Zinc in PDB 4qa3: Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)

All present enzymatic activity of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa):
3.5.1.98;

The structure of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa), PDB code: 4qa3 was solved by C.Decroos, C.B.Bowman, J.-A.S.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 2.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.186, 83.094, 94.297, 90.00, 95.94, 90.00
R / Rfree (%)	17.8 / 23.4

The structure of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa) also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa) (pdb code 4qa3). 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 T311M HDAC8 in Complex with Trichostatin A (Tsa), PDB code: 4qa3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:31.2 occ:1.00 OD2 A:ASP267 2.0 31.1 1.0 OD2 A:ASP178 2.1 29.7 1.0 O2 A:TSN501 2.2 39.6 1.0 ND1 A:HIS180 2.2 28.4 1.0 O1 A:TSN501 2.6 38.4 1.0 C13 A:TSN501 2.8 37.9 1.0 CG A:ASP178 2.9 30.0 1.0 N1 A:TSN501 3.0 37.6 1.0 CE1 A:HIS180 3.0 32.6 1.0 OD1 A:ASP178 3.1 28.2 1.0 CG A:ASP267 3.1 32.3 1.0 CG A:HIS180 3.3 27.6 1.0 OD1 A:ASP267 3.6 32.7 1.0 CB A:HIS180 3.7 31.0 1.0 N A:HIS180 3.8 29.2 1.0 C12 A:TSN501 4.1 33.5 1.0 CA A:GLY304 4.1 31.2 1.0 NE2 A:HIS180 4.2 33.7 1.0 N A:LEU179 4.2 27.6 1.0 CD2 A:HIS180 4.3 29.2 1.0 CB A:ASP267 4.3 33.6 1.0 CB A:ASP178 4.4 29.7 1.0 CA A:HIS180 4.4 31.2 1.0 CB A:LEU179 4.4 28.0 1.0 N A:GLY304 4.6 32.0 1.0 C11 A:TSN501 4.6 38.4 1.0 OH A:TYR306 4.6 44.8 1.0 C A:LEU179 4.7 29.0 1.0 CA A:LEU179 4.7 28.3 1.0 NE2 A:HIS142 4.7 26.1 1.0 O2 A:GOL505 5.0 31.5 0.6 CE1 A:TYR306 5.0 41.8 1.0 NE2 A:HIS143 5.0 28.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:45.0 occ:1.00 OD2 B:ASP178 2.0 40.8 1.0 OD2 B:ASP267 2.2 41.5 1.0 ND1 B:HIS180 2.3 42.2 1.0 O2 B:TSN404 2.5 47.3 1.0 O1 B:TSN404 2.5 58.6 1.0 CG B:ASP178 2.7 40.3 1.0 OD1 B:ASP178 2.8 37.9 1.0 C13 B:TSN404 3.0 48.5 1.0 N1 B:TSN404 3.0 55.9 1.0 CE1 B:HIS180 3.2 44.9 1.0 CG B:ASP267 3.2 40.0 1.0 CG B:HIS180 3.3 40.2 1.0 OD1 B:ASP267 3.6 41.8 1.0 CB B:HIS180 3.7 40.3 1.0 N B:HIS180 3.7 41.2 1.0 CA B:GLY304 3.9 41.6 1.0 CB B:ASP178 4.1 41.6 1.0 N B:LEU179 4.2 41.3 1.0 C12 B:TSN404 4.2 48.1 1.0 CA B:HIS180 4.3 39.9 1.0 NE2 B:HIS180 4.4 46.7 1.0 N B:GLY304 4.4 41.4 1.0 CD2 B:HIS180 4.4 41.5 1.0 NE2 B:HIS142 4.4 36.8 1.0 CB B:LEU179 4.5 39.0 1.0 CB B:ASP267 4.5 35.2 1.0 C B:LEU179 4.6 41.7 1.0 CA B:LEU179 4.7 41.1 1.0 CE1 B:HIS142 4.8 41.7 1.0 NE2 B:HIS143 4.8 45.1 1.0 C11 B:TSN404 4.9 46.4 1.0 C B:ASP178 4.9 37.3 1.0 C B:GLY304 5.0 39.8 1.0 CA B:ASP178 5.0 36.0 1.0

C.Decroos, C.M.Bowman, J.A.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia De Lange Syndrome Spectrum Disorders. Acs Chem.Biol. V. 9 2157 2014.
ISSN: ISSN 1554-8929
PubMed: 25075551
DOI: 10.1021/CB5003762