Cadmium in the structure of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato (pdb 3r52)

The binding sites of Cadmium atom in the structure of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato (pdb code 3r52). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3r52 structure was solved by K.L.LIU, W.C.CHANG, S.T.JENG, Y.S.CHENG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 26.0-2.1 Space group P1211 a (A) 59.280 b (A) 83.710 c (A) 65.060 alpha (°) 90.00 beta (°) 112.76 gamma (°) 90.00 Rfactor (%) 18.8 Rfree (%) 24.3 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 3r52 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3r52. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ser18, B: Asn19, B: Gly20, B: Tyr97, B: Asn98, B: Asp145, B: Gyp200, B: Hoh158, B: Hoh166, B: Hoh167, B: Hoh402, conact list: Atom Atom Distance (A) Cd O B:Ser18 4.37 Cd CB B:Ser18 3.50 Cd OG B:Ser18 2.66 Cd C B:Ser18 3.94 Cd CA B:Ser18 4.36 Cd O B:Asn19 2.44 Cd N B:Asn19 3.76 Cd CB B:Asn19 4.65 Cd C B:Asn19 3.56 Cd CA B:Asn19 4.15 Cd N B:Gly20 4.67 Cd CA B:Gly20 4.98 Cd CB B:Tyr97 4.86 Cd CD2 B:Tyr97 4.69 Cd O B:Asn98 4.39 Cd N B:Asn98 4.82 Cd CB B:Asp145 4.91 Cd OD1 B:Asp145 4.22 Cd CG B:Asp145 4.90 Cd O4 B:Gyp200 4.62 Cd O B:Hoh158 2.72 Cd O B:Hoh166 2.76 Cd O B:Hoh167 2.88 Cd O B:Hoh402 4.52 interactive model: Cadmium binding site 2 out of 3 in 3r52 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3r52. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ser18, C: Asn19, C: Gly20, C: Tyr97, C: Asn98, C: Asp145, D: Leu3, C: Gyp200, C: Hoh257, C: Hoh259, C: Hoh426, D: Hoh201, D: Hoh258, conact list: Atom Atom Distance (A) Cd O C:Ser18 4.37 Cd CB C:Ser18 3.41 Cd OG C:Ser18 2.71 Cd C C:Ser18 3.97 Cd CA C:Ser18 4.34 Cd O C:Asn19 2.57 Cd N C:Asn19 3.85 Cd CB C:Asn19 4.84 Cd C C:Asn19 3.68 Cd CA C:Asn19 4.28 Cd N C:Gly20 4.80 Cd CD1 C:Tyr97 4.79 Cd O C:Asn98 4.12 Cd N C:Asn98 4.68 Cd OD1 C:Asp145 4.30 Cd O D:Leu3 3.99 Cd C D:Leu3 4.84 Cd O4 C:Gyp200 4.48 Cd O C:Hoh257 4.48 Cd O C:Hoh259 4.17 Cd O C:Hoh426 2.68 Cd O D:Hoh201 2.54 Cd O D:Hoh258 2.75 interactive model: Cadmium binding site 3 out of 3 in 3r52 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3r52. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Leu3, D: Ser18, D: Asn19, D: Gly20, D: Tyr97, D: Asn98, D: Asp145, D: Gyp200, C: Hoh171, C: Hoh175, D: Hoh155, D: Hoh280, D: Hoh284, D: Hoh346, D: Hoh464, conact list: Atom Atom Distance (A) Cd O C:Leu3 4.25 Cd O D:Ser18 4.43 Cd CB D:Ser18 3.69 Cd OG D:Ser18 2.83 Cd C D:Ser18 4.05 Cd CA D:Ser18 4.50 Cd O D:Asn19 2.51 Cd N D:Asn19 3.89 Cd CB D:Asn19 4.73 Cd C D:Asn19 3.64 Cd CA D:Asn19 4.24 Cd N D:Gly20 4.74 Cd CD1 D:Tyr97 4.52 Cd O D:Asn98 4.17 Cd N D:Asn98 4.69 Cd CB D:Asp145 5.00 Cd OD1 D:Asp145 4.13 Cd CG D:Asp145 4.81 Cd O4 D:Gyp200 4.57 Cd O C:Hoh171 2.67 Cd O C:Hoh175 2.61 Cd O D:Hoh155 2.61 Cd O D:Hoh280 4.90 Cd O D:Hoh284 4.44 Cd O D:Hoh346 2.70 Cd O D:Hoh464 4.76 interactive model: