Iodine 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
Zinc	(Zn)	1 atom
Potassium	(K)	2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985, PDB code: 7o2r:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 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 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 ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:I803 b:68.3 occ:1.00 CA A:SER513 3.9 31.5 1.0 CD2 A:HIS516 4.0 36.2 1.0 CB A:SER513 4.1 27.2 1.0 NE2 A:HIS516 4.4 40.6 1.0 N A:SER513 4.4 29.9 1.0 NZ A:LYS512 4.6 58.3 1.0 CG A:LYS512 4.8 44.5 1.0 C A:LYS512 4.8 31.6 1.0

Iodine binding site 2 out of 6 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 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 ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:I804 b:59.1 occ:1.00 O A:HOH968 3.3 27.7 1.0 NE2 A:HIS463 3.4 41.2 1.0 C A:SER531 3.9 28.6 1.0 CA A:SER531 3.9 27.7 1.0 CD2 A:HIS463 4.0 41.6 1.0 N A:ILE532 4.0 29.8 1.0 C A:ILE532 4.1 30.8 1.0 O A:ILE532 4.2 32.0 1.0 N4 A:V05801 4.3 58.3 1.0 O A:SER531 4.3 24.5 1.0 N A:PHE533 4.3 31.6 1.0 CB A:SER531 4.4 26.8 1.0 CE1 A:HIS463 4.4 37.2 1.0 CE1 A:PHE583 4.5 35.0 1.0 CD2 A:PHE533 4.5 37.4 1.0 CA A:ILE532 4.6 29.5 1.0 CB A:PHE533 4.7 32.7 1.0 N5 A:V05801 4.7 57.7 1.0 CD1 A:PHE583 4.8 31.3 1.0 N3 A:V05801 4.9 62.7 1.0

Iodine binding site 3 out of 6 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 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 ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:I805 b:58.8 occ:1.00 N A:PHE643 3.9 27.0 1.0 CD1 A:PHE642 4.0 28.0 1.0 CE1 A:PHE642 4.2 26.3 1.0 CB A:PHE643 4.3 34.8 1.0 CA A:PHE642 4.3 29.0 1.0 CG A:PHE642 4.5 26.1 1.0 O A:ALA641 4.6 31.2 1.0 C A:PHE642 4.6 26.7 1.0 CA A:PHE643 4.7 30.7 1.0 CZ A:PHE642 4.9 24.7 1.0

Iodine binding site 4 out of 6 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 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 ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:I806 b:79.1 occ:1.00 O A:HOH901 3.3 41.8 1.0 N A:GLY655 3.5 33.2 1.0 CA A:GLY655 3.7 35.3 1.0 CG A:LEU656 3.9 46.4 1.0 C A:GLY655 3.9 39.5 1.0 CB A:LYS653 4.0 35.9 1.0 CA A:LYS653 4.1 32.8 1.0 CD1 A:LEU656 4.1 47.7 1.0 C A:LYS653 4.1 34.5 1.0 N A:VAL654 4.2 33.9 1.0 O A:GLY655 4.2 35.7 1.0 OE1 A:GLU624 4.4 63.9 1.0 N A:LEU656 4.5 41.6 1.0 NE2 A:GLN620 4.6 25.2 1.0 CD2 A:LEU656 4.6 47.4 1.0 CD A:LYS653 4.6 41.9 1.0 C A:VAL654 4.7 33.1 1.0 O A:LYS653 4.8 36.7 1.0 CB A:GLU624 4.8 44.5 1.0 CG A:LYS653 4.9 38.1 1.0

Iodine binding site 5 out of 6 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 Iodine with other atoms in the I binding site number 5 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:I807 b:81.4 occ:1.00 CG A:GLN728 4.0 39.1 1.0 OG A:SER731 4.2 33.0 1.0 CB A:SER731 4.2 32.3 1.0 CA A:GLN728 4.2 30.8 1.0 CB A:GLN728 4.4 37.3 1.0 O A:GLN728 4.5 34.7 1.0 O A:HOH952 4.9 24.3 1.0 C A:GLN728 4.9 30.8 1.0

Iodine binding site 6 out of 6 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 Iodine with other atoms in the I binding site number 6 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:I808 b:90.1 occ:1.00 CB A:PRO464 4.0 34.2 1.0 CG A:PRO464 4.0 35.5 1.0 CG A:PRO711 4.1 42.1 1.0 CD2 A:LEU712 4.4 55.4 1.0 CB A:PRO711 4.5 40.7 1.0 C11 A:V05801 4.5 59.6 1.0 CD A:PRO464 4.6 35.9 1.0 CG A:LEU712 4.9 47.8 1.0 C10 A:V05801 5.0 57.6 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