Zinc in the structure of Crystal Structure of A Hdac-Like Protein With 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb 2gh6)

The binding sites of Zinc atom in the structure of Crystal Structure of A Hdac-Like Protein With 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb code 2gh6). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2gh6 structure was solved by T.K.NIELSEN, C.HILDMANN, D.RIESTER, D.WEGENER, A.SCHWIENHORST, R.FICNER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.8-2.2 Space group P1211 a (A) 68.507 b (A) 94.897 c (A) 123.301 alpha (°) 90.00 beta (°) 104.28 gamma (°) 90.00 Rfactor (%) 15.8 Rfree (%) 21.4 Zinc Binding Sites: Zinc binding site 1 out of 4 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His142, A: His143, A: Asp180, A: Val181, A: His182, A: Asp268, A: Gly310, A: Gly311, A: Tyr312, A: Cf39452, conact list: Atom Atom Distance (A) Zn NE2 A:His142 3.99 Zn CE1 A:His142 4.50 Zn NE2 A:His143 4.68 Zn CB A:Asp180 4.17 Zn OD2 A:Asp180 2.48 Zn C A:Asp180 4.90 Zn OD1 A:Asp180 2.19 Zn CG A:Asp180 2.65 Zn CA A:Asp180 4.90 Zn N A:Val181 4.44 Zn CG1 A:Val181 4.59 Zn NE2 A:His182 4.26 Zn N A:His182 4.07 Zn CB A:His182 3.77 Zn ND1 A:His182 2.25 Zn CD2 A:His182 4.42 Zn CE1 A:His182 3.07 Zn CG A:His182 3.36 Zn CA A:His182 4.56 Zn CB A:Asp268 4.33 Zn OD2 A:Asp268 1.98 Zn OD1 A:Asp268 3.47 Zn CG A:Asp268 3.05 Zn N A:Gly310 4.44 Zn C A:Gly310 4.83 Zn CA A:Gly310 4.08 Zn N A:Gly311 4.85 Zn CE2 A:Tyr312 4.27 Zn CZ A:Tyr312 4.77 Zn OH A:Tyr312 4.26 Zn C9 A:Cf39452 3.90 Zn C11 A:Cf39452 3.85 Zn C11 A:Cf39452 3.44 Zn F2 A:Cf39452 3.55 Zn O2 A:Cf39452 1.77 Zn O2 A:Cf39452 2.11 Zn C13 A:Cf39452 2.78 Zn C13 A:Cf39452 2.70 Zn F3 A:Cf39452 4.63 Zn C15 A:Cf39452 3.70 Zn F1 A:Cf39452 4.53 interactive model: Zinc binding site 2 out of 4 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His142, B: His143, B: Asp180, B: Val181, B: His182, B: Asp268, B: Gly310, B: Gly311, B: Tyr312, B: Cf39552, conact list: Atom Atom Distance (A) Zn NE2 B:His142 4.10 Zn CE1 B:His142 4.51 Zn NE2 B:His143 4.68 Zn CB B:Asp180 4.10 Zn OD2 B:Asp180 2.56 Zn C B:Asp180 4.83 Zn OD1 B:Asp180 2.05 Zn CG B:Asp180 2.62 Zn CA B:Asp180 4.80 Zn N B:Val181 4.40 Zn CG1 B:Val181 4.37 Zn NE2 B:His182 4.28 Zn N B:His182 4.10 Zn CB B:His182 3.80 Zn ND1 B:His182 2.27 Zn CD2 B:His182 4.45 Zn CE1 B:His182 3.09 Zn CG B:His182 3.39 Zn CA B:His182 4.58 Zn CB B:Asp268 4.29 Zn OD2 B:Asp268 1.92 Zn OD1 B:Asp268 3.44 Zn CG B:Asp268 3.00 Zn N B:Gly310 4.49 Zn C B:Gly310 4.81 Zn CA B:Gly310 4.19 Zn N B:Gly311 4.89 Zn CE2 B:Tyr312 4.23 Zn CZ B:Tyr312 4.80 Zn OH B:Tyr312 4.40 Zn C9 B:Cf39552 3.83 Zn C11 B:Cf39552 3.72 Zn C11 B:Cf39552 3.29 Zn F2 B:Cf39552 3.57 Zn O2 B:Cf39552 1.91 Zn O2 B:Cf39552 2.25 Zn C13 B:Cf39552 2.77 Zn C13 B:Cf39552 2.70 Zn F3 B:Cf39552 4.69 Zn C15 B:Cf39552 3.73 Zn F1 B:Cf39552 4.54 interactive model: Zinc binding site 3 out of 4 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His142, C: His143, C: Asp180, C: Val181, C: His182, C: Asp268, C: Gly310, C: Gly311, C: Tyr312, C: Cf39652, conact list: Atom Atom Distance (A) Zn NE2 C:His142 3.92 Zn CE1 C:His142 4.43 Zn NE2 C:His143 4.55 Zn CB C:Asp180 4.21 Zn OD2 C:Asp180 2.55 Zn OD1 C:Asp180 2.14 Zn CG C:Asp180 2.68 Zn CA C:Asp180 4.98 Zn N C:Val181 4.52 Zn CG1 C:Val181 4.52 Zn NE2 C:His182 4.33 Zn N C:His182 4.30 Zn CB C:His182 3.70 Zn ND1 C:His182 2.28 Zn CD2 C:His182 4.43 Zn CE1 C:His182 3.17 Zn CG C:His182 3.34 Zn CA C:His182 4.65 Zn CB C:Asp268 4.42 Zn OD2 C:Asp268 2.05 Zn OD1 C:Asp268 3.67 Zn CG C:Asp268 3.18 Zn N C:Gly310 4.38 Zn C C:Gly310 4.83 Zn CA C:Gly310 4.07 Zn N C:Gly311 4.88 Zn CE2 C:Tyr312 4.30 Zn CZ C:Tyr312 4.79 Zn OH C:Tyr312 4.28 Zn C9 C:Cf39652 3.94 Zn C11 C:Cf39652 3.69 Zn C11 C:Cf39652 3.67 Zn F2 C:Cf39652 3.33 Zn O2 C:Cf39652 1.76 Zn O2 C:Cf39652 2.07 Zn C13 C:Cf39652 2.66 Zn C13 C:Cf39652 2.73 Zn F3 C:Cf39652 4.52 Zn C15 C:Cf39652 3.57 Zn F1 C:Cf39652 4.39 interactive model: Zinc binding site 4 out of 4 in 2gh6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2gh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His142, D: His143, D: Asp180, D: Val181, D: His182, D: Asp268, D: Gly310, D: Gly311, D: Tyr312, D: Cf39752, conact list: Atom Atom Distance (A) Zn NE2 D:His142 3.94 Zn CE1 D:His142 4.37 Zn NE2 D:His143 4.63 Zn CB D:Asp180 4.13 Zn OD2 D:Asp180 2.55 Zn C D:Asp180 4.76 Zn OD1 D:Asp180 2.10 Zn CG D:Asp180 2.65 Zn CA D:Asp180 4.84 Zn N D:Val181 4.33 Zn C D:Val181 5.00 Zn CG1 D:Val181 4.42 Zn NE2 D:His182 4.33 Zn N D:His182 4.10 Zn CB D:His182 3.64 Zn ND1 D:His182 2.27 Zn CD2 D:His182 4.40 Zn CE1 D:His182 3.18 Zn CG D:His182 3.30 Zn CA D:His182 4.51 Zn CB D:Asp268 4.32 Zn OD2 D:Asp268 1.99 Zn OD1 D:Asp268 3.48 Zn CG D:Asp268 3.05 Zn N D:Gly310 4.50 Zn C D:Gly310 4.90 Zn CA D:Gly310 4.23 Zn N D:Gly311 4.97 Zn CE2 D:Tyr312 4.34 Zn CZ D:Tyr312 4.89 Zn OH D:Tyr312 4.39 Zn C9 D:Cf39752 3.95 Zn C11 D:Cf39752 3.76 Zn C11 D:Cf39752 3.75 Zn F2 D:Cf39752 3.51 Zn O2 D:Cf39752 1.89 Zn O2 D:Cf39752 2.12 Zn C13 D:Cf39752 2.77 Zn C13 D:Cf39752 2.82 Zn F3 D:Cf39752 4.71 Zn C15 D:Cf39752 3.71 Zn F1 D:Cf39752 4.44 interactive model: