Cadmium in the structure of Crystal Structure Of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 At 2.2 Angstrom Resolution in the Presence of Calcium and Cademium (pdb 3jqx)

The binding sites of Cadmium atom in the structure of Crystal Structure Of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 At 2.2 Angstrom Resolution in the Presence of Calcium and Cademium (pdb code 3jqx). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3jqx structure was solved by J.SAKON, S.T.L.PHILOMINATHAN, R.BAUER, O.MATSUSHITA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.7-2.2 Space group P212121 a (A) 61.567 b (A) 64.589 c (A) 96.010 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.6 Rfree (%) 25 Cadmium Binding Sites: Cadmium binding site 1 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3jqx. 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: Glu908, A: Glu910, A: Asn912, A: Thr931, A: Ile932, A: Glu933, A: Asp937, A: Asp939, A: Tyr1011, A: Ca2001, A: Hoh85, conact list: Atom Atom Distance (A) Cd OE1 A:Glu908 2.59 Cd OE2 A:Glu908 2.66 Cd CD A:Glu908 2.98 Cd CG A:Glu908 4.49 Cd OE1 A:Glu910 4.67 Cd OE2 A:Glu910 2.54 Cd CD A:Glu910 3.77 Cd CG A:Glu910 4.57 Cd OD1 A:Asn912 4.55 Cd O A:Thr931 2.45 Cd N A:Thr931 4.28 Cd CB A:Thr931 4.95 Cd C A:Thr931 3.56 Cd CA A:Thr931 4.52 Cd N A:Ile932 4.32 Cd C A:Ile932 4.99 Cd CA A:Ile932 4.29 Cd N A:Glu933 4.61 Cd CG A:Glu933 4.67 Cd CB A:Asp937 4.69 Cd OD2 A:Asp937 2.39 Cd OD1 A:Asp937 3.56 Cd CG A:Asp937 3.32 Cd CB A:Asp939 4.36 Cd OD2 A:Asp939 2.56 Cd OD1 A:Asp939 2.51 Cd CG A:Asp939 2.87 Cd OH A:Tyr1011 4.31 Cd CA A:Ca2001 3.69 Cd O A:Hoh85 3.14 interactive model: Cadmium binding site 2 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3jqx. 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: Ser914, A: Lys915, A: Glu916, A: Hoh131, A: Hoh186, conact list: Atom Atom Distance (A) Cd CB A:Ser914 4.74 Cd N A:Lys915 4.62 Cd CB A:Lys915 4.63 Cd OE1 A:Glu916 2.84 Cd OE2 A:Glu916 2.17 Cd CD A:Glu916 2.88 Cd CG A:Glu916 4.43 Cd O A:Hoh131 2.73 Cd O A:Hoh186 4.83 interactive model: Cadmium binding site 3 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3jqx. 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: Glu970, A: Gly995, A: Arg996, conact list: Atom Atom Distance (A) Cd OE1 A:Glu970 3.44 Cd OE2 A:Glu970 2.24 Cd CD A:Glu970 3.15 Cd CG A:Glu970 4.46 Cd C A:Gly995 4.91 Cd CA A:Gly995 4.21 Cd N A:Arg996 4.51 interactive model: Cadmium binding site 4 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3jqx. 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: B: Glu908, B: Glu910, B: Asn912, B: Thr931, B: Ile932, B: Glu933, B: Asp937, B: Asp939, B: Tyr1011, B: Ca2001, B: Hoh14, B: Hoh54, conact list: Atom Atom Distance (A) Cd OE1 B:Glu908 2.79 Cd OE2 B:Glu908 2.54 Cd CD B:Glu908 3.02 Cd CG B:Glu908 4.54 Cd OE1 B:Glu910 4.46 Cd OE2 B:Glu910 2.35 Cd CD B:Glu910 3.57 Cd CG B:Glu910 4.35 Cd ND2 B:Asn912 4.99 Cd OD1 B:Asn912 4.56 Cd O B:Thr931 2.35 Cd N B:Thr931 4.29 Cd C B:Thr931 3.48 Cd CA B:Thr931 4.43 Cd N B:Ile932 4.26 Cd C B:Ile932 4.95 Cd CA B:Ile932 4.26 Cd N B:Glu933 4.52 Cd CG B:Glu933 4.81 Cd CB B:Asp937 4.70 Cd OD2 B:Asp937 2.49 Cd OD1 B:Asp937 3.56 Cd CG B:Asp937 3.35 Cd CB B:Asp939 4.35 Cd OD2 B:Asp939 2.51 Cd OD1 B:Asp939 2.48 Cd CG B:Asp939 2.85 Cd CE2 B:Tyr1011 4.99 Cd OH B:Tyr1011 4.29 Cd CA B:Ca2001 3.63 Cd O B:Hoh14 2.86 Cd O B:Hoh54 4.59 interactive model: Cadmium binding site 5 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3jqx. 