Cadmium in the structure of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody (pdb 1d5i)

The binding sites of Cadmium atom in the structure of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody (pdb code 1d5i). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1d5i structure was solved by E.C.MUNDORFF, M.A.HANSON, P.G.SCHULTZ, R.C.STEVENS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group P1211 a (A) 53.170 b (A) 64.130 c (A) 75.950 alpha (°) 90.00 beta (°) 99.53 gamma (°) 90.00 Rfactor (%) 21.6 Rfree (%) 26.3 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 1d5i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1d5i. 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: Asp167, L: Asp170, L: Thr172, L: Ser174, H: Gly162, H: His164, L: Hoh241, L: Hoh242, L: Hoh243, L: Hoh244, L: Hoh304, H: Hoh280, conact list: Atom Atom Distance (A) Cd ND2 L:Asn137 4.78 Cd OD1 L:Asn137 4.97 Cd CB L:Asn138 4.44 Cd ND2 L:Asn138 2.24 Cd OD1 L:Asn138 3.40 Cd CG L:Asn138 3.15 Cd OD2 L:Asp167 4.83 Cd OD2 L:Asp170 4.61 Cd OD1 L:Asp170 5.00 Cd OG1 L:Thr172 4.92 Cd OG L:Ser174 4.74 Cd CA H:Gly162 4.88 Cd NE2 H:His164 2.99 Cd ND1 H:His164 3.68 Cd CD2 H:His164 4.32 Cd CE1 H:His164 2.47 Cd CG H:His164 4.65 Cd O L:Hoh241 2.44 Cd O L:Hoh242 2.40 Cd O L:Hoh243 2.33 Cd O L:Hoh244 4.02 Cd O L:Hoh304 2.68 Cd O H:Hoh280 4.28 interactive model: Cadmium binding site 2 out of 3 in 1d5i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1d5i. 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: Glu93, L: Hoh233, L: Hoh312, conact list: Atom Atom Distance (A) Cd OE1 L:Glu93 2.44 Cd CB L:Glu93 4.70 Cd OE2 L:Glu93 3.89 Cd CD L:Glu93 2.89 Cd CG L:Glu93 3.13 Cd O L:Hoh233 4.13 Cd O L:Hoh312 1.62 interactive model: Cadmium binding site 3 out of 3 in 1d5i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1d5i. 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, L: Hoh292, L: Hoh293, L: Hoh313, conact list: Atom Atom Distance (A) Cd NH2 L:Arg61 4.54 Cd NH1 L:Arg61 4.61 Cd OE1 L:Glu79 4.40 Cd OE1 L:Glu81 2.48 Cd OE2 L:Glu81 2.31 Cd CD L:Glu81 2.70 Cd CG L:Glu81 4.21 Cd O L:Hoh292 3.98 Cd O L:Hoh293 2.25 Cd O L:Hoh313 1.59 interactive model: