Zinc in PDB 5g0h: Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A, PDB code: 5g0h was solved by Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.43 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.980, 48.230, 73.780, 90.00, 103.22, 90.00
R / Rfree (%)	15.02 / 17.41

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A (pdb code 5g0h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A, PDB code: 5g0h:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-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 Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1804 b:16.4 occ:0.90 O1 A:E1Z1801 1.9 20.3 0.9 OD2 A:ASP705 2.0 17.2 1.0 OD1 A:ASP612 2.1 15.2 1.0 ND1 A:HIS614 2.1 15.3 1.0 O2 A:E1Z1801 2.3 17.9 0.9 OD2 A:ASP612 2.7 13.6 1.0 CG A:ASP612 2.7 12.6 1.0 N1 A:E1Z1801 2.7 27.9 0.9 C13 A:E1Z1801 2.8 22.8 0.9 CG A:ASP705 3.0 17.9 1.0 CE1 A:HIS614 3.0 15.6 1.0 CG A:HIS614 3.2 14.9 1.0 OD1 A:ASP705 3.4 14.3 1.0 CB A:HIS614 3.6 12.8 1.0 N A:HIS614 4.0 10.4 1.0 NE2 A:HIS573 4.1 16.5 1.0 C12 A:E1Z1801 4.2 19.6 0.9 CB A:ASP612 4.2 10.9 1.0 NE2 A:HIS614 4.2 15.7 1.0 CA A:GLY743 4.3 13.9 1.0 CD2 A:HIS614 4.3 15.7 1.0 CB A:ASP705 4.3 12.7 1.0 CG1 A:VAL613 4.4 15.4 1.0 OH A:TYR745 4.4 22.5 1.0 CA A:HIS614 4.4 12.9 1.0 N A:VAL613 4.5 12.2 1.0 N A:GLY743 4.6 13.2 1.0 CE1 A:HIS573 4.6 15.7 1.0 NE2 A:HIS574 4.6 17.1 1.0 CE2 A:TYR745 4.6 17.1 1.0 C11 A:E1Z1801 4.7 15.6 0.9 C A:ASP612 4.9 12.4 1.0 CA A:ASP612 4.9 10.0 1.0 CZ A:TYR745 5.0 21.7 1.0 C A:VAL613 5.0 13.1 1.0

Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias. Structural Insights Into HDAC6 Tubulin Deacetylation and Its Selective Inhibition Nat.Chem.Biol. V. 12 748 2016.
ISSN: ISSN 1552-4450
PubMed: 27454931
DOI: 10.1038/NCHEMBIO.2140