Cadmium in the structure of Diels Alder Catalytic Antibody With Transition State Analogue (pdb 1a4k)

The binding sites of Cadmium atom in the structure of Diels Alder Catalytic Antibody With Transition State Analogue (pdb code 1a4k). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1a4k structure was solved by B.W.SPILLER, F.E.ROMESBURG, P.G.SCHULTZ, R.C.STEVENS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.4 Space group P212121 a (A) 69.316 b (A) 96.823 c (A) 172.730 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.1 Rfree (%) 29.1 Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1a4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1a4k. 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: L: Arg61, L: Glu79, L: Glu81, conact list: Atom Atom Distance (A) Cd CZ L:Arg61 4.71 Cd NE L:Arg61 4.54 Cd NH2 L:Arg61 4.05 Cd OE1 L:Glu79 2.48 Cd OE2 L:Glu79 3.35 Cd CD L:Glu79 3.26 Cd CG L:Glu79 4.68 Cd OE1 L:Glu81 2.80 Cd OE2 L:Glu81 4.18 Cd CD L:Glu81 3.83 interactive model: Cadmium binding site 2 out of 4 in 1a4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1a4k. 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: L: Asn137, L: Asn138, L: Asp170, L: Ser174, H: Gly162, H: His164, L: Hoh5049, L: Hoh5050, L: Hoh5051, L: Hoh5057, H: Hoh3092, conact list: Atom Atom Distance (A) Cd ND2 L:Asn137 4.71 Cd OD1 L:Asn137 4.83 Cd CB L:Asn138 4.55 Cd ND2 L:Asn138 2.25 Cd OD1 L:Asn138 3.33 Cd CG L:Asn138 3.17 Cd OD2 L:Asp170 4.14 Cd OG L:Ser174 4.93 Cd O H:Gly162 4.82 Cd NE2 H:His164 3.14 Cd ND1 H:His164 3.69 Cd CD2 H:His164 4.14 Cd CE1 H:His164 2.82 Cd CG H:His164 4.43 Cd O L:Hoh5049 2.91 Cd O L:Hoh5050 4.14 Cd O L:Hoh5051 3.22 Cd O L:Hoh5057 2.53 Cd O H:Hoh3092 4.18 interactive model: Cadmium binding site 3 out of 4 in 1a4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1a4k. 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: Arg61, A: Glu79, A: Glu81, A: Hoh5051, A: Hoh5055, conact list: Atom Atom Distance (A) Cd CZ A:Arg61 4.86 Cd NE A:Arg61 4.53 Cd NH2 A:Arg61 4.40 Cd OE1 A:Glu79 2.61 Cd CB A:Glu79 4.92 Cd OE2 A:Glu79 4.29 Cd CD A:Glu79 3.75 Cd CG A:Glu79 4.91 Cd OE1 A:Glu81 3.55 Cd OE2 A:Glu81 2.78 Cd CD A:Glu81 3.33 Cd CG A:Glu81 4.47 Cd O A:Hoh5051 2.50 Cd O A:Hoh5055 2.57 interactive model: Cadmium binding site 4 out of 4 in 1a4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1a4k. 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: Asn137, A: Asn138, A: Asp170, A: Thr172, A: Ser174, B: Gly162, B: His164, A: Hoh5059, A: Hoh5061, A: Hoh5065, A: Hoh5071, B: Hoh3102, conact list: Atom Atom Distance (A) Cd ND2 A:Asn137 4.80 Cd OD1 A:Asn137 4.85 Cd CB A:Asn138 4.61 Cd ND2 A:Asn138 2.34 Cd OD1 A:Asn138 3.66 Cd CG A:Asn138 3.35 Cd OD2 A:Asp170 4.04 Cd OG1 A:Thr172 4.90 Cd OG A:Ser174 4.85 Cd O B:Gly162 4.85 Cd CA B:Gly162 4.80 Cd NE2 B:His164 3.52 Cd ND1 B:His164 3.46 Cd CD2 B:His164 4.63 Cd CE1 B:His164 2.62 Cd CG B:His164 4.61 Cd O A:Hoh5059 3.05 Cd O A:Hoh5061 2.79 Cd O A:Hoh5065 4.24 Cd O A:Hoh5071 2.80 Cd O B:Hoh3102 3.71 interactive model: