Cadmium in the structure of A Structural Analysis of Metal Substitutions in Thermolysin (pdb 1lne)

The binding sites of Cadmium atom in the structure of A Structural Analysis of Metal Substitutions in Thermolysin (pdb code 1lne). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1lne structure was solved by D.R.HOLLAND, A.C.HAUSRATH, D.JUERS, B.W.MATTHEWS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P6122 a (A) 93.888 b (A) 93.888 c (A) 131.164 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) n/a Rfree (%) n/a Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1lne Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1lne. 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: E: His142, E: Glu143, E: His146, E: Tyr157, E: Glu166, E: Ser169, E: His231, E: Val1321, E: Hoh907, E: Hoh1058, E: Hoh1059, conact list: Atom Atom Distance (A) Cd NE2 E:His142 2.16 Cd ND1 E:His142 4.38 Cd CD2 E:His142 3.15 Cd CE1 E:His142 3.21 Cd CG E:His142 4.35 Cd OE1 E:Glu143 3.99 Cd OE1 E:Glu143 4.09 Cd OE2 E:Glu143 2.62 Cd OE2 E:Glu143 4.72 Cd CD E:Glu143 3.65 Cd CD E:Glu143 4.73 Cd NE2 E:His146 2.18 Cd ND1 E:His146 4.29 Cd CD2 E:His146 3.17 Cd CE1 E:His146 3.15 Cd CG E:His146 4.32 Cd CZ E:Tyr157 4.94 Cd OH E:Tyr157 3.90 Cd OE1 E:Glu166 2.99 Cd OE2 E:Glu166 2.11 Cd CD E:Glu166 2.87 Cd CG E:Glu166 4.36 Cd CB E:Ser169 4.87 Cd NE2 E:His231 4.26 Cd CD2 E:His231 4.98 Cd O E:Val1321 4.54 Cd N E:Val1321 4.09 Cd C E:Val1321 4.45 Cd CA E:Val1321 3.94 Cd O E:Hoh907 2.35 Cd O E:Hoh1058 4.27 Cd O E:Hoh1059 2.34 interactive model: Cadmium binding site 2 out of 4 in 1lne Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1lne. 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: E: Glu177, E: Lys182, E: Asn183, E: Pro184, E: Asp185, E: Glu190, E: Asp191, E: Ca901, E: Hoh931, E: Hoh979, E: Hoh981, conact list: Atom Atom Distance (A) Cd OE1 E:Glu177 3.78 Cd OE2 E:Glu177 2.54 Cd CD E:Glu177 3.30 Cd CG E:Glu177 4.31 Cd O E:Lys182 3.82 Cd C E:Lys182 4.90 Cd O E:Asn183 2.43 Cd CB E:Asn183 4.26 Cd C E:Asn183 3.59 Cd CA E:Asn183 4.60 Cd O E:Pro184 4.94 Cd N E:Pro184 4.32 Cd C E:Pro184 4.28 Cd CA E:Pro184 4.21 Cd N E:Asp185 4.16 Cd CB E:Asp185 4.45 Cd OD2 E:Asp185 2.32 Cd OD1 E:Asp185 3.65 Cd CG E:Asp185 3.25 Cd CA E:Asp185 4.88 Cd OE1 E:Glu190 4.31 Cd OE2 E:Glu190 2.31 Cd CD E:Glu190 3.33 Cd CG E:Glu190 3.66 Cd OD2 E:Asp191 4.08 Cd OD1 E:Asp191 4.08 Cd CG E:Asp191 4.39 Cd CA E:Ca901 3.78 Cd O E:Hoh931 2.35 Cd O E:Hoh979 4.63 Cd O E:Hoh981 2.34 interactive model: Cadmium binding site 3 out of 4 in 1lne Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1lne. 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: E: Asp57, E: Ala58, E: Asp59, E: Asn60, E: Gln61, E: Phe62, E: Asp67, E: Hoh908, E: Hoh910, E: Hoh911, E: Hoh934, E: Hoh988, E: Hoh999, E: Hoh1038, E: Hoh1053, conact list: Atom Atom Distance (A) Cd CB E:Asp57 4.26 Cd OD2 E:Asp57 2.71 Cd OD1 E:Asp57 2.14 Cd CG E:Asp57 2.76 Cd N E:Ala58 4.61 Cd N E:Asp59 4.23 Cd CB E:Asp59 4.59 Cd OD2 E:Asp59 3.62 Cd C E:Asp59 4.93 Cd OD1 E:Asp59 2.34 Cd CG E:Asp59 3.25 Cd CA E:Asp59 4.81 Cd N E:Asn60 4.71 Cd O E:Gln61 2.26 Cd N E:Gln61 3.93 Cd CB E:Gln61 4.29 Cd C E:Gln61 3.43 Cd CA E:Gln61 4.12 Cd N E:Phe62 4.47 Cd CA E:Phe62 4.67 Cd OD2 E:Asp67 4.58 Cd O E:Hoh908 2.30 Cd O E:Hoh910 2.03 Cd O E:Hoh911 2.35 Cd O E:Hoh934 4.46 Cd O E:Hoh988 3.91 Cd O E:Hoh999 4.35 Cd O E:Hoh1038 4.22 Cd O E:Hoh1053 4.64 interactive model: Cadmium binding site 4 out of 4 in 1lne Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1lne. 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: E: Arg203, E: Tyr211, E: Asp213, E: His231, E: Ile232, E: Hoh954, E: Hoh1055, E: Hoh1056, E: Hoh1057, conact list: Atom Atom Distance (A) Cd CD E:Arg203 4.47 Cd CG E:Arg203 4.30 Cd O E:Tyr211 4.95 Cd CB E:Asp213 4.36 Cd OD2 E:Asp213 2.55 Cd OD1 E:Asp213 2.52 Cd CG E:Asp213 2.87 Cd O E:His231 2.73 Cd CB E:His231 4.44 Cd C E:His231 3.73 Cd CA E:His231 4.74 Cd N E:Ile232 4.43 Cd CG1 E:Ile232 4.67 Cd CA E:Ile232 4.27 Cd O E:Hoh954 4.27 Cd O E:Hoh1055 2.47 Cd O E:Hoh1056 2.58 Cd O E:Hoh1057 2.77 interactive model: