Zinc in PDB 2gh6: Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6 was solved by T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.84 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.507, 94.897, 123.301, 90.00, 104.28, 90.00
R / Rfree (%)	15.8 / 21.4

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Potassium	(K)	8 atoms

The binding sites of Zinc atom in the 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 within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9451 b:31.0 occ:0.50 O2 A:CF39452 1.8 17.8 0.5 OD2 A:ASP268 2.0 17.1 1.0 O2 A:CF39452 2.1 14.5 0.5 OD1 A:ASP180 2.2 16.0 1.0 ND1 A:HIS182 2.2 16.8 1.0 OD2 A:ASP180 2.5 15.4 1.0 CG A:ASP180 2.6 17.4 1.0 C13 A:CF39452 2.7 23.5 0.5 C13 A:CF39452 2.8 24.0 0.5 CG A:ASP268 3.1 15.2 1.0 CE1 A:HIS182 3.1 17.5 1.0 CG A:HIS182 3.4 15.8 1.0 C11 A:CF39452 3.4 25.3 0.5 OD1 A:ASP268 3.5 14.0 1.0 F2 A:CF39452 3.6 26.0 1.0 C15 A:CF39452 3.7 23.1 1.0 CB A:HIS182 3.8 16.0 1.0 C11 A:CF39452 3.9 25.6 0.5 C9 A:CF39452 3.9 27.9 1.0 NE2 A:HIS142 4.0 15.6 1.0 N A:HIS182 4.1 16.0 1.0 CA A:GLY310 4.1 17.3 1.0 CB A:ASP180 4.2 15.7 1.0 NE2 A:HIS182 4.3 14.4 1.0 OH A:TYR312 4.3 21.4 1.0 CE2 A:TYR312 4.3 17.3 1.0 CB A:ASP268 4.3 16.8 1.0 CD2 A:HIS182 4.4 12.9 1.0 N A:VAL181 4.4 16.5 1.0 N A:GLY310 4.4 16.9 1.0 CE1 A:HIS142 4.5 16.3 1.0 F1 A:CF39452 4.5 26.7 1.0 CA A:HIS182 4.6 16.5 1.0 CG1 A:VAL181 4.6 14.0 1.0 F3 A:CF39452 4.6 24.6 1.0 NE2 A:HIS143 4.7 17.1 1.0 CZ A:TYR312 4.8 17.3 1.0 C A:GLY310 4.8 17.9 1.0 N A:GLY311 4.8 18.5 1.0 C A:ASP180 4.9 16.5 1.0 CA A:ASP180 4.9 16.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn9551 b:26.9 occ:0.50 O2 B:CF39552 1.9 5.5 0.5 OD2 B:ASP268 1.9 17.1 1.0 OD1 B:ASP180 2.0 14.6 1.0 O2 B:CF39552 2.2 6.9 0.5 ND1 B:HIS182 2.3 13.6 1.0 OD2 B:ASP180 2.6 17.3 1.0 CG B:ASP180 2.6 16.1 1.0 C13 B:CF39552 2.7 17.9 0.5 C13 B:CF39552 2.8 17.4 0.5 CG B:ASP268 3.0 16.2 1.0 CE1 B:HIS182 3.1 11.8 1.0 C11 B:CF39552 3.3 20.1 0.5 CG B:HIS182 3.4 15.7 1.0 OD1 B:ASP268 3.4 14.9 1.0 F2 B:CF39552 3.6 18.9 1.0 C11 B:CF39552 3.7 19.2 0.5 C15 B:CF39552 3.7 18.2 1.0 CB B:HIS182 3.8 14.9 1.0 C9 B:CF39552 3.8 23.2 1.0 CB B:ASP180 4.1 15.3 1.0 NE2 B:HIS142 4.1 16.3 1.0 N B:HIS182 4.1 16.9 1.0 CA B:GLY310 4.2 15.7 1.0 CE2 B:TYR312 4.2 22.2 1.0 NE2 B:HIS182 4.3 12.0 1.0 CB B:ASP268 4.3 16.2 1.0 CG1 B:VAL181 4.4 16.9 1.0 N B:VAL181 4.4 17.6 1.0 OH B:TYR312 4.4 18.8 1.0 CD2 B:HIS182 4.4 11.0 1.0 N B:GLY310 4.5 16.0 1.0 CE1 B:HIS142 4.5 13.6 1.0 F1 B:CF39552 4.5 19.7 1.0 CA B:HIS182 4.6 16.6 1.0 NE2 B:HIS143 4.7 19.4 1.0 F3 B:CF39552 4.7 20.6 1.0 CZ B:TYR312 4.8 22.2 1.0 CA B:ASP180 4.8 17.3 1.0 C B:GLY310 4.8 16.2 1.0 C B:ASP180 4.8 17.2 1.0 N B:GLY311 4.9 17.