Iodine 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
Zinc	(Zn)	2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756, PDB code: 7o2p:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 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 Iodine with other atoms in the I 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:I805 b:35.4 occ:1.00 N A:LYS672 3.7 30.0 1.0 CA A:GLY671 4.1 28.3 1.0 CG B:PRO464 4.2 30.1 1.0 CB A:LYS672 4.3 33.2 1.0 CD B:PRO464 4.3 27.8 1.0 CB B:PRO464 4.4 29.8 1.0 CD2 B:LEU712 4.4 28.5 1.0 C A:GLY671 4.4 27.2 1.0 S1 B:UZW801 4.4 30.6 1.0 CA A:LYS672 4.5 28.3 1.0 CE A:LYS672 4.6 45.2 1.0 CG B:LEU712 4.6 27.3 1.0 CG A:LYS672 4.6 40.8 1.0 CG B:PRO711 4.7 34.5 1.0 CB B:PRO711 4.8 34.3 1.0 O B:HOH943 4.9 33.1 1.0 NH2 A:ARG636 5.0 26.8 1.0 C11 B:UZW801 5.0 25.3 1.0

Iodine binding site 2 out of 4 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 Iodine with other atoms in the I 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 A:I806 b:41.4 occ:1.00 NE2 A:HIS463 3.3 25.1 1.0 CD2 A:HIS463 3.7 27.8 1.0 CA A:SER531 3.9 28.8 1.0 C A:SER531 3.9 28.0 1.0 N A:ILE532 4.0 26.6 1.0 C10 A:UZW801 4.1 26.6 1.0 C A:ILE532 4.4 25.2 1.0 CE1 A:PHE583 4.5 27.0 1.0 O A:SER531 4.5 25.6 1.0 CB A:SER531 4.5 28.8 1.0 N A:PHE533 4.5 23.6 1.0 CD2 A:PHE533 4.5 20.6 1.0 CE1 A:HIS463 4.6 25.2 1.0 C9 A:UZW801 4.6 24.5 1.0 O A:ILE532 4.6 26.4 1.0 O A:HOH991 4.6 46.9 1.0 CA A:ILE532 4.7 26.3 1.0 CD1 A:PHE583 4.9 26.0 1.0 CB A:PHE533 4.9 23.2 1.0 ND2 A:ASN457 4.9 27.7 1.0 CG A:HIS463 5.0 25.7 1.0

Iodine binding site 3 out of 4 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 Iodine with other atoms in the I binding site number 3 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:I812 b:38.0 occ:1.00 N B:LYS672 3.7 32.1 1.0 CA B:GLY671 3.8 28.3 1.0 CG A:PRO464 4.1 24.9 1.0 CD A:PRO464 4.2 26.4 1.0 C B:GLY671 4.3 29.2 1.0 CB A:PRO464 4.4 25.9 1.0 CB A:PRO711 4.5 26.4 1.0 CB B:LYS672 4.5 44.9 1.0 S1 A:UZW801 4.5 31.8 1.0 CD2 A:LEU712 4.5 30.5 1.0 CA B:LYS672 4.7 38.5 1.0 CG A:PRO711 4.7 28.8 1.0 CG A:LEU712 4.7 29.1 1.0 CG B:LYS672 4.7 52.5 1.0

Iodine binding site 4 out of 4 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 Iodine with other atoms in the I binding site number 4 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:I805 b:40.1 occ:1.00 NE2 B:HIS463 3.6 26.5 1.0 N B:ILE532 3.9 29.8 1.0 CD2 B:HIS463 4.0 25.9 1.0 C10 B:UZW801 4.0 25.3 1.0 C B:SER531 4.0 29.3 1.0 CA B:SER531 4.0 29.4 1.0 C B:ILE532 4.1 31.3 1.0 O B:ILE532 4.3 33.0 1.0 N B:PHE533 4.3 32.4 1.0 CE1 B:PHE583 4.4 27.0 1.0 CD2 B:PHE533 4.5 38.2 1.0 CB B:SER531 4.5 28.4 1.0 CA B:ILE532 4.5 30.4 1.0 C9 B:UZW801 4.5 22.9 1.0 O B:SER531 4.6 28.2 1.0 OG B:SER531 4.7 32.1 1.0 CD1 B:PHE583 4.8 27.3 1.0 O B:HOH968 4.8 27.8 1.0 ND2 B:ASN457 4.8 34.5 1.0 CB B:PHE533 4.8 36.4 1.0 CE1 B:HIS463 4.8 29.0 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