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: B: Ser914, B: Lys915, B: Glu916, conact list: Atom Atom Distance (A) Cd CB B:Ser914 4.39 Cd OG B:Ser914 4.83 Cd N B:Lys915 4.47 Cd CB B:Lys915 4.60 Cd CA B:Lys915 4.98 Cd N B:Glu916 4.54 Cd OE1 B:Glu916 2.27 Cd OE2 B:Glu916 2.44 Cd CD B:Glu916 2.59 Cd CG B:Glu916 4.01 interactive model: Cadmium binding site 6 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 3jqx. 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: B: Glu970, B: Gly995, B: Arg996, B: Hoh132, B: Hoh147, B: Hoh178, conact list: Atom Atom Distance (A) Cd OE1 B:Glu970 2.79 Cd OE2 B:Glu970 2.50 Cd CD B:Glu970 2.98 Cd CG B:Glu970 4.47 Cd CA B:Gly995 4.89 Cd N B:Arg996 4.63 Cd CB B:Arg996 4.91 Cd O B:Hoh132 3.16 Cd O B:Hoh147 4.68 Cd O B:Hoh178 3.75 interactive model: Cadmium binding site 7 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 3jqx. 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: Glu908, C: Glu910, C: Asn912, C: Thr931, C: Ile932, C: Glu933, C: Asp937, C: Asp939, C: Tyr1011, C: Ca2001, C: Hoh56, conact list: Atom Atom Distance (A) Cd OE1 C:Glu908 2.63 Cd OE2 C:Glu908 2.53 Cd CD C:Glu908 2.94 Cd CG C:Glu908 4.46 Cd OE1 C:Glu910 4.70 Cd OE2 C:Glu910 2.59 Cd CD C:Glu910 3.74 Cd CG C:Glu910 4.32 Cd ND2 C:Asn912 4.97 Cd OD1 C:Asn912 4.57 Cd O C:Thr931 2.28 Cd N C:Thr931 4.26 Cd C C:Thr931 3.48 Cd CA C:Thr931 4.50 Cd N C:Ile932 4.27 Cd CA C:Ile932 4.29 Cd N C:Glu933 4.65 Cd OE2 C:Glu933 4.39 Cd CD C:Glu933 4.84 Cd CG C:Glu933 4.42 Cd CB C:Asp937 4.69 Cd OD2 C:Asp937 2.40 Cd OD1 C:Asp937 3.45 Cd CG C:Asp937 3.29 Cd CB C:Asp939 4.40 Cd OD2 C:Asp939 2.57 Cd OD1 C:Asp939 2.46 Cd CG C:Asp939 2.87 Cd CE2 C:Tyr1011 4.97 Cd OH C:Tyr1011 4.29 Cd CA C:Ca2001 3.65 Cd O C:Hoh56 2.96 interactive model: Cadmium binding site 8 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 3jqx. 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: Ser914, C: Lys915, C: Glu916, C: Hoh45, C: Hoh123, C: Hoh160, conact list: Atom Atom Distance (A) Cd CB C:Ser914 4.63 Cd N C:Lys915 4.38 Cd CB C:Lys915 4.46 Cd CG C:Lys915 4.99 Cd CA C:Lys915 4.96 Cd NZ C:Lys915 4.52 Cd N C:Glu916 4.79 Cd OE1 C:Glu916 2.23 Cd OE2 C:Glu916 2.59 Cd CD C:Glu916 2.77 Cd CG C:Glu916 4.32 Cd O C:Hoh45 2.88 Cd O C:Hoh123 3.07 Cd O C:Hoh160 4.06 interactive model: Cadmium binding site 9 out of 9 in 3jqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 3jqx. 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: Glu970, C: Pro994, C: Gly995, C: Arg996, C: Hoh145, conact list: Atom Atom Distance (A) Cd OE1 C:Glu970 2.66 Cd OE2 C:Glu970 2.36 Cd CD C:Glu970 2.84 Cd CG C:Glu970 4.36 Cd O C:Pro994 4.64 Cd C C:Gly995 4.96 Cd CA C:Gly995 4.17 Cd N C:Arg996 4.60 Cd O C:Hoh145 2.69 interactive model: