Cadmium in the structure of X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin With A Cubic Space Group (pdb 2fcn)

The binding sites of Cadmium atom in the structure of X-Ray Crystal Structure of A Chemically Synthesized [D-VAL35]Ubiquitin With A Cubic Space Group (pdb code 2fcn). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2fcn structure was solved by D.BANG, A.V.GRIBENKO, V.TERESHKO, A.A.KOSSIAKOFF, S.B.KENT, G.I.MAKHATADZE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.2 Space group P4332 a (A) 106.152 b (A) 106.152 c (A) 106.152 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) 27.8 Cadmium Binding Sites: Cadmium binding site 1 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2fcn. 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: Lys63, A: Glu64, A: Act101, A: Act102, A: Hoh103, A: Hoh1012, conact list: Atom Atom Distance (A) Cd CE A:Lys63 4.86 Cd CD A:Lys63 4.81 Cd NZ A:Lys63 4.71 Cd OE1 A:Glu64 2.56 Cd OE2 A:Glu64 2.19 Cd CD A:Glu64 2.71 Cd CG A:Glu64 4.22 Cd O A:Act101 2.55 Cd CH3 A:Act101 4.23 Cd C A:Act101 2.75 Cd OXT A:Act101 2.17 Cd O A:Act102 3.71 Cd CH3 A:Act102 4.33 Cd C A:Act102 3.22 Cd OXT A:Act102 2.18 Cd O A:Hoh103 2.74 Cd O A:Hoh1012 4.02 interactive model: Cadmium binding site 2 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2fcn. 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: Glu18, A: Asp21, A: Asn25, A: Lys29, A: Hoh201, conact list: Atom Atom Distance (A) Cd N A:Glu18 4.35 Cd CB A:Glu18 4.25 Cd OE2 A:Glu18 4.08 Cd CD A:Glu18 4.47 Cd CG A:Glu18 3.73 Cd CA A:Glu18 4.99 Cd CB A:Asp21 4.32 Cd OD2 A:Asp21 2.49 Cd OD1 A:Asp21 2.40 Cd CG A:Asp21 2.82 Cd CB A:Asn25 4.80 Cd ND2 A:Asn25 4.19 Cd CG A:Asn25 4.92 Cd CE A:Lys29 3.35 Cd CD A:Lys29 4.84 Cd NZ A:Lys29 3.59 Cd O A:Hoh201 2.85 interactive model: Cadmium binding site 3 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2fcn. 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: Leu1, A: Gln2, A: Glu16, A: Act301, A: Hoh1004, A: Hoh1021, A: Hoh1025, conact list: Atom Atom Distance (A) Cd O A:Leu1 3.39 Cd N A:Leu1 2.24 Cd CB A:Leu1 4.58 Cd C A:Leu1 3.38 Cd CA A:Leu1 3.23 Cd N A:Gln2 4.20 Cd CB A:Gln2 4.88 Cd CA A:Gln2 4.99 Cd OE1 A:Glu16 2.17 Cd OE2 A:Glu16 2.88 Cd CD A:Glu16 2.84 Cd CG A:Glu16 4.30 Cd O A:Act301 2.62 Cd CH3 A:Act301 4.27 Cd C A:Act301 2.79 Cd OXT A:Act301 2.16 Cd O A:Hoh1004 4.75 Cd O A:Hoh1021 4.98 Cd O A:Hoh1025 4.73 interactive model: Cadmium binding site 4 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2fcn. 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: Glu24, A: Lys27, A: Asp52, A: Cd401, conact list: Atom Atom Distance (A) Cd OE1 A:Glu24 2.18 Cd OE2 A:Glu24 3.23 Cd CD A:Glu24 3.05 Cd CG A:Glu24 4.48 Cd CD A:Lys27 4.99 Cd NZ A:Lys27 4.30 Cd CB A:Asp52 3.77 Cd OD2 A:Asp52 4.55 Cd OD1 A:Asp52 2.49 Cd CG A:Asp52 3.46 Cd CD A:Cd401 4.42 interactive model: Cadmium binding site 5 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2fcn. 