Cadmium in the structure of Structural Basis For Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases (pdb 1guy)

The binding sites of Cadmium atom in the structure of Structural Basis For Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases (pdb code 1guy). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1guy structure was solved by B.DALHUS, M.SARINEN, U.H.SAUER, P.EKLUND, K.JOHANSSON, A.KARLSSON, S.RAMASWAMY, A.BJORK, B.SYNSTAD, K.NATERSTAD, R.SIREVAG, H.EKLUND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-2.2 Space group P3121 a (A) 106.670 b (A) 106.670 c (A) 103.990 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.4 Rfree (%) 19.7 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 1guy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1guy. 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: Glu165, C: Glu238, C: Lys244, C: Arg246, A: Hoh2079, C: Hoh2106, conact list: Atom Atom Distance (A) Cd OE1 A:Glu165 2.82 Cd OE2 A:Glu165 2.52 Cd CD A:Glu165 3.00 Cd CG A:Glu165 4.46 Cd OE1 C:Glu238 4.23 Cd OE2 C:Glu238 4.47 Cd CD C:Glu238 4.76 Cd CE C:Lys244 4.42 Cd NZ C:Lys244 4.21 Cd NH1 C:Arg246 4.96 Cd O A:Hoh2079 4.01 Cd O C:Hoh2106 2.42 interactive model: Cadmium binding site 2 out of 5 in 1guy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1guy. 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: Glu281, A: Hoh2145, A: Hoh2146, A: Hoh2147, A: Hoh2149, conact list: Atom Atom Distance (A) Cd OE1 A:Glu281 2.58 Cd OE2 A:Glu281 2.78 Cd CD A:Glu281 3.02 Cd CG A:Glu281 4.49 Cd O A:Hoh2145 4.79 Cd O A:Hoh2146 4.30 Cd O A:Hoh2147 4.72 Cd O A:Hoh2149 4.73 interactive model: Cadmium binding site 3 out of 5 in 1guy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1guy. 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: Asp200, A: Hoh2102, conact list: Atom Atom Distance (A) Cd CB A:Asp200 4.24 Cd OD2 A:Asp200 2.24 Cd OD1 A:Asp200 2.53 Cd CG A:Asp200 2.72 Cd O A:Hoh2102 4.61 interactive model: Cadmium binding site 4 out of 5 in 1guy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1guy. 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: Glu238, A: Lys244, C: Glu165, A: Hoh2121, A: Hoh2123, C: Hoh2070, conact list: Atom Atom Distance (A) Cd OE1 A:Glu238 4.33 Cd OE2 A:Glu238 4.40 Cd CD A:Glu238 4.78 Cd CE A:Lys244 4.45 Cd NZ A:Lys244 4.31 Cd OE1 C:Glu165 2.76 Cd OE2 C:Glu165 2.62 Cd CD C:Glu165 3.01 Cd CG C:Glu165 4.47 Cd O A:Hoh2121 2.40 Cd O A:Hoh2123 2.90 Cd O C:Hoh2070 4.15 interactive model: Cadmium binding site 5 out of 5 in 1guy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1guy. 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: C: Glu159, C: Hoh2063, C: Hoh2064, C: Hoh2090, conact list: Atom Atom Distance (A) Cd O C:Glu159 4.62 Cd OE1 C:Glu159 2.90 Cd OE2 C:Glu159 2.64 Cd CD C:Glu159 3.10 Cd CG C:Glu159 4.57 Cd CA C:Glu159 4.98 Cd O C:Hoh2063 3.44 Cd O C:Hoh2064 2.65 Cd O C:Hoh2090 3.36 interactive model: