Zinc in PDB 5g0g: Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A, PDB code: 5g0g 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)	46.505 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.470, 93.010, 118.470, 90.00, 90.00, 90.00
R / Rfree (%)	13.89 / 16.96

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A (pdb code 5g0g). 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 CD1 in Complex with Trichostatin A, PDB code: 5g0g:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio HDAC6 CD1 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 Danio Rerio HDAC6 CD1 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1419 b:26.0 occ:0.62 O1 A:TSN1427 2.0 25.8 1.0 OD2 A:ASP323 2.0 20.9 1.0 OD1 A:ASP230 2.1 20.7 1.0 O2 A:TSN1427 2.2 24.4 1.0 ND1 A:HIS232 2.2 20.4 1.0 OD2 A:ASP230 2.4 20.6 1.0 CG A:ASP230 2.6 19.5 1.0 C13 A:TSN1427 2.7 26.5 1.0 N1 A:TSN1427 2.7 30.3 1.0 CE1 A:HIS232 3.0 22.1 1.0 CG A:ASP323 3.0 22.2 1.0 CG A:HIS232 3.3 20.4 1.0 OD1 A:ASP323 3.4 21.3 1.0 CB A:HIS232 3.7 21.2 1.0 CA A:GLY361 4.0 20.6 1.0 C12 A:TSN1427 4.0 26.7 1.0 N A:HIS232 4.0 20.1 1.0 CB A:ASP230 4.1 19.1 1.0 NE2 A:HIS232 4.2 21.6 1.0 NE2 A:HIS192 4.3 22.0 1.0 N A:GLY361 4.3 21.2 1.0 CD2 A:HIS232 4.3 20.9 1.0 CB A:ASP323 4.3 21.9 1.0 N A:VAL231 4.4 18.8 1.0 CG1 A:VAL231 4.4 20.8 1.0 CA A:HIS232 4.5 20.5 1.0 OH A:TYR363 4.5 29.2 1.0 CE2 A:TYR363 4.6 26.2 1.0 C11 A:TSN1427 4.6 26.4 1.0 CE1 A:HIS192 4.7 19.2 1.0 C A:GLY361 4.8 21.9 1.0 C A:ASP230 4.8 18.5 1.0 CA A:ASP230 4.8 18.9 1.0 N A:GLY362 4.9 22.4 1.0 C A:VAL231 4.9 20.3 1.0 NE2 A:HIS193 4.9 22.1 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