Zinc in PDB 1c3r: Crystal Structure of An Hdac Homolog Complexed with Trichostatin A

The structure of Crystal Structure of An Hdac Homolog Complexed with Trichostatin A, PDB code: 1c3r was solved by M.S.Finnin, J.R.Donigian, N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.400, 94.400, 156.300, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 25.8

The binding sites of Zinc atom in the Crystal Structure of An Hdac Homolog Complexed with Trichostatin A (pdb code 1c3r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of An Hdac Homolog Complexed with Trichostatin A, PDB code: 1c3r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of An Hdac Homolog Complexed with Trichostatin A


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 An Hdac Homolog Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:32.5 occ:1.00 OD2 A:ASP258 1.9 33.2 1.0 OD2 A:ASP168 2.1 34.7 1.0 ND1 A:HIS170 2.1 31.0 1.0 O1 A:TSN502 2.2 28.8 1.0 O2 A:TSN502 2.4 25.8 1.0 N1 A:TSN502 2.6 31.2 1.0 C13 A:TSN502 2.8 29.0 1.0 CG A:ASP168 2.9 28.1 1.0 CE1 A:HIS170 3.0 24.3 1.0 CG A:ASP258 3.0 29.1 1.0 OD1 A:ASP168 3.0 25.4 1.0 CG A:HIS170 3.1 30.3 1.0 OD1 A:ASP258 3.4 29.9 1.0 CB A:HIS170 3.5 23.2 1.0 N A:HIS170 3.8 21.6 1.0 NE2 A:HIS170 4.2 21.9 1.0 CA A:GLY295 4.2 23.3 1.0 CD2 A:HIS170 4.2 22.9 1.0 C12 A:TSN502 4.2 27.4 1.0 CA A:HIS170 4.3 24.8 1.0 CB A:ASP258 4.3 25.1 1.0 O A:HOH707 4.3 45.1 1.0 CB A:ASP168 4.3 27.1 1.0 N A:ALA169 4.3 21.3 1.0 OH A:TYR297 4.3 19.5 1.0 NE2 A:HIS131 4.4 24.2 1.0 C A:ALA169 4.6 26.6 1.0 N A:GLY295 4.7 19.9 1.0 CE1 A:TYR297 4.7 20.2 1.0 C A:GLY295 4.8 19.0 1.0 CA A:ALA169 4.8 25.0 1.0 C A:ASP168 4.9 24.2 1.0 C11 A:TSN502 4.9 32.0 1.0 CE1 A:HIS131 4.9 20.5 1.0 CB A:ALA169 5.0 21.2 1.0 O A:GLY295 5.0 19.4 1.0 CA A:ASP168 5.0 24.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of An Hdac Homolog Complexed with Trichostatin A


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 An Hdac Homolog Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:28.2 occ:1.00 OD2 B:ASP258 1.9 18.7 1.0 OD2 B:ASP168 2.0 18.4 1.0 ND1 B:HIS170 2.1 19.1 1.0 O1 B:TSN504 2.2 24.7 1.0 O2 B:TSN504 2.5 30.2 1.0 N1 B:TSN504 2.8 27.2 1.0 CG B:ASP168 2.8 24.9 1.0 C13 B:TSN504 2.9 28.3 1.0 OD1 B:ASP168 3.0 22.0 1.0 CG B:ASP258 3.0 21.6 1.0 CE1 B:HIS170 3.0 19.4 1.0 CG B:HIS170 3.1 18.9 1.0 OD1 B:ASP258 3.4 17.7 1.0 CB B:HIS170 3.5 21.3 1.0 N B:HIS170 3.8 18.8 1.0 CA B:GLY295 4.1 16.5 1.0 NE2 B:HIS170 4.2 20.4 1.0 CD2 B:HIS170 4.2 19.0 1.0 CB B:ASP258 4.3 12.8 1.0 C12 B:TSN504 4.3 23.5 1.0 N B:ALA169 4.3 15.5 1.0 CA B:HIS170 4.3 22.7 1.0 CB B:ASP168 4.3 21.2 1.0 NE2 B:HIS131 4.4 17.2 1.0 OH B:TYR297 4.4 17.8 1.0 C B:ALA169 4.6 21.8 1.0 N B:GLY295 4.6 17.1 1.0 CE1 B:TYR297 4.7 19.8 1.0 C B:GLY295 4.8 19.5 1.0 CA B:ALA169 4.8 18.7 1.0 CE1 B:HIS131 4.8 15.3 1.0 C B:ASP168 4.8 23.0 1.0 CB B:ALA169 4.9 12.0 1.0 C11 B:TSN504 4.9 27.2 1.0 O B:GLY295 5.0 16.3 1.0 CA B:ASP168 5.0 22.0 1.0

M.S.Finnin, J.R.Donigian, A.Cohen, V.M.Richon, R.A.Rifkind, P.A.Marks, R.Breslow, N.P.Pavletich. Structures of A Histone Deacetylase Homologue Bound to the Tsa and Saha Inhibitors. Nature V. 401 188 1999.
ISSN: ISSN 0028-0836
PubMed: 10490031
DOI: 10.1038/43710