PHE765 4.8 11.5 1.0 CB A:ASP766 4.8 13.1 1.0 CG2 A:THR771 4.8 13.4 1.0 C A:LEU769 4.8 12.6 1.0 O A:ALA764 4.9 13.6 1.0

Calcium binding site 2 out of 2 in the CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CBM62 in Complex with 6-Alpha-D-Galactosyl-Mannotriose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1879 b:12.7 occ:1.00 OE1 B:GLU869 2.3 13.2 1.0 O B:LYS763 2.3 12.8 1.0 O B:ASP768 2.3 11.2 1.0 O B:ALA868 2.4 11.4 1.0 OD1 B:ASP766 2.5 12.9 1.0 OG1 B:THR771 2.5 13.9 1.0 O B:THR771 2.6 13.3 1.0 C B:THR771 3.4 12.6 1.0 CG B:ASP766 3.5 13.0 1.0 C B:ASP768 3.5 10.8 1.0 CD B:GLU869 3.5 10.2 1.0 C B:LYS763 3.5 13.9 1.0 C B:ALA868 3.6 9.6 1.0 CB B:THR771 3.7 15.1 1.0 OD2 B:ASP766 3.8 14.2 1.0 CA B:THR771 3.9 13.8 1.0 N B:ASP768 4.0 11.4 1.0 N B:THR771 4.0 13.8 1.0 CA B:ALA764 4.2 10.2 1.0 CA B:ASP768 4.2 11.9 1.0 OE2 B:GLU869 4.3 14.9 1.0 CA B:ALA868 4.4 10.4 1.0 N B:ALA764 4.4 11.6 1.0 N B:PHE772 4.4 13.2 1.0 CB B:ASP768 4.4 12.4 1.0 CA B:GLU869 4.4 10.6 1.0 CA B:LYS763 4.5 13.1 1.0 CB B:GLU869 4.5 10.1 1.0 N B:LEU769 4.5 10.1 1.0 C B:ALA764 4.5 9.9 1.0 N B:GLU869 4.5 9.2 1.0 N B:ASP766 4.6 10.4 1.0 CG B:GLU869 4.6 11.9 1.0 CA B:LEU769 4.6 11.4 1.0 CB B:ALA868 4.6 10.8 1.0 CB B:LYS763 4.7 10.3 1.0 CA B:PHE772 4.8 12.7 1.0 CB B:ASP766 4.8 12.8 1.0 N B:PHE765 4.8 11.6 1.0 N B:GLY767 4.8 12.1 1.0 C B:LEU769 4.8 11.9 1.0 CG2 B:THR771 4.9 14.8 1.0 O B:ALA764 4.9 12.5 1.0

C.Y.Montanier, M.A.S.Correia, J.E.Flint, Y.Zhu, A.Basle, L.S.Mckee, J.A.M.Prates, S.J.Polizzi, P.M.Coutinho, R.J.Lewis, B.Henrissat, C.M.G.A.Fontes, H.J.Gilbert. A Novel, Noncatalytic Carbohydrate-Binding Module Displays Specificity For Galactose-Containing Polysaccharides Through Calcium-Mediated Oligomerization. J.Biol.Chem. V. 286 22499 2011.
ISSN: ISSN 0021-9258
PubMed: 21454512
DOI: 10.1074/JBC.M110.217372