Zinc in PDB 6cgp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032, PDB code: 6cgp was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.08 / 2.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.310, 64.950, 140.499, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032 (pdb code 6cgp). 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 Maip-032, PDB code: 6cgp:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032


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 Maip-032 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:35.0 occ:1.00 OD2 A:ASP705 2.0 30.6 1.0 O16 A:F1Y804 2.0 48.3 1.0 OD1 A:ASP612 2.2 36.9 1.0 O A:HOH903 2.2 27.4 1.0 ND1 A:HIS614 2.4 33.3 1.0 OD2 A:ASP612 2.5 30.4 1.0 CG A:ASP612 2.7 32.8 1.0 N15 A:F1Y804 2.9 46.4 1.0 CG A:ASP705 3.1 36.6 1.0 CG A:HIS614 3.3 36.8 1.0 CE1 A:HIS614 3.4 33.7 1.0 CB A:HIS614 3.5 31.6 1.0 OD1 A:ASP705 3.6 36.5 1.0 O14 A:F1Y804 3.6 50.2 1.0 C13 A:F1Y804 3.6 43.9 1.0 N A:HIS614 3.9 26.3 1.0 CB A:ASP612 4.2 28.4 1.0 NE2 A:HIS573 4.2 30.5 1.0 CA A:GLY743 4.3 35.2 1.0 CA A:HIS614 4.3 29.9 1.0 CB A:ASP705 4.3 38.5 1.0 CG1 A:VAL613 4.4 33.4 1.0 CD2 A:HIS614 4.4 36.4 1.0 NE2 A:HIS614 4.4 40.4 1.0 OH A:TYR745 4.5 39.0 1.0 N A:VAL613 4.5 30.8 1.0 CE1 A:HIS573 4.5 27.4 1.0 NE2 A:HIS574 4.7 37.6 1.0 CE2 A:TYR745 4.8 38.4 1.0 N A:GLY743 4.8 32.9 1.0 C A:VAL613 4.9 31.3 1.0 C A:ASP612 4.9 31.0 1.0 C10 A:F1Y804 4.9 44.4 1.0 CA A:ASP612 5.0 29.1 1.0

M.K.W.Mackwitz, A.Hamacher, J.D.Osko, J.Held, A.Scholer, D.W.Christianson, M.U.Kassack, F.K