Cadmium in the structure of Homing Endonuclease/Dna Complex (pdb 1ipp)

The binding sites of Cadmium atom in the structure of Homing Endonuclease/Dna Complex (pdb code 1ipp). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1ipp structure was solved by K.E.FLICK, M.S.JURICA, R.J.MONNAT JR., B.L.STODDARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.2 Space group P3121 a (A) 113.900 b (A) 113.900 c (A) 88.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.2 Rfree (%) 31.6 Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1ipp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1ipp. 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: Arg122, A: Cys125, A: Cys132, A: Val133, A: His134, A: Cys138, A: Hoh327, A: Hoh457, conact list: Atom Atom Distance (A) Cd CZ A:Arg122 4.89 Cd NE A:Arg122 4.87 Cd NH2 A:Arg122 4.41 Cd CB A:Cys125 3.56 Cd SG A:Cys125 2.65 Cd CB A:Cys132 3.38 Cd SG A:Cys132 2.72 Cd C A:Cys132 4.62 Cd CA A:Cys132 4.03 Cd N A:Val133 4.59 Cd NE2 A:His134 4.46 Cd N A:His134 4.34 Cd CB A:His134 3.75 Cd ND1 A:His134 2.43 Cd CD2 A:His134 4.55 Cd CE1 A:His134 3.32 Cd CG A:His134 3.44 Cd CA A:His134 4.71 Cd N A:Cys138 4.11 Cd CB A:Cys138 3.39 Cd SG A:Cys138 2.67 Cd CA A:Cys138 4.34 Cd O A:Hoh327 3.84 Cd O A:Hoh457 2.99 interactive model: Cadmium binding site 2 out of 4 in 1ipp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1ipp. 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: His40, A: Cys41, A: Tyr42, A: Cys100, A: Asn102, A: Cys105, A: Asn107, A: His110, conact list: Atom Atom Distance (A) Cd O A:His40 4.55 Cd C A:His40 4.78 Cd N A:Cys41 4.47 Cd CB A:Cys41 3.40 Cd SG A:Cys41 2.65 Cd C A:Cys41 4.94 Cd CA A:Cys41 3.77 Cd N A:Tyr42 4.99 Cd CB A:Cys100 3.16 Cd SG A:Cys100 2.63 Cd CA A:Cys100 4.66 Cd O A:Asn102 4.94 Cd CB A:Asn102 4.34 Cd ND2 A:Asn102 4.63 Cd CG A:Asn102 4.99 Cd CB A:Cys105 3.25 Cd SG A:Cys105 2.62 Cd CA A:Cys105 4.75 Cd CB A:Asn107 4.68 Cd NE2 A:His110 4.39 Cd CB A:His110 3.58 Cd ND1 A:His110 2.31 Cd CD2 A:His110 4.44 Cd CE1 A:His110 3.26 Cd CG A:His110 3.31 interactive model: Cadmium binding site 3 out of 4 in 1ipp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1ipp. 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: Arg122, B: Cys125, B: Cys132, B: Val133, B: His134, B: Cys138, A: Hoh453, B: Hoh334, B: Hoh340, B: Hoh352, conact list: Atom Atom Distance (A) Cd CZ B:Arg122 4.94 Cd NE B:Arg122 4.97 Cd NH2 B:Arg122 4.29 Cd CB B:Cys125 3.47 Cd SG B:Cys125 2.62 Cd CA B:Cys125 4.92 Cd CB B:Cys132 3.44 Cd SG B:Cys132 2.66 Cd C B:Cys132 4.77 Cd CA B:Cys132 4.10 Cd N B:Val133 4.76 Cd NE2 B:His134 4.42 Cd N B:His134 4.52 Cd CB B:His134 3.74 Cd ND1 B:His134 2.39 Cd CD2 B:His134 4.50 Cd CE1 B:His134 3.29 Cd CG B:His134 3.41 Cd CA B:His134 4.78 Cd N B:Cys138 4.07 Cd CB B:Cys138 3.32 Cd SG B:Cys138 2.61 Cd CA B:Cys138 4.26 Cd O A:Hoh453 4.72 Cd O B:Hoh334 3.65 Cd O B:Hoh340 4.98 Cd O B:Hoh352 4.67 interactive model: Cadmium binding site 4 out of 4 in 1ipp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1ipp. 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: His40, B: Cys41, B: Cys100, B: Asn102, B: Cys105, B: Asn107, B: His110, B: Hoh370, conact list: Atom Atom Distance (A) Cd O B:His40 4.69 Cd C B:His40 4.90 Cd N B:Cys41 4.51 Cd CB B:Cys41 3.42 Cd SG B:Cys41 2.67 Cd C B:Cys41 4.95 Cd CA B:Cys41 3.78 Cd CB B:Cys100 3.24 Cd SG B:Cys100 2.63 Cd CA B:Cys100 4.73 Cd CB B:Asn102 4.35 Cd ND2 B:Asn102 4.26 Cd CG B:Asn102 4.79 Cd CB B:Cys105 3.27 Cd SG B:Cys105 2.64 Cd CA B:Cys105 4.75 Cd CB B:Asn107 4.78 Cd NE2 B:His110 4.47 Cd CB B:His110 3.56 Cd ND1 B:His110 2.38 Cd CD2 B:His110 4.49 Cd CE1 B:His110 3.35 Cd CG B:His110 3.34 Cd O B:Hoh370 4.39 interactive model: