Zinc in PDB 5w5k: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70, PDB code: 5w5k was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.14 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.290, 170.940, 151.370, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 (pdb code 5w5k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70, PDB code: 5w5k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:17.1 occ:1.00 O04 A:K70804 2.0 30.0 1.0 OD1 A:ASP612 2.1 16.7 1.0 OD2 A:ASP705 2.1 14.9 1.0 O A:HOH921 2.1 16.4 1.0 ND1 A:HIS614 2.2 18.3 1.0 N03 A:K70804 2.4 22.6 1.0 CG A:ASP612 2.7 15.0 1.0 OD2 A:ASP612 2.7 13.0 1.0 CG A:HIS614 3.1 16.4 1.0 CG A:ASP705 3.1 15.7 1.0 CE1 A:HIS614 3.1 17.2 1.0 C02 A:K70804 3.3 21.5 1.0 CB A:HIS614 3.4 11.0 1.0 OD1 A:ASP705 3.6 16.2 1.0 O01 A:K70804 3.7 21.4 1.0 N A:HIS614 3.7 12.3 1.0 CA A:HIS614 4.2 13.5 1.0 CG1 A:VAL613 4.2 11.2 1.0 CB A:ASP612 4.2 13.9 1.0 NE2 A:HIS614 4.2 16.0 1.0 CD2 A:HIS614 4.2 14.2 1.0 NE2 A:HIS573 4.3 14.4 1.0 CB A:ASP705 4.4 13.6 1.0 N A:VAL613 4.4 13.3 1.0 C05 A:K70804 4.5 22.8 1.0 CE1 A:HIS573 4.5 14.4 1.0 NE2 A:HIS574 4.6 16.5 1.0 CA A:GLY743 4.6 13.5 1.0 C A:VAL613 4.7 12.7 1.0 CE2 A:TYR745 4.7 17.1 1.0 OH A:TYR745 4.8 27.2 1.0 C A:ASP612 4.9 13.4 1.0 C06 A:K70804 4.9 22.3 1.0 CA A:VAL613 5.0 13.2 1.0 CA A:ASP612 5.0 12.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:15.9 occ:1.00 OD1 B:ASP612 2.1 15.5 1.0 O B:HOH902 2.1 15.5 1.0 O04 B:K70804 2.1 28.4 1.0 OD2 B:ASP705 2.1 15.8 1.0 ND1 B:HIS614 2.1 15.6 1.0 N03 B:K70804 2.6 23.8 1.0 CG B:ASP612 2.8 15.4 1.0 OD2 B:ASP612 2.8 16.6 1.0 CG B:HIS614 3.1 16.4 1.0 CE1 B:HIS614 3.1 18.0 1.0 CG B:ASP705 3.2 15.2 1.0 CB B:HIS614 3.3 12.5 1.0 C02 B:K70804 3.4 20.8 1.0 O01 B:K70804 3.6 20.5 1.0 OD1 B:ASP705 3.7 16.6 1.0 N B:HIS614 3.7 14.9 1.0 CA B:HIS614 4.1 14.6 1.0 CG1 B:VAL613 4.2 13.6 1.0 NE2 B:HIS573 4.2 16.1 1.0 CD2 B:HIS614 4.2 17.1 1.0 NE2 B:HIS614 4.2 18.2 1.0 CB B:ASP612 4.2 14.3 1.0 CE1 B:HIS573 4.4 14.4 1.0 N B:VAL613 4.4 11.1 1.0 CB B:ASP705 4.4 13.2 1.0 NE2 B:HIS574 4.5 17.1 1.0 C05 B:K70804 4.6 20.4 1.0 CA B:GLY743 4.7 15.9 1.0 C B:VAL613 4.7 13.8 1.0 OH B:TYR745 4.7 19.9 1.0 CE2 B:TYR745 4.7 14.4 1.0 C06 B:K70804 4.9 24.8 1.0 C B:ASP612 4.9 12.5 1.0 CA B:VAL613 5.0 12.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:23.8 occ:1.00 OD2 C:ASP705 2.0 18.7 1.0 O04 C:K70804 2.0 25.1 1.0 OD1 C:ASP612 2.0 19.1 1.0 O C:HOH906 2.1 20.0 1.0 ND1 C:HIS614 2.3 16.4 1.0 OD2 C:ASP612 2.5 14.6 1.0 N03 C:K70804 2.5 20.6 1.0 CG C:ASP612 2.6 15.6 1.0 CG C:ASP705 3.1 17.7 1.0 CG C:HIS614 3.3 17.8 1.0 CE1 C:HIS614 3.3 20.1 1.0 C02 C:K70804 3.4 21.7 1.0 CB C:HIS614 3.5 14.7 1.0 OD1 C:ASP705 3.5 17.6 1.0 O01 C:K70804 3.8 22.5 1.0 N C:HIS614 3.8 13.9 1.0 CB C:ASP612 4.0 16.0 1.0 NE2 C:HIS573 4.2 18.4 1.0 CG1 C:VAL613 4.3 17.0 1.0 CA C:HIS614 4.3 14.3 1.0 CB C:ASP705 4.3 17.7 1.0 N C:VAL613 4.4 14.7 1.0 CE1 C:HIS573 4.4 15.8 1.0 NE2 C:HIS614 4.4 17.8 1.0 CD2 C:HIS614 4.4 19.1 1.0 CA C:GLY743 4.4 16.9 1.0 NE2 C:HIS574 4.4 18.5 1.0 C05 C:K70804 4.6 22.7 1.0 OH C:TYR745 4.7 21.4 1.0 N C:GLY743 4.7 19.6 1.0 C C:VAL613 4.8 14.2 1.0 CE2 C:TYR745 4.8 18.1 1.0 C C:ASP612 4.8 14.4 1.0 CA C:ASP612 4.9 14.8 1.0 CA C:VAL613 5.0 16.0 1.0

K.Vogerl, N.Ong, J.Senger, D.Herp, K.Schmidtkunz, M.Marek, M.Muller, K.Bartel, T.B.Shaik, N.J.Porter, D.Robaa, D.W.Christianson, C.Romier, W.Sippl, M.Jung, F.Bracher. Synthesis and Biological Investigation of Phenothiazine-Based Benzhydroxamic Acids As Selective Histone Deacetylase 6 Inhibitors. J.Med.Chem. V. 62 1138 2019.
ISSN: ISSN 0022-2623
PubMed: 30645113
DOI: 10.1021/ACS.JMEDCHEM.8B01090