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: Asp39, A: Cd400, conact list: Atom Atom Distance (A) Cd CB A:Asp39 4.49 Cd OD2 A:Asp39 3.41 Cd OD1 A:Asp39 2.15 Cd CG A:Asp39 3.14 Cd CD A:Cd400 4.42 interactive model: Cadmium binding site 6 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2fcn. 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: Gly53, A: Arg54, A: Thr55, A: Asp58, conact list: Atom Atom Distance (A) Cd O A:Gly53 4.87 Cd C A:Arg54 4.99 Cd NH1 A:Arg54 4.52 Cd CA A:Arg54 4.62 Cd N A:Thr55 4.48 Cd CB A:Thr55 4.88 Cd CG2 A:Thr55 4.23 Cd OG1 A:Thr55 4.44 Cd CB A:Asp58 4.28 Cd OD2 A:Asp58 2.17 Cd OD1 A:Asp58 2.64 Cd CG A:Asp58 2.78 interactive model: Cadmium binding site 7 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2fcn. 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: Lys6, B: His68, B: Hoh2005, conact list: Atom Atom Distance (A) Cd CE B:Lys6 4.43 Cd CD B:Lys6 4.16 Cd CG B:Lys6 4.74 Cd NZ B:Lys6 4.14 Cd NE2 B:His68 4.30 Cd CB B:His68 3.33 Cd ND1 B:His68 2.23 Cd CD2 B:His68 4.26 Cd CE1 B:His68 3.23 Cd CG B:His68 3.11 Cd CA B:His68 4.44 Cd O B:Hoh2005 3.85 interactive model: Cadmium binding site 8 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 2fcn. 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: Glu18, B: Asp21, B: Asn25, B: Lys29, conact list: Atom Atom Distance (A) Cd N B:Glu18 4.55 Cd OE1 B:Glu18 2.94 Cd CB B:Glu18 4.24 Cd CD B:Glu18 4.06 Cd CG B:Glu18 4.53 Cd CB B:Asp21 4.40 Cd OD2 B:Asp21 2.91 Cd OD1 B:Asp21 2.19 Cd CG B:Asp21 2.94 Cd CA B:Asp21 4.98 Cd ND2 B:Asn25 4.24 Cd CG B:Asn25 4.99 Cd CE B:Lys29 4.36 Cd NZ B:Lys29 3.49 interactive model: Cadmium binding site 9 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 2fcn. 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: Leu1, B: Gln2, B: Glu16, B: Val17, conact list: Atom Atom Distance (A) Cd O B:Leu1 3.30 Cd N B:Leu1 2.22 Cd CB B:Leu1 4.17 Cd C B:Leu1 3.30 Cd CA B:Leu1 3.29 Cd N B:Gln2 4.03 Cd CA B:Gln2 4.88 Cd OE1 B:Glu16 3.22 Cd OE2 B:Glu16 2.17 Cd CD B:Glu16 3.00 Cd CG B:Glu16 4.31 Cd O B:Val17 4.03 Cd N B:Val17 4.98 interactive model: Cadmium binding site 10 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 2fcn. 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: Glu24, B: Asp39, B: Asp52, B: Cd801, conact list: Atom Atom Distance (A) Cd OE1 B:Glu24 2.89 Cd OE2 B:Glu24 3.17 Cd CD B:Glu24 3.32 Cd CG B:Glu24 4.69 Cd OD1 B:Asp39 4.49 Cd CB B:Asp52 3.66 Cd OD2 B:Asp52 4.10 Cd OD1 B:Asp52 2.13 Cd CG B:Asp52 3.13 Cd CD B:Cd801 4.39 interactive model: Cadmium binding site 11 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 2fcn. 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: Glu24, B: Asp39, B: Cd800, conact list: Atom Atom Distance (A) Cd OE1 B:Glu24 4.94 Cd CB B:Asp39 4.67 Cd OD2 B:Asp39 3.18 Cd OD1 B:Asp39 2.47 Cd CG B:Asp39 3.23 Cd CD B:Cd800 4.39 interactive model: Cadmium binding site 12 out of 12 in 2fcn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 2fcn. 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: Arg54, B: Thr55, B: Asp58, conact list: Atom Atom Distance (A) Cd CG B:Arg54 4.72 Cd N B:Thr55 4.96 Cd OG1 B:Thr55 4.15 Cd CB B:Asp58 4.28 Cd OD2 B:Asp58 2.63 Cd OD1 B:Asp58 2.57 Cd CG B:Asp58 2.90 interactive model: