Calcium in PDB 2w87: Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide.

The structure of Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide., PDB code: 2w87 was solved by C.Montainer, A.L.V.Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.G.A.Fontes, G.J.Davies, A.B.Boraston, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.15 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.850, 45.450, 48.910, 71.79, 89.74, 81.28
R / Rfree (%)	14.3 / 19.3

The binding sites of Calcium atom in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide. (pdb code 2w87). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide., PDB code: 2w87:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1148 b:11.7 occ:1.00 OD1 A:ASN40 2.3 11.2 1.0 O A:THR41 2.4 10.7 1.0 O6A A:GCU1150 2.4 13.3 1.0 O A:HOH2054 2.4 14.8 1.0 O A:HOH2126 2.5 11.8 1.0 O A:HOH2132 2.5 11.4 1.0 OD1 A:ASN43 2.6 14.5 0.5 OD1 A:ASN43 2.6 18.6 0.5 O4 A:GCU1150 2.7 14.9 1.0 C6 A:GCU1150 3.5 13.9 1.0 CG A:ASN40 3.5 10.7 1.0 C A:THR41 3.6 11.5 1.0 CG A:ASN43 3.7 13.4 0.5 CG A:ASN43 3.8 17.1 0.5 C4 A:GCU1150 3.9 13.2 1.0 C5 A:GCU1150 3.9 14.0 1.0 N A:THR41 4.0 10.8 1.0 OG1 A:THR41 4.1 11.5 1.0 ND2 A:ASN40 4.2 13.7 1.0 C A:ASN40 4.3 10.5 1.0 ND2 A:ASN43 4.3 12.1 0.5 CA A:THR41 4.3 10.7 1.0 OD1 A:ASN130 4.3 10.1 1.0 NH1 A:ARG75 4.4 12.0 1.0 ND2 A:ASN43 4.4 18.9 0.5 O A:HOH2051 4.4 25.4 1.0 O A:LEU128 4.4 11.7 1.0 C A:ASN42 4.5 13.0 1.0 O6B A:GCU1150 4.5 14.2 1.0 N A:ASN43 4.6 13.8 1.0 N A:ASN42 4.6 12.0 1.0 O A:ASN42 4.7 12.4 1.0 CA A:ASN40 4.7 10.6 1.0 O A:HOH2146 4.7 26.8 1.0 CB A:ASN40 4.7 10.8 1.0 O A:GLU126 4.7 14.1 1.0 O A:ASN40 4.8 12.0 1.0 CB A:THR41 4.9 10.7 1.0 CA A:ASN42 4.9 12.9 1.0 CB A:ASN43 4.9 14.2 0.5 C3 A:GCU1150 4.9 13.7 1.0 CB A:ASN43 5.0 15.3 0.5 OAN A:UNL1151 5.0 27.4 1.0 CA A:ASN43 5.0 14.7 0.5 CA A:ASN43 5.0 14.1 0.5

Calcium binding site 2 out of 4 in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1149 b:11.0 occ:1.00 OE1 A:GLN13 2.2 11.6 1.0 O A:THR34 2.4 12.6 1.0 O A:ASP132 2.4 9.2 1.0 O A:GLY37 2.4 10.5 1.0 OD1 A:ASP132 2.4 10.4 1.0 OE1 A:GLU14 2.5 11.0 1.0 OE2 A:GLU14 2.5 12.3 1.0 CD A:GLU14 2.8 12.3 1.0 C A:ASP132 3.4 10.1 1.0 CD A:GLN13 3.4 12.8 1.0 C A:THR34 3.4 14.4 1.0 CG A:ASP132 3.5 9.8 1.0 C A:GLY37 3.5 11.4 1.0 CA A:ASP132 3.9 9.6 1.0 NE2 A:GLN13 4.1 13.0 1.0 N A:THR34 4.1 14.2 1.0 N A:GLY37 4.2 13.1 1.0 OG1 A:THR34 4.2 13.0 1.0 CB A:ASP132 4.3 10.0 1.0 N A:GLY35 4.3 14.8 1.0 OD2 A:ASP132 4.3 12.5 1.0 CA A:GLY35 4.3 14.8 1.0 CA A:THR34 4.3 14.1 1.0 CG A:GLU14 4.4 13.2 1.0 N A:PHE38 4.4 10.3 1.0 CA A:GLY37 4.5 12.0 1.0 O A:HOH2008 4.5 10.6 1.0 CA A:PHE38 4.5 9.9 1.0 N A:SER133 4.5 9.8 1.0 CB A:GLN13 4.5 12.6 1.0 CG A:GLN13 4.5 12.0 1.0 C A:GLY35 4.7 14.9 1.0 CB A:PHE33 4.7 13.4 1.0 CB A:SER133 4.7 11.6 1.0 CA A:GLN13 4.8 12.5 1.0 N A:GLU14 4.8 12.7 1.0 N A:SER36 4.8 14.4 1.0 CA A:SER133 4.9 11.0 1.0 CB A:THR34 4.9 14.2 1.0

