Cadmium in the structure of Cytochrome Domain of Cellobiose Dehydrogenase, pH 4.6 (pdb 1d7c)

The binding sites of Cadmium atom in the structure of Cytochrome Domain of Cellobiose Dehydrogenase, pH 4.6 (pdb code 1d7c). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1d7c structure was solved by B.M.HALLBERG, T.BERGFORS, K.BACKBRO, C.DIVNE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-1.9 Space group P65 a (A) 139.400 b (A) 139.400 c (A) 53.940 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.7 Rfree (%) 22 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 1d7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1d7c. 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: Pro21, A: Val22, A: Asp24, B: Phe166, B: Hem401, A: Hoh1629, A: Hoh1662, A: Hoh1672, A: Hoh1733, B: Hoh1628, B: Hoh2633, conact list: Atom Atom Distance (A) Cd O A:Pro21 2.37 Cd CB A:Pro21 4.24 Cd C A:Pro21 3.36 Cd CA A:Pro21 3.74 Cd O A:Val22 4.81 Cd N A:Val22 4.55 Cd C A:Val22 4.90 Cd CA A:Val22 4.91 Cd N A:Asp24 4.84 Cd CB A:Asp24 4.25 Cd OD2 A:Asp24 2.47 Cd OD1 A:Asp24 2.35 Cd CG A:Asp24 2.71 Cd CA A:Asp24 4.81 Cd CZ B:Phe166 4.93 Cd CBA B:Hem401 4.14 Cd CGA B:Hem401 2.62 Cd O2A B:Hem401 2.42 Cd O1A B:Hem401 2.20 Cd O A:Hoh1629 1.80 Cd O A:Hoh1662 4.37 Cd O A:Hoh1672 4.73 Cd O A:Hoh1733 4.34 Cd O B:Hoh1628 2.26 Cd O B:Hoh2633 4.55 interactive model: Cadmium binding site 2 out of 5 in 1d7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1d7c. 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: Phe13, A: Pro106, A: Glu107, A: Tyr184, A: Leu185, A: Asn186, A: Gly187, A: Asp188, A: Hoh1709, A: Hoh1721, A: Hoh1740, conact list: Atom Atom Distance (A) Cd CZ A:Phe13 4.98 Cd CB A:Pro106 4.86 Cd CD A:Pro106 4.50 Cd CG A:Pro106 4.30 Cd OE1 A:Glu107 3.59 Cd OE2 A:Glu107 2.54 Cd CD A:Glu107 3.46 Cd CG A:Glu107 4.85 Cd O A:Tyr184 3.67 Cd C A:Tyr184 4.76 Cd O A:Leu185 4.40 Cd C A:Leu185 4.64 Cd O A:Asn186 3.81 Cd N A:Asn186 4.76 Cd C A:Asn186 3.45 Cd CA A:Asn186 4.54 Cd O A:Gly187 3.95 Cd N A:Gly187 2.65 Cd C A:Gly187 3.48 Cd CA A:Gly187 2.08 Cd N A:Asp188 4.48 Cd O A:Hoh1709 2.98 Cd O A:Hoh1721 2.68 Cd O A:Hoh1740 4.43 interactive model: Cadmium binding site 3 out of 5 in 1d7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1d7c. 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: Asn186, A: Gly187, A: Asp188, A: Hoh1768, conact list: Atom Atom Distance (A) Cd O A:Asn186 4.48 Cd O A:Gly187 4.67 Cd C A:Gly187 4.92 Cd CB A:Asp188 4.80 Cd OD2 A:Asp188 3.77 Cd OD1 A:Asp188 2.68 Cd CG A:Asp188 3.53 Cd CA A:Asp188 4.99 Cd O A:Hoh1768 3.02 interactive model: Cadmium binding site 4 out of 5 in 1d7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1d7c. 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: Val22, A: His23, A: Trp143, A: Asp165, A: Phe166, B: Val22, B: His23, B: Trp143, B: Asp165, B: Phe166, A: Hoh1612, A: Hoh1627, A: Hoh1677, A: Hoh2642, B: Hoh2612, B: Hoh2627, B: Hoh2677, conact list: Atom Atom Distance (A) Cd CG2 A:Val22 4.62 Cd CE1 A:His23 4.97 Cd CH2 A:Trp143 4.60 Cd CB A:Asp165 4.27 Cd OD2 A:Asp165 2.36 Cd OD1 A:Asp165 2.45 Cd CG A:Asp165 2.76 Cd O A:Phe166 4.33 Cd CB B:Val22 4.96 Cd CG2 B:Val22 4.56 Cd CG1 B:Val22 4.95 Cd CE1 B:His23 4.93 Cd CH2 B:Trp143 4.62 Cd CB B:Asp165 4.24 Cd OD2 B:Asp165 2.28 Cd OD1 B:Asp165 2.48 Cd CG B:Asp165 2.74 Cd O B:Phe166 4.32 Cd O A:Hoh1612 4.55 Cd O A:Hoh1627 2.37 Cd O A:Hoh1677 4.55 Cd O A:Hoh2642 4.82 Cd O B:Hoh2612 4.59 Cd O B:Hoh2627 2.38 Cd O B:Hoh2677 4.76 interactive model: Cadmium binding site 5 out of 5 in 1d7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1d7c. 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: Phe166, B: Pro21, B: Val22, B: Asp24, A: Hem401, A: Hoh1633, A: Hoh2628, A: Hoh2629, A: Hoh2754, B: Hoh2662, B: Hoh2672, conact list: Atom Atom Distance (A) Cd CZ A:Phe166 4.94 Cd O B:Pro21 2.38 Cd CB B:Pro21 4.23 Cd C B:Pro21 3.37 Cd CA B:Pro21 3.76 Cd O B:Val22 4.86 Cd N B:Val22 4.58 Cd C B:Val22 4.94 Cd CA B:Val22 4.96 Cd N B:Asp24 4.84 Cd CB B:Asp24 4.27 Cd OD2 B:Asp24 2.48 Cd OD1 B:Asp24 2.36 Cd CG B:Asp24 2.75 Cd CA B:Asp24 4.80 Cd CBA A:Hem401 4.16 Cd CGA A:Hem401 2.64 Cd O2A A:Hem401 2.48 Cd O1A A:Hem401 2.22 Cd O A:Hoh1633 4.52 Cd O A:Hoh2628 2.41 Cd O A:Hoh2629 2.04 Cd O A:Hoh2754 4.26 Cd O B:Hoh2662 4.50 Cd O B:Hoh2672 4.52 interactive model: