Calcium in PDB 2vzq: C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid

The structure of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid, PDB code: 2vzq was solved by A.Lammerts Van Bueren, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.06 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.925, 54.772, 81.341, 90.00, 100.16, 90.00
R / Rfree (%)	17.1 / 21.7

The structure of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid (pdb code 2vzq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid, PDB code: 2vzq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1129 b:14.6 occ:1.00 OE1 A:GLN7 2.3 11.5 1.0 OD1 A:ASP123 2.3 8.9 1.0 O A:GLY29 2.4 14.7 1.0 OE1 A:GLU9 2.4 13.7 1.0 O A:THR26 2.5 12.6 1.0 O A:ASP123 2.5 12.0 1.0 OE2 A:GLU9 2.6 12.7 1.0 CD A:GLU9 2.8 13.8 1.0 CG A:ASP123 3.4 12.6 1.0 CD A:GLN7 3.4 16.3 1.0 C A:ASP123 3.5 12.6 1.0 C A:GLY29 3.5 14.4 1.0 C A:THR26 3.5 12.4 1.0 CA A:ASP123 3.9 13.2 1.0 N A:THR26 4.1 12.6 1.0 CB A:GLN7 4.2 11.0 1.0 CB A:ASP123 4.2 12.5 1.0 OD2 A:ASP123 4.3 14.8 1.0 CA A:PHE30 4.3 14.2 1.0 N A:PHE30 4.3 15.6 1.0 CG A:GLN7 4.3 14.0 1.0 N A:GLY29 4.3 14.9 1.0 OG1 A:THR26 4.3 12.1 1.0 NE2 A:GLN7 4.3 16.2 1.0 CG A:GLU9 4.4 13.5 1.0 N A:GLY27 4.4 12.7 1.0 CA A:GLY27 4.4 13.0 1.0 CA A:THR26 4.4 13.2 1.0 CA A:GLY29 4.5 14.4 1.0 N A:ALA8 4.6 11.3 1.0 N A:LYS124 4.6 13.4 1.0 CB A:TYR25 4.6 11.9 1.0 CA A:GLN7 4.7 12.0 1.0 CB A:LYS124 4.7 11.3 1.0 CB A:PHE30 4.7 13.9 1.0 C A:GLY27 4.8 13.9 1.0 N A:THR28 4.9 14.9 1.0

Calcium binding site 2 out of 4 in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1130 b:16.6 occ:1.00 O A:TYR33 2.3 12.2 1.0 OD1 A:ASN32 2.3 12.9 1.0 O6 A:UNF1128 2.4 17.3 1.0 OD1 A:ASN35 2.4 13.1 1.0 O A:HOH2204 2.5 12.5 1.0 O A:HOH2086 2.6 20.5 1.0 O A:HOH2206 2.7 15.2 1.0 C6 A:UNF1128 3.4 19.0 1.0 CG A:ASN32 3.5 12.5 1.0 C A:TYR33 3.5 14.3 1.0 CG A:ASN35 3.5 14.2 1.0 N A:TYR33 4.0 12.8 1.0 NH1 A:ARG67 4.0 14.2 1.0 ND2 A:ASN32 4.0 11.4 1.0 C4 A:UNF1128 4.1 18.2 1.0 O3' A:UNF1128 4.1 30.9 1.0 C5 A:UNF1128 4.2 18.9 1.0 ND2 A:ASN35 4.2 16.4 1.0 N A:ASN35 4.2 14.8 1.0 OAN A:UNF1128 4.2 17.3 1.0 CA A:TYR33 4.3 13.7 1.0 C A:ASN32 4.3 12.3 1.0 C A:ASP34 4.3 14.6 1.0 O A:GLY119 4.4 14.8 1.0 O A:HOH2082 4.5 15.3 1.0 OD1 A:ASN121 4.5 12.6 1.0 N A:ASP34 4.5 14.2 1.0 CA A:ASP34 4.5 14.8 1.0 CB A:TYR33 4.6 13.8 1.0 CA A:ASN35 4.7 15.9 1.0 CB A:ASN35 4.7 16.4 1.0 CB A:ASN32 4.7 12.1 1.0 CA A:ASN32 4.7 12.0 1.0 O A:HOH2085 4.7 22.8 1.0 O A:ASN32 4.8 12.0 1.0 O A:ASP34 4.8 14.0 1.0 O A:ASN117 4.8 17.1 1.0

