Zinc in PDB 7o2r: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985, PDB code: 7o2r was solved by K.Zrubek, G.Sandrone, C.D.Cukier, A.Stevenazzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 2.30
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.966, 84.212, 94.977, 90, 90, 90
R / Rfree (%)	19.9 / 26

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Iodine	(I)	6 atoms
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 (pdb code 7o2r). 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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985, PDB code: 7o2r:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985


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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:51.9 occ:1.00 O2 A:V05801 2.1 54.5 1.0 ND1 A:HIS614 2.2 24.8 1.0 OD2 A:ASP705 2.2 31.9 1.0 OD1 A:ASP612 2.2 27.2 1.0 O A:HOH910 2.3 33.2 1.0 OD2 A:ASP612 2.5 27.8 1.0 N1 A:V05801 2.6 46.9 1.0 CG A:ASP612 2.7 27.4 1.0 CG A:ASP705 3.1 28.8 1.0 CG A:HIS614 3.1 26.4 1.0 CE1 A:HIS614 3.2 23.9 1.0 CB A:HIS614 3.3 26.8 1.0 OD1 A:ASP705 3.4 22.9 1.0 C1 A:V05801 3.5 48.9 1.0 N A:HIS614 3.8 29.2 1.0 NE2 A:HIS573 4.0 34.2 1.0 O1 A:V05801 4.0 52.8 1.0 CB A:ASP612 4.2 26.6 1.0 CA A:HIS614 4.2 28.9 1.0 CG1 A:VAL613 4.2 27.9 1.0 CD2 A:HIS614 4.3 25.5 1.0 NE2 A:HIS614 4.3 25.1 1.0 N A:VAL613 4.3 27.7 1.0 CA A:GLY743 4.3 34.2 1.0 CE1 A:HIS573 4.4 30.8 1.0 CB A:ASP705 4.4 30.6 1.0 OH A:TYR745 4.5 34.8 1.0 C2 A:V05801 4.5 49.0 1.0 N A:GLY743 4.6 35.7 1.0 NE2 A:HIS574 4.7 30.1 1.0 C13 A:V05801 4.7 50.5 1.0 C A:ASP612 4.7 25.4 1.0 CE2 A:TYR745 4.8 36.5 1.0 CA A:ASP612 4.8 25.6 1.0 C A:VAL613 4.8 28.0 1.0

G.Sandrone, C.D.Cukier, K.Zrubek, M.Marchini, B.Vergani, G.Caprini, G.Fossati, C.Steinkuhler, A.Stevenazzi. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00425