Zinc in PDB 5edu: Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A:
3.5.1.98;

The structure of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5edu was solved by Y.Hai, D.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.54 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.262, 149.032, 216.333, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 27.5

The structure of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A (pdb code 5edu). 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 Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5edu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex 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 Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2502 b:62.6 occ:1.00 O1 B:TSN2501 2.0 74.9 1.0 OD2 B:ASP742 2.1 45.4 1.0 OD1 B:ASP649 2.2 55.3 1.0 ND1 B:HIS651 2.2 39.8 1.0 O2 B:TSN2501 2.3 75.5 1.0 N1 B:TSN2501 2.6 73.8 1.0 C13 B:TSN2501 2.7 72.6 1.0 OD2 B:ASP649 2.8 54.7 1.0 CG B:ASP649 2.8 53.0 1.0 CE1 B:HIS651 3.1 39.4 1.0 CG B:ASP742 3.1 45.5 1.0 CG B:HIS651 3.2 37.5 1.0 CB B:HIS651 3.5 35.2 1.0 OD1 B:ASP742 3.6 47.5 1.0 N B:HIS651 3.9 30.9 1.0 C12 B:TSN2501 4.0 68.8 1.0 CA B:GLY780 4.1 32.1 1.0 NE2 B:HIS651 4.2 37.6 1.0 NE2 B:HIS610 4.2 29.6 1.0 CD2 B:HIS651 4.3 36.9 1.0 CB B:ASP649 4.3 46.3 1.0 CA B:HIS651 4.3 31.4 1.0 CB B:ASP742 4.4 42.5 1.0 OH B:TYR782 4.4 44.7 1.0 CG1 B:VAL650 4.4 31.3 1.0 CE1 B:HIS610 4.4 29.6 1.0 C11 B:TSN2501 4.4 66.1 1.0 N B:VAL650 4.4 36.1 1.0 N B:GLY780 4.6 29.8 1.0 CE2 B:TYR782 4.6 39.4 1.0 CE1 B:HIS611 4.8 37.4 1.0 C B:VAL650 4.9 35.5 1.0 CZ B:TYR782 5.0 40.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex 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 Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:41.3 occ:1.00 OD2 A:ASP742 2.1 43.6 1.0 ND1 A:HIS651 2.1 34.2 1.0 O1 A:TSN904 2.2 66.0 1.0 OD1 A:ASP649 2.2 31.8 1.0 O2 A:TSN904 2.6 64.3 1.0 N1 A:TSN904 2.8 65.3 1.0 CG A:ASP649 2.9 30.4 1.0 OD2 A:ASP649 2.9 30.4 1.0 C13 A:TSN904 2.9 62.5 1.0 CE1 A:HIS651 3.0 34.8 1.0 CG A:HIS651 3.1 34.7 1.0 CG A:ASP742 3.2 39.0 1.0 CB A:HIS651 3.5 33.4 1.0 OD1 A:ASP742 3.7 41.1 1.0 N A:HIS651 3.9 27.2 1.0 CA A:GLY780 4.1 39.0 1.0 CG1 A:VAL650 4.1 27.8 1.0 NE2 A:HIS651 4.2 35.7 1.0 C12 A:TSN904 4.2 58.9 1.0 CD2 A:HIS651 4.2 35.6 1.0 CA A:HIS651 4.3 31.2 1.0 CB A:ASP742 4.3 31.8 1.0 CB A:ASP649 4.4 29.1 1.0 NE2 A:HIS610 4.4 33.6 1.0 OH A:TYR782 4.4 40.9 1.0 N A:VAL650 4.4 24.3 1.0 N A:GLY780 4.6 39.2 1.0 CE2 A:TYR782 4.6 33.5 1.0 CE1 A:HIS610 4.6 33.0 1.0 C11 A:TSN904 4.7 57.1 1.0 NE2 A:HIS611 4.7 35.8 1.0 C A:VAL650 4.8 25.1 1.0 CA A:VAL650 5.0 24.7 1.0

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134