Calcium binding site 3 out of 4 in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1128 b:12.7 occ:1.00 OE1 B:GLN7 2.2 10.9 1.0 OE1 B:GLU9 2.4 11.4 1.0 O B:GLY29 2.4 11.7 1.0 O B:THR26 2.4 11.4 1.0 OD1 B:ASP123 2.4 9.6 1.0 O B:ASP123 2.5 10.1 1.0 OE2 B:GLU9 2.6 11.1 1.0 CD B:GLU9 2.8 12.8 1.0 CD B:GLN7 3.3 13.5 1.0 CG B:ASP123 3.5 12.4 1.0 C B:ASP123 3.5 10.6 1.0 C B:GLY29 3.5 12.9 1.0 C B:THR26 3.5 11.5 1.0 CA B:ASP123 3.9 11.0 1.0 N B:THR26 4.1 11.5 1.0 CB B:GLN7 4.1 10.8 1.0 CG B:GLN7 4.2 10.4 1.0 NE2 B:GLN7 4.2 15.5 1.0 N B:GLY29 4.2 11.8 1.0 OD2 B:ASP123 4.2 12.6 1.0 N B:PHE30 4.3 13.3 1.0 CA B:PHE30 4.3 11.6 1.0 CB B:ASP123 4.3 10.8 1.0 OG1 B:THR26 4.3 11.8 1.0 CG B:GLU9 4.4 12.8 1.0 CA B:GLY27 4.4 11.5 1.0 CA B:THR26 4.4 11.8 1.0 N B:GLY27 4.4 11.9 1.0 CA B:GLY29 4.5 11.7 1.0 CA B:GLN7 4.6 10.7 1.0 N B:ALA8 4.6 11.3 1.0 CB B:TYR25 4.6 10.4 1.0 N B:LYS124 4.6 10.6 1.0 CB B:PHE30 4.7 11.9 1.0 C B:GLY27 4.7 12.3 1.0 CB B:LYS124 4.7 9.7 1.0 N B:THR28 4.8 11.7 1.0

Calcium binding site 4 out of 4 in the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa in Complex with Digalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1129 b:14.2 occ:1.00 O6 B:UNF1133 2.4 16.0 1.0 OD1 B:ASN35 2.4 15.2 1.0 O B:TYR33 2.4 11.6 1.0 OD1 B:ASN32 2.4 11.3 1.0 O B:HOH2225 2.5 13.2 1.0 O B:HOH2102 2.6 14.7 1.0 O B:HOH2227 2.6 10.8 1.0 C6 B:UNF1133 3.4 15.8 1.0 CG B:ASN35 3.6 14.4 1.0 C B:TYR33 3.6 12.9 1.0 CG B:ASN32 3.6 8.4 1.0 NH1 B:ARG67 3.9 15.1 1.0 N B:TYR33 4.1 12.4 1.0 C4 B:UNF1133 4.1 17.0 1.0 ND2 B:ASN32 4.1 10.0 1.0 C5 B:UNF1133 4.2 18.1 1.0 OAN B:UNF1133 4.2 13.6 1.0 O3' B:UNF1133 4.2 29.6 1.0 ND2 B:ASN35 4.2 15.6 1.0 N B:ASN35 4.2 13.4 1.0 CA B:TYR33 4.3 11.8 1.0 C B:ASN32 4.3 11.3 1.0 C B:ASP34 4.3 13.3 1.0 OD1 B:ASN121 4.4 12.8 1.0 O B:GLY119 4.4 11.6 1.0 CA B:ASP34 4.5 13.6 1.0 O B:HOH2093 4.6 16.3 1.0 N B:ASP34 4.6 11.8 1.0 CB B:TYR33 4.6 12.7 1.0 O B:HOH2100 4.6 20.5 1.0 CA B:ASN35 4.7 13.7 1.0 CB B:ASN35 4.7 14.7 1.0 O B:ASN117 4.7 13.2 1.0 CA B:ASN32 4.7 10.8 1.0 CB B:ASN32 4.8 11.9 1.0 O B:ASN32 4.8 12.0 1.0 O B:ASP34 4.8 13.2 1.0 CZ B:ARG67 4.9 12.3 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