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn9651 b:31.3 occ:0.50 O2 C:CF39652 1.8 16.3 0.5 OD2 C:ASP268 2.0 16.2 1.0 O2 C:CF39652 2.1 12.0 0.5 OD1 C:ASP180 2.1 17.9 1.0 ND1 C:HIS182 2.3 20.4 1.0 OD2 C:ASP180 2.6 18.6 1.0 C13 C:CF39652 2.7 23.6 0.5 CG C:ASP180 2.7 18.4 1.0 C13 C:CF39652 2.7 22.1 0.5 CE1 C:HIS182 3.2 21.4 1.0 CG C:ASP268 3.2 16.4 1.0 F2 C:CF39652 3.3 24.9 1.0 CG C:HIS182 3.3 20.2 1.0 C15 C:CF39652 3.6 22.0 1.0 OD1 C:ASP268 3.7 16.6 1.0 C11 C:CF39652 3.7 23.6 0.5 C11 C:CF39652 3.7 25.1 0.5 CB C:HIS182 3.7 17.9 1.0 NE2 C:HIS142 3.9 15.1 1.0 C9 C:CF39652 3.9 27.5 1.0 CA C:GLY310 4.1 17.5 1.0 CB C:ASP180 4.2 17.1 1.0 OH C:TYR312 4.3 20.4 1.0 CE2 C:TYR312 4.3 18.4 1.0 N C:HIS182 4.3 18.7 1.0 NE2 C:HIS182 4.3 19.9 1.0 N C:GLY310 4.4 17.4 1.0 F1 C:CF39652 4.4 23.6 1.0 CB C:ASP268 4.4 17.3 1.0 CD2 C:HIS182 4.4 20.2 1.0 CE1 C:HIS142 4.4 16.2 1.0 N C:VAL181 4.5 17.7 1.0 F3 C:CF39652 4.5 23.8 1.0 CG1 C:VAL181 4.5 16.7 1.0 NE2 C:HIS143 4.5 14.9 1.0 CA C:HIS182 4.7 18.1 1.0 CZ C:TYR312 4.8 18.7 1.0 C C:GLY310 4.8 17.8 1.0 N C:GLY311 4.9 18.1 1.0 CA C:ASP180 5.0 17.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn9751 b:29.7 occ:0.50 O2 D:CF39752 1.9 15.4 0.5 OD2 D:ASP268 2.0 15.7 1.0 OD1 D:ASP180 2.1 23.4 1.0 O2 D:CF39752 2.1 16.3 0.5 ND1 D:HIS182 2.3 21.4 1.0 OD2 D:ASP180 2.5 21.7 1.0 CG D:ASP180 2.6 20.9 1.0 C13 D:CF39752 2.8 23.0 0.5 C13 D:CF39752 2.8 23.3 0.5 CG D:ASP268 3.1 15.9 1.0 CE1 D:HIS182 3.2 21.8 1.0 CG D:HIS182 3.3 20.1 1.0 OD1 D:ASP268 3.5 15.9 1.0 F2 D:CF39752 3.5 24.9 1.0 CB D:HIS182 3.6 17.7 1.0 C15 D:CF39752 3.7 23.7 1.0 C11 D:CF39752 3.7 26.0 0.5 C11 D:CF39752 3.8 25.9 0.5 NE2 D:HIS142 3.9 21.1 1.0 C9 D:CF39752 3.9 28.4 1.0 N D:HIS182 4.1 17.4 1.0 CB D:ASP180 4.1 18.8 1.0 CA D:GLY310 4.2 18.1 1.0 CB D:ASP268 4.3 15.4 1.0 N D:VAL181 4.3 18.3 1.0 NE2 D:HIS182 4.3 19.9 1.0 CE2 D:TYR312 4.3 16.7 1.0 CE1 D:HIS142 4.4 18.1 1.0 OH D:TYR312 4.4 20.4 1.0 CD2 D:HIS182 4.4 22.1 1.0 CG1 D:VAL181 4.4 16.5 1.0 F1 D:CF39752 4.4 23.3 1.0 N D:GLY310 4.5 17.9 1.0 CA D:HIS182 4.5 17.6 1.0 NE2 D:HIS143 4.6 17.7 1.0 F3 D:CF39752 4.7 24.8 1.0 C D:ASP180 4.8 19.2 1.0 CA D:ASP180 4.8 19.4 1.0 CZ D:TYR312 4.9 18.1 1.0 C D:GLY310 4.9 18.3 1.0 N D:GLY311 5.0 18.4 1.0 C D:VAL181 5.0 17.3 1.0

T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner. Complex Structure of A Bacterial Class 2 Histone Deacetylase Homologue with A Trifluoromethylketone Inhibitor. Acta Crystallogr.,Sect.F V. 63 270 2007.
ISSN: ESSN 1744-3091
PubMed: 17401192
DOI: 10.1107/S1744309107012377