Cadmium in the structure of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus At PH4.5 (pdb 1ib4)

The binding sites of Cadmium atom in the structure of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus At PH4.5 (pdb code 1ib4). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1ib4 structure was solved by S.W.CHO, W.SHIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.1-2.0 Space group P1211 a (A) 56.100 b (A) 96.400 c (A) 57.770 alpha (°) 90.00 beta (°) 107.30 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 21.7 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 1ib4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1ib4. 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: A: Gln179, A: His202, A: Asp231, B: Glu95, B: Gly99, B: Gly100, A: Hoh1232, A: Hoh1249, A: Hoh1305, conact list: Atom Atom Distance (A) Cd O A:Gln179 4.37 Cd NE2 A:His202 2.32 Cd ND1 A:His202 4.45 Cd CD2 A:His202 3.19 Cd CE1 A:His202 3.38 Cd CG A:His202 4.40 Cd CB A:Asp231 4.55 Cd OD2 A:Asp231 3.73 Cd OD1 A:Asp231 2.57 Cd CG A:Asp231 3.39 Cd OE1 B:Glu95 2.67 Cd OE2 B:Glu95 1.91 Cd CD B:Glu95 2.64 Cd CG B:Glu95 4.10 Cd C B:Gly99 4.64 Cd CA B:Gly99 4.59 Cd N B:Gly100 3.90 Cd CA B:Gly100 4.64 Cd O A:Hoh1232 4.76 Cd O A:Hoh1249 3.32 Cd O A:Hoh1305 4.18 interactive model: Cadmium binding site 2 out of 3 in 1ib4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1ib4. 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: A: Glu95, A: Gly99, A: Gly100, B: Gln179, B: His202, B: Asp231, B: Hoh1114, B: Hoh1309, conact list: Atom Atom Distance (A) Cd OE1 A:Glu95 2.60 Cd OE2 A:Glu95 2.25 Cd CD A:Glu95 2.77 Cd CG A:Glu95 4.25 Cd C A:Gly99 4.89 Cd CA A:Gly99 4.62 Cd N A:Gly100 4.18 Cd CA A:Gly100 4.93 Cd O B:Gln179 4.61 Cd NE2 B:His202 2.52 Cd ND1 B:His202 4.63 Cd CD2 B:His202 3.27 Cd CE1 B:His202 3.62 Cd CG B:His202 4.51 Cd CB B:Asp231 4.36 Cd OD2 B:Asp231 3.16 Cd OD1 B:Asp231 2.72 Cd CG B:Asp231 3.24 Cd O B:Hoh1114 4.24 Cd O B:Hoh1309 1.72 interactive model: Cadmium binding site 3 out of 3 in 1ib4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1ib4. 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: Asp285, B: Asp313, B: Hoh1042, B: Hoh1262, conact list: Atom Atom Distance (A) Cd CB B:Asp285 4.47 Cd OD2 B:Asp285 2.41 Cd OD1 B:Asp285 4.43 Cd CG B:Asp285 3.60 Cd CA B:Asp285 4.99 Cd CB B:Asp313 4.59 Cd OD2 B:Asp313 2.36 Cd OD1 B:Asp313 3.17 Cd CG B:Asp313 3.14 Cd O B:Hoh1042 4.74 Cd O B:Hoh1262 3.79 interactive model: