Calcium in PDB 2xfd: VCBM60 in Complex with Cellobiose

The structure of VCBM60 in Complex with Cellobiose, PDB code: 2xfd was solved by C.Montanier, J.E.Flint, D.N.Bolam, H.Xie, Z.Liu, A.Rogowski, D.P.Weiner, D.Nurizzo, S.M.Roberts, J.P.Turkenburg, G.J.Davies, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.04 / 1.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.610, 41.990, 80.080, 90.00, 90.00, 90.00
R / Rfree (%)	11.699 / 14.795

The binding sites of Calcium atom in the VCBM60 in Complex with Cellobiose (pdb code 2xfd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the VCBM60 in Complex with Cellobiose, PDB code: 2xfd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the VCBM60 in Complex with Cellobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of VCBM60 in Complex with Cellobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1111 b:10.2 occ:1.00 O A:HIS100 2.3 10.2 1.0 OD2 A:ASP60 2.3 9.3 1.0 O A:ARG59 2.4 9.8 1.0 O A:HOH2100 2.4 14.2 1.0 OD1 A:ASP55 2.4 10.3 1.0 O3 A:CBI1113 2.5 13.2 1.0 O2 A:CBI1113 2.6 12.6 1.0 C3 A:CBI1113 3.3 13.1 1.0 CG A:ASP55 3.4 11.1 1.0 CG A:ASP60 3.4 8.7 1.0 C2 A:CBI1113 3.4 12.3 1.0 C A:HIS100 3.4 8.5 1.0 C A:ARG59 3.6 6.8 1.0 OD2 A:ASP55 3.7 12.3 1.0 CA A:HIS100 4.0 7.9 1.0 OD1 A:ASP60 4.1 13.2 1.0 O A:ALA56 4.1 12.3 1.0 O A:HOH2170 4.2 16.4 1.0 CA A:ASP60 4.3 6.0 1.0 O A:HOH2169 4.3 31.1 1.0 N A:ASP60 4.3 6.4 1.0 CB A:ASP60 4.4 7.0 1.0 CE2 A:PHE52 4.5 7.3 1.0 CB A:HIS100 4.5 9.5 1.0 N A:CYS101 4.5 9.7 1.0 O A:HOH2107 4.6 21.5 1.0 CA A:ARG59 4.6 8.4 1.0 CB A:ASP55 4.7 10.5 1.0 N A:ARG59 4.7 9.9 1.0 C4 A:CBI1113 4.7 16.1 1.0 C1 A:CBI1113 4.8 14.3 1.0 CZ A:PHE52 4.8 6.8 1.0 CA A:CYS101 5.0 10.4 1.0 N A:ALA56 5.0 11.1 1.0

Calcium binding site 2 out of 2 in the VCBM60 in Complex with Cellobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of VCBM60 in Complex with Cellobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1112 b:6.0 occ:1.00 OE1 A:GLN74 2.3 6.8 1.0 OD1 A:ASP64 2.3 6.5 1.0 OE2 A:GLU97 2.3 7.6 1.0 O A:HOH2110 2.4 12.0 1.0 OE2 A:GLU76 2.5 5.5 1.0 O A:ASP64 2.5 4.5 1.0 OE1 A:GLU76 2.5 8.4 1.0 CD A:GLU76 2.8 6.1 1.0 C A:ASP64 3.4 4.3 1.0 CD A:GLU97 3.5 6.7 1.0 CD A:GLN74 3.5 6.8 1.0 CG A:ASP64 3.5 6.3 1.0 CA A:ASP64 3.7 4.9 1.0 CG A:GLU97 4.0 6.0 1.0 CB A:ASP64 4.2 5.0 1.0 CB A:GLN74 4.3 4.7 1.0 CG A:GLU76 4.3 6.8 1.0 NE2 A:GLN74 4.4 10.4 1.0 CG A:GLN74 4.4 5.9 1.0 O A:HOH2155 4.4 18.1 0.5 O A:HOH2111 4.5 17.3 1.0 OD2 A:ASP64 4.5 8.6 1.0 N A:TYR65 4.5 3.9 1.0 OE1 A:GLU97 4.5 9.5 1.0 N A:ALA75 4.6 3.8 1.0 O A:HOH2126 4.6 30.1 1.0 O A:HOH2156 4.7 22.0 0.5 CA A:GLN74 4.7 3.8 1.0 CB A:TYR65 4.8 4.7 1.0 O A:VAL63 4.8 5.3 1.0 CD2 A:TYR65 4.8 6.2 1.0

C.Montanier, J.E.Flint, D.N.Bolam, H.Xie, Z.Liu, A.Rogowski, D.P.Weiner, S.Ratnaparkhe, D.Nurizzo, S.M.Roberts, J.P.Turkenburg, G.J.Davies, H.J.Gilbert. Circular Permutation Provides An Evolutionary Link Between Two Families of Calcium-Dependent Carbohydrate Binding Modules. J.Biol.Chem. V. 285 31742 2010.
ISSN: ISSN 0021-9258
PubMed: 20659893
DOI: 10.1074/JBC.M110.142133