Calcium in the structure of Concanavalin From Canavalia Brasiliensis (pdb 1azd)

The binding sites of Calcium atom in the structure of Concanavalin From Canavalia Brasiliensis (pdb code 1azd). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1azd structure was solved by J.SANZ-APARICIO, J.HERMOSO, T.B.GRANGEIRO, J.J.CALVETE, B.S.CAVADA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-3.0 Space group P212121 a (A) 71.290 b (A) 71.650 c (A) 190.960 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16 Rfree (%) 24 Calcium Binding Sites: Calcium binding site 1 out of 4 in 1azd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1azd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp10, A: Tyr12, A: Pro13, A: Asn14, A: Asp19, A: His24, A: Asp208, A: Arg228, A: Mn239, conact list: Atom Atom Distance (A) Ca CB A:Asp10 4.44 Ca OD2 A:Asp10 2.65 Ca OD1 A:Asp10 2.48 Ca CG A:Asp10 2.92 Ca O A:Tyr12 2.52 Ca N A:Tyr12 4.61 Ca CB A:Tyr12 4.80 Ca C A:Tyr12 3.75 Ca CA A:Tyr12 4.60 Ca N A:Pro13 4.70 Ca C A:Pro13 4.88 Ca CA A:Pro13 4.74 Ca N A:Asn14 4.06 Ca CB A:Asn14 4.22 Ca ND2 A:Asn14 4.44 Ca OD1 A:Asn14 2.28 Ca CG A:Asn14 3.46 Ca CA A:Asn14 4.81 Ca OD2 A:Asp19 2.77 Ca OD1 A:Asp19 4.34 Ca CG A:Asp19 3.90 Ca CE1 A:His24 4.88 Ca O A:Asp208 4.60 Ca OD1 A:Asp208 4.66 Ca O A:Arg228 4.56 Ca CB A:Arg228 4.57 Ca CA A:Arg228 4.66 Ca MN A:Mn239 4.34 interactive model: Calcium binding site 2 out of 4 in 1azd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1azd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp10, B: Tyr12, B: Pro13, B: Asn14, B: Asp19, B: His24, B: Asp208, B: Arg228, B: Mn239, conact list: Atom Atom Distance (A) Ca CB B:Asp10 4.47 Ca OD2 B:Asp10 2.69 Ca OD1 B:Asp10 2.49 Ca CG B:Asp10 2.95 Ca O B:Tyr12 2.57 Ca N B:Tyr12 4.63 Ca CB B:Tyr12 4.78 Ca C B:Tyr12 3.78 Ca CA B:Tyr12 4.61 Ca N B:Pro13 4.74 Ca C B:Pro13 4.92 Ca CA B:Pro13 4.79 Ca N B:Asn14 4.09 Ca CB B:Asn14 4.24 Ca ND2 B:Asn14 4.42 Ca OD1 B:Asn14 2.27 Ca CG B:Asn14 3.45 Ca CA B:Asn14 4.84 Ca OD2 B:Asp19 2.84 Ca OD1 B:Asp19 4.39 Ca CG B:Asp19 3.96 Ca CE1 B:His24 4.95 Ca O B:Asp208 4.50 Ca OD1 B:Asp208 4.57 Ca O B:Arg228 4.53 Ca CB B:Arg228 4.51 Ca CA B:Arg228 4.58 Ca MN B:Mn239 4.46 interactive model: Calcium binding site 3 out of 4 in 1azd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1azd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp10, C: Tyr12, C: Pro13, C: Asn14, C: Asp19, C: His24, C: Asp208, C: Arg228, C: Mn239, conact list: Atom Atom Distance (A) Ca CB C:Asp10 4.48 Ca OD2 C:Asp10 2.68 Ca OD1 C:Asp10 2.51 Ca CG C:Asp10 2.95 Ca O C:Tyr12 2.55 Ca N C:Tyr12 4.64 Ca CB C:Tyr12 4.80 Ca C C:Tyr12 3.77 Ca CA C:Tyr12 4.61 Ca N C:Pro13 4.72 Ca C C:Pro13 4.88 Ca CA C:Pro13 4.76 Ca N C:Asn14 4.06 Ca CB C:Asn14 4.21 Ca ND2 C:Asn14 4.40 Ca OD1 C:Asn14 2.24 Ca CG C:Asn14 3.43 Ca CA C:Asn14 4.80 Ca OD2 C:Asp19 2.77 Ca OD1 C:Asp19 4.34 Ca CG C:Asp19 3.90 Ca CE1 C:His24 4.91 Ca O C:Asp208 4.57 Ca OD1 C:Asp208 4.40 Ca O C:Arg228 4.53 Ca CB C:Arg228 4.54 Ca CA C:Arg228 4.61 Ca MN C:Mn239 4.41 interactive model: Calcium binding site 4 out of 4 in 1azd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1azd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp10, D: Tyr12, D: Pro13, D: Asn14, D: Asp19, D: His24, D: Asp208, D: Arg228, D: Mn239, conact list: Atom Atom Distance (A) Ca CB D:Asp10 4.44 Ca OD2 D:Asp10 2.65 Ca OD1 D:Asp10 2.47 Ca CG D:Asp10 2.91 Ca O D:Tyr12 2.53 Ca N D:Tyr12 4.61 Ca CB D:Tyr12 4.77 Ca C D:Tyr12 3.75 Ca CA D:Tyr12 4.60 Ca N D:Pro13 4.71 Ca C D:Pro13 4.89 Ca CA D:Pro13 4.75 Ca N D:Asn14 4.07 Ca CB D:Asn14 4.24 Ca ND2 D:Asn14 4.44 Ca OD1 D:Asn14 2.28 Ca CG D:Asn14 3.46 Ca CA D:Asn14 4.83 Ca OD2 D:Asp19 2.80 Ca OD1 D:Asp19 4.36 Ca CG D:Asp19 3.93 Ca CE1 D:His24 4.90 Ca O D:Asp208 4.60 Ca OD1 D:Asp208 4.63 Ca O D:Arg228 4.56 Ca CB D:Arg228 4.57 Ca CA D:Arg228 4.64 Ca MN D:Mn239 4.43 interactive model: