Calcium in PDB 2vzp: Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa

The structure of Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa, PDB code: 2vzp 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)	81.65 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.573, 57.022, 81.699, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 14.9

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

Calcium binding site 1 out of 4 in the Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1128 b:3.1 occ:1.00 OE1 A:GLN7 2.3 4.2 1.0 OD1 A:ASP123 2.3 3.7 1.0 O A:GLY29 2.3 3.3 1.0 O A:THR26 2.3 4.3 1.0 OE1 A:GLU9 2.4 4.1 1.0 OE2 A:GLU9 2.5 4.4 1.0 O A:ASP123 2.6 3.0 1.0 CD A:GLU9 2.8 4.1 1.0 CG A:ASP123 3.4 3.4 1.0 CD A:GLN7 3.4 4.7 1.0 C A:THR26 3.4 3.7 1.0 C A:GLY29 3.5 3.6 1.0 C A:ASP123 3.5 2.9 1.0 CA A:ASP123 3.9 3.1 1.0 N A:THR26 4.1 3.7 1.0 CB A:GLN7 4.2 4.6 1.0 OG1 A:THR26 4.2 4.4 1.0 OD2 A:ASP123 4.2 3.6 1.0 N A:GLY29 4.2 4.5 1.0 CB A:ASP123 4.2 3.2 1.0 CA A:PHE30 4.3 3.6 1.0 NE2 A:GLN7 4.3 5.0 1.0 CG A:GLN7 4.3 4.9 1.0 N A:PHE30 4.3 3.7 1.0 N A:GLY27 4.3 4.2 1.0 CG A:GLU9 4.4 5.0 1.0 CA A:THR26 4.4 4.1 1.0 CA A:GLY27 4.4 4.6 1.0 CA A:GLY29 4.5 4.3 1.0 N A:ALA8 4.6 3.7 1.0 CA A:GLN7 4.6 3.6 1.0 N A:LYS124 4.6 2.9 1.0 CB A:TYR25 4.6 4.3 1.0 C A:GLY27 4.7 4.5 1.0 CB A:PHE30 4.8 3.6 1.0 CB A:LYS124 4.8 3.7 1.0 N A:THR28 4.8 5.0 1.0 CB A:THR26 4.9 4.4 1.0 O A:HOH2024 5.0 11.7 1.0

Calcium binding site 2 out of 4 in the Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1129 b:8.2 occ:1.00 C2 A:EDO1130 2.2 6.7 0.5 O A:TYR33 2.3 5.9 1.0 OD1 A:ASN32 2.4 5.5 1.0 O A:HOH2217 2.4 6.9 1.0 OD1 A:ASN35 2.5 11.1 1.0 O2 A:EDO1130 2.6 14.5 0.5 O A:HOH2233 2.6 10.1 1.0 O A:HOH2221 2.7 8.4 1.0 O2 A:EDO1130 2.7 7.3 0.5 C2 A:EDO1130 2.8 21.1 0.5 C A:TYR33 3.4 4.5 1.0 CG A:ASN32 3.5 4.8 1.0 C1 A:EDO1130 3.5 8.9 0.5 CG A:ASN35 3.6 9.8 1.0 NH1 A:ARG67 3.9 11.7 1.0 C1 A:EDO1130 3.9 23.2 0.5 N A:TYR33 4.0 4.0 1.0 ND2 A:ASN32 4.1 7.5 1.0 CA A:TYR33 4.2 4.1 1.0 ND2 A:ASN35 4.3 17.5 1.0 C A:ASN32 4.3 4.2 1.0 C A:ASP34 4.3 5.7 1.0 O A:GLY119 4.3 4.6 1.0 O1 A:EDO1130 4.4 14.0 0.5 N A:ASN35 4.4 6.6 1.0 N A:ASP34 4.4 5.0 1.0 OD1 A:ASN121 4.4 4.8 1.0 O A:HOH2099 4.5 6.7 1.0 O A:HOH2089 4.5 26.2 1.0 CA A:ASP34 4.5 5.2 1.0 CB A:TYR33 4.5 4.5 1.0 CB A:ASN32 4.7 4.9 1.0 O A:ASP34 4.7 6.2 1.0 CA A:ASN32 4.7 3.3 1.0 O1 A:EDO1131 4.7 12.0 1.0 O A:HOH2229 4.7 26.7 1.0 CZ A:ARG67 4.8 11.0 1.0 CB A:ASN35 4.8 9.8 1.0 O A:ASN32 4.8 4.4 1.0 CA A:ASN35 4.8 7.5 1.0 O A:ASN117 4.8 9.4 1.0

Calcium binding site 3 out of 4 in the Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1128 b:3.2 occ:1.00 OE1 B:GLN7 2.3 3.6 1.0 OD1 B:ASP123 2.3 3.9 1.0 O B:GLY29 2.3 4.1 1.0 O B:THR26 2.4 4.5 1.0 OE1 B:GLU9 2.4 3.6 1.0 OE2 B:GLU9 2.5 4.3 1.0 O B:ASP123 2.5 2.9 1.0 CD B:GLU9 2.9 3.8 1.0 CD B:GLN7 3.4 4.0 1.0 CG B:ASP123 3.4 3.5 1.0 C B:GLY29 3.5 4.7 1.0 C B:THR26 3.5 4.4 1.0 C B:ASP123 3.5 2.6 1.0 CA B:ASP123 3.9 3.2 1.0 N B:THR26 4.2 4.7 1.0 CB B:GLN7 4.2 3.7 1.0 N B:GLY29 4.2 5.1 1.0 NE2 B:GLN7 4.2 4.5 1.0 CB B:ASP123 4.2 3.5 1.0 OD2 B:ASP123 4.3 4.0 1.0 CG B:GLN7 4.3 4.4 1.0 CA B:PHE30 4.3 4.0 1.0 N B:PHE30 4.3 4.5 1.0 CG B:GLU9 4.3 4.9 1.0 N B:GLY27 4.3 5.1 1.0 OG1 B:THR26 4.4 4.3 1.0 CA B:THR26 4.4 4.7 1.0 CA B:GLY27 4.4 5.2 1.0 CA B:GLY29 4.5 5.2 1.0 N B:LYS124 4.6 3.0 1.0 CA B:GLN7 4.6 3.1 1.0 N B:ALA8 4.6 3.6 1.0 CB B:TYR25 4.7 5.9 1.0 CB B:LYS124 4.7 3.3 1.0 C B:GLY27 4.7 5.4 1.0 N B:THR28 4.8 5.5 1.0 CB B:PHE30 4.8 4.7 1.0 O B:HOH2095 4.9 12.0 1.0

Calcium binding site 4 out of 4 in the Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Atomic Resolution Structure of the C-Terminal CBM35 From Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1129 b:12.3 occ:1.00 C2 B:EDO1130 2.2 15.2 1.0 O B:TYR33 2.2 6.3 1.0 OD1 B:ASN32 2.3 6.7 1.0 O B:HOH2235 2.4 8.3 1.0 OD1 B:ASN35 2.6 9.6 0.5 O2 B:EDO1130 2.7 11.6 1.0 O B:HOH2239 2.7 8.5 1.0 O B:HOH2097 2.8 15.1 1.0 C B:TYR33 3.4 5.6 1.0 CG B:ASN32 3.5 6.1 1.0 C1 B:EDO1130 3.5 18.3 1.0 CG B:ASN35 3.7 6.9 0.5 N B:TYR33 3.8 4.7 1.0 OD1 B:ASN35 4.0 15.5 0.5 NH1 B:ARG67 4.0 8.5 1.0 CA B:TYR33 4.1 4.8 1.0 C B:ASN32 4.1 4.9 1.0 ND2 B:ASN32 4.2 9.3 1.0 O B:GLY119 4.3 5.2 1.0 ND2 B:ASN35 4.3 11.2 0.5 OD1 B:ASN121 4.4 6.1 1.0 O B:HOH2249 4.4 21.8 1.0 O1 B:EDO1130 4.4 18.9 1.0 C B:ASP34 4.4 6.7 1.0 CB B:TYR33 4.4 5.1 1.0 N B:ASP34 4.5 5.6 1.0 O B:HOH2098 4.5 25.5 1.0 O B:HOH2104 4.5 8.6 1.0 CA B:ASN32 4.5 4.4 1.0 CB B:ASN32 4.6 5.5 1.0 CA B:ASP34 4.6 6.5 1.0 N B:ASN35 4.6 8.3 1.0 CG B:ASN35 4.7 11.5 0.5 O B:ASP34 4.7 7.3 1.0 O B:ASN32 4.7 5.6 1.0 O B:ASN117 4.9 9.9 1.0 CZ B:ARG67 4.9 7.9 1.0 CB B:ASN35 4.9 7.8 0.5

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