Calcium binding site 3 out of 4 in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1150 b:11.8 occ:1.00 O B:THR41 2.4 10.7 1.0 O6A B:GCU1148 2.4 14.2 1.0 OD1 B:ASN40 2.4 10.6 1.0 O B:HOH2141 2.5 10.4 1.0 OD1 B:ASN43 2.5 10.7 0.5 O B:HOH2139 2.5 10.9 1.0 O B:HOH2061 2.5 15.1 1.0 OD1 B:ASN43 2.6 18.0 0.5 O4 B:GCU1148 2.7 12.8 1.0 C6 B:GCU1148 3.4 14.2 1.0 CG B:ASN40 3.6 12.1 1.0 C B:THR41 3.6 12.3 1.0 CG B:ASN43 3.6 12.8 0.5 CG B:ASN43 3.8 16.9 0.5 C4 B:GCU1148 3.8 13.0 1.0 C5 B:GCU1148 3.9 13.8 1.0 N B:THR41 4.0 10.3 1.0 OG1 B:THR41 4.1 11.7 1.0 ND2 B:ASN43 4.2 10.8 0.5 ND2 B:ASN40 4.2 15.8 1.0 C B:ASN40 4.3 11.0 1.0 OD1 B:ASN130 4.3 11.0 1.0 NH1 B:ARG75 4.3 12.9 1.0 CA B:THR41 4.3 10.8 1.0 O B:LEU128 4.4 10.9 1.0 ND2 B:ASN43 4.5 19.4 0.5 O B:HOH2056 4.5 15.7 0.6 O6B B:GCU1148 4.5 16.0 1.0 C B:ASN42 4.5 14.1 1.0 N B:ASN43 4.6 14.2 1.0 N B:ASN42 4.6 12.7 1.0 CA B:ASN40 4.7 11.4 1.0 O B:ASN42 4.7 13.1 1.0 O B:GLU126 4.7 14.6 1.0 CB B:ASN40 4.7 11.4 1.0 O B:ASN40 4.7 10.0 1.0 O B:HOH2154 4.8 22.1 1.0 O B:HOH2060 4.9 34.5 1.0 CB B:ASN43 4.9 14.5 0.5 CB B:THR41 4.9 10.1 1.0 CA B:ASN42 4.9 13.6 1.0 CA B:ASN43 5.0 14.4 0.5 CA B:ASN43 5.0 15.1 0.5 C3 B:GCU1148 5.0 12.6 1.0 CB B:ASN43 5.0 15.8 0.5

Calcium binding site 4 out of 4 in the Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xyl-CBM35 in Complex with Glucuronic Acid Containing Disaccharide. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1151 b:10.8 occ:1.00 OE1 B:GLN13 2.2 10.7 1.0 O B:THR34 2.3 13.4 1.0 O B:GLY37 2.3 11.0 1.0 OD1 B:ASP132 2.4 10.8 1.0 O B:ASP132 2.4 8.3 1.0 OE1 B:GLU14 2.5 10.2 1.0 OE2 B:GLU14 2.5 11.3 1.0 CD B:GLU14 2.8 11.7 1.0 C B:ASP132 3.4 10.1 1.0 CD B:GLN13 3.4 10.8 1.0 C B:THR34 3.5 14.1 1.0 CG B:ASP132 3.5 10.6 1.0 C B:GLY37 3.5 12.2 1.0 CA B:ASP132 3.8 10.0 1.0 N B:THR34 4.1 13.5 1.0 NE2 B:GLN13 4.1 12.6 1.0 N B:GLY37 4.2 13.6 1.0 OG1 B:THR34 4.2 13.9 1.0 CB B:ASP132 4.3 10.6 1.0 OD2 B:ASP132 4.3 12.4 1.0 CG B:GLU14 4.3 11.3 1.0 N B:GLY35 4.3 15.2 1.0 CA B:THR34 4.3 14.4 1.0 CA B:GLY35 4.4 14.8 1.0 N B:PHE38 4.4 10.9 1.0 CA B:GLY37 4.4 12.3 1.0 O B:HOH2010 4.4 3.6 0.5 CA B:PHE38 4.4 10.9 1.0 CB B:GLN13 4.5 11.4 1.0 N B:SER133 4.5 9.2 1.0 CG B:GLN13 4.5 10.9 1.0 C B:GLY35 4.7 14.9 1.0 CB B:PHE33 4.7 13.6 1.0 N B:GLU14 4.7 11.2 1.0 CA B:GLN13 4.8 10.9 1.0 CB B:SER133 4.8 11.7 1.0 N B:SER36 4.8 14.5 1.0 CB B:THR34 4.9 14.3 1.0 CA B:SER133 4.9 10.8 1.0

C.Montanier, A.L.Van Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.G.A.Fontes, G.J.Davies, A.B.Boraston, H.J.Gilbert. Evidence That Family 35 Carbohydrate Binding Modules Display Conserved Specificity But Divergent Function. Proc.Natl.Acad.Sci.Usa V. 106 3065 2009.
ISSN: ISSN 0027-8424
PubMed: 19218457
DOI: 10.1073/PNAS.0808972106