Potassium 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
Iodine	(I)	6 atoms

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

Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K809 b:28.2 occ:1.00 O A:HOH906 2.6 24.5 1.0 O A:PHE623 2.6 34.9 1.0 O A:VAL629 2.7 36.8 1.0 O A:TYR662 2.8 29.1 1.0 O A:ASP626 2.9 35.4 1.0 O A:HOH947 3.1 26.4 1.0 C A:TYR662 3.5 28.8 1.0 C A:PHE623 3.6 31.3 1.0 CB A:TYR662 3.7 31.3 1.0 CB A:PHE623 3.8 26.8 1.0 C A:VAL629 3.9 32.7 1.0 C A:ASP626 4.1 36.8 1.0 CA A:TYR662 4.2 29.6 1.0 N A:ASN663 4.3 30.6 1.0 N A:TYR631 4.4 27.6 1.0 CA A:PHE623 4.4 29.9 1.0 N A:ASP626 4.4 36.7 1.0 N A:GLU624 4.4 33.4 1.0 CA A:GLU624 4.4 39.0 1.0 CA A:LEU630 4.5 31.9 1.0 CB A:ASP626 4.5 41.5 1.0 C A:GLU624 4.6 35.1 1.0 CA A:ASP626 4.6 36.8 1.0 O A:GLU624 4.6 34.0 1.0 N A:LEU630 4.7 33.0 1.0 O A:GLY659 4.7 39.6 1.0 CA A:ASN663 4.7 27.5 1.0 CB A:ASN663 4.8 24.0 1.0 CB A:TYR631 4.9 28.9 1.0 C A:LEU630 4.9 27.3 1.0 CA A:VAL629 5.0 33.8 1.0

Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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:K810 b:35.2 occ:1.00 O A:LEU634 2.5 29.8 1.0 OG A:SER633 2.6 25.1 1.0 O A:ASP612 2.6 26.0 1.0 O A:ASP610 2.7 20.3 1.0 O A:HIS614 2.8 26.5 1.0 OD1 A:ASP610 2.9 28.4 1.0 CG A:ASP610 3.3 30.1 1.0 C A:ASP610 3.4 25.2 1.0 C A:LEU634 3.6 30.2 1.0 CB A:SER633 3.7 29.8 1.0 C A:ASP612 3.7 25.4 1.0 CB A:ASP610 3.8 26.2 1.0 C A:HIS614 3.8 29.2 1.0 N A:LEU634 3.9 27.6 1.0 CB A:HIS635 4.0 25.3 1.0 OD2 A:ASP610 4.0 29.1 1.0 CA A:SER633 4.0 29.1 1.0 N A:ASP612 4.0 26.8 1.0 CA A:ASP610 4.2 26.1 1.0 N A:TRP611 4.2 24.7 1.0 ND1 A:HIS635 4.3 29.1 1.0 C A:SER633 4.3 28.3 1.0 CA A:HIS615 4.3 31.2 1.0 CA A:ASP612 4.3 25.6 1.0 O A:HOH925 4.4 28.8 1.0 C A:TRP611 4.4 26.5 1.0 N A:HIS615 4.5 30.1 1.0 CA A:LEU634 4.5 30.2 1.0 N A:HIS635 4.5 26.6 1.0 CA A:TRP611 4.5 27.4 1.0 CA A:HIS635 4.5 27.7 1.0 N A:HIS614 4.5 29.2 1.0 CB A:ASP612 4.5 26.6 1.0 N A:GLY616 4.5 36.3 1.0 OH A:TYR631 4.6 31.3 1.0 CG A:HIS635 4.6 27.6 1.0 C A:VAL613 4.7 28.0 1.0 N A:VAL613 4.8 27.7 1.0 C A:HIS615 4.8 33.6 1.0 CE1 A:HIS573 4.9 30.8 1.0 CA A:HIS614 4.9 28.9 1.0 OD1 A:ASP612 4.9 27.2 1.0 ND1 A:HIS573 5.0 29.2 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