Zinc in PDB 7o2p: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756, PDB code: 7o2p 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)	45.42 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.483, 90.753, 71.964, 90, 95.64, 90
R / Rfree (%)	19.5 / 26.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756 also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Iodine	(I)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756 (pdb code 7o2p). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756, PDB code: 7o2p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 ITF3756 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:33.7 occ:1.00 OD2 A:ASP705 2.0 23.8 1.0 O2 A:UZW801 2.0 51.8 1.0 OD1 A:ASP612 2.1 19.2 1.0 O A:HOH911 2.2 29.1 1.0 ND1 A:HIS614 2.2 20.3 1.0 N1 A:UZW801 2.7 37.7 1.0 CG A:ASP612 2.7 20.8 1.0 OD2 A:ASP612 2.7 22.4 1.0 CG A:ASP705 3.0 20.9 1.0 CE1 A:HIS614 3.1 22.1 1.0 CG A:HIS614 3.3 21.9 1.0 OD1 A:ASP705 3.3 19.9 1.0 CB A:HIS614 3.6 21.7 1.0 C1 A:UZW801 3.6 34.4 1.0 N A:HIS614 3.8 20.2 1.0 O1 A:UZW801 4.0 42.5 1.0 NE2 A:HIS573 4.1 26.7 1.0 CB A:ASP612 4.2 20.9 1.0 NE2 A:HIS614 4.3 21.6 1.0 CG1 A:VAL613 4.3 23.2 1.0 CA A:HIS614 4.3 19.8 1.0 CB A:ASP705 4.3 20.1 1.0 CD2 A:HIS614 4.3 22.1 1.0 CA A:GLY743 4.4 21.1 1.0 N A:VAL613 4.4 18.1 1.0 OH A:TYR745 4.5 25.1 1.0 CE1 A:HIS573 4.5 28.1 1.0 NE2 A:HIS574 4.6 23.8 1.0 CE2 A:TYR745 4.7 22.8 1.0 N A:GLY743 4.7 20.4 1.0 C2 A:UZW801 4.7 26.8 1.0 C A:VAL613 4.8 18.9 1.0 C A:ASP612 4.8 21.6 1.0 CA A:ASP612 4.9 20.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:32.7 occ:1.00 OD1 B:ASP612 2.0 18.2 1.0 OD2 B:ASP705 2.1 23.6 1.0 ND1 B:HIS614 2.1 19.5 1.0 O2 B:UZW801 2.2 40.8 1.0 O B:HOH906 2.3 30.6 1.0 CG B:ASP612 2.7 19.6 1.0 N1 B:UZW801 2.8 31.1 1.0 OD2 B:ASP612 2.8 16.9 1.0 CG B:ASP705 3.1 23.8 1.0 CE1 B:HIS614 3.1 19.5 1.0 CG B:HIS614 3.2 19.0 1.0 OD1 B:ASP705 3.4 20.9 1.0 CB B:HIS614 3.5 19.3 1.0 C1 B:UZW801 3.7 34.2 1.0 N B:HIS614 3.9 20.5 1.0 NE2 B:HIS573 3.9 21.1 1.0 CB B:ASP612 4.1 19.6 1.0 O1 B:UZW801 4.2 42.1 1.0 NE2 B:HIS614 4.2 17.9 1.0 CD2 B:HIS614 4.3 18.9 1.0 CA B:HIS614 4.3 18.3 1.0 CE1 B:HIS573 4.4 20.1 1.0 N B:VAL613 4.4 19.4 1.0 OH B:TYR745 4.4 26.0 1.0 CB B:ASP705 4.4 22.7 1.0 CG1 B:VAL613 4.4 19.9 1.0 CA B:GLY743 4.4 22.1 1.0 NE2 B:HIS574 4.5 21.3 1.0 CE2 B:TYR745 4.7 28.4 1.0 C B:ASP612 4.8 20.4 1.0 N B:GLY743 4.8 23.9 1.0 C B:VAL613 4.8 19.3 1.0 CA B:ASP612 4.8 20.0 1.0 C2 B:UZW801 4.8 30.2 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