Zinc in PDB 7uk2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390, PDB code: 7uk2 was solved by F.Erdogan, H.-S.Seo, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.06 / 1.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.263, 83.135, 93.276, 90, 90, 90
R / Rfree (%)	19.9 / 22.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390 (pdb code 7uk2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390, PDB code: 7uk2:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Complexed with Nn-390 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:15.2 occ:1.00 OD2 A:ASP705 2.1 10.6 1.0 OD1 A:ASP612 2.1 8.0 1.0 O20 A:O2L801 2.2 10.2 1.0 ND1 A:HIS614 2.2 6.7 1.0 O21 A:O2L801 2.4 17.4 1.0 OD2 A:ASP612 2.6 11.3 1.0 N19 A:O2L801 2.7 23.2 1.0 CG A:ASP612 2.7 10.6 1.0 C18 A:O2L801 2.8 18.8 1.0 CE1 A:HIS614 3.0 15.1 1.0 CG A:ASP705 3.1 8.9 1.0 CG A:HIS614 3.3 6.9 1.0 OD1 A:ASP705 3.5 8.7 1.0 CB A:HIS614 3.7 8.8 1.0 N A:HIS614 3.9 5.4 1.0 NE2 A:HIS573 4.1 7.8 1.0 CB A:ASP612 4.2 7.8 1.0 NE2 A:HIS614 4.2 11.5 1.0 C17 A:O2L801 4.2 16.3 1.0 CG1 A:VAL613 4.3 7.1 1.0 CA A:GLY743 4.3 9.4 1.0 CD2 A:HIS614 4.3 9.3 1.0 N A:VAL613 4.4 7.2 1.0 OH A:TYR745 4.4 11.8 1.0 CB A:ASP705 4.4 10.1 1.0 CA A:HIS614 4.4 9.6 1.0 CE1 A:HIS573 4.6 10.4 1.0 CE2 A:TYR745 4.6 11.6 1.0 N A:GLY743 4.7 9.9 1.0 NE2 A:HIS574 4.7 13.9 1.0 C16 A:O2L801 4.8 18.4 1.0 C A:VAL613 4.9 12.0 1.0 C A:ASP612 4.9 9.3 1.0 CA A:ASP612 4.9 9.9 1.0

H.K.Garcha, N.Nawar, H.Sorger, F.Erdogan, M.M.K.Aung, A.Sedighi, P.Manaswiyoungkul, H.S.Seo, S.Schonefeldt, D.Poloske, S.Dhe-Paganon, H.A.Neubauer, S.M.Mustjoki, M.Herling, E.D.De Araujo, R.Moriggl, P.T.Gunning. High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor Nn-429 in Natural Killer (Nk)/T-Cell Lymphoma. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 36355493
DOI: 10.3390/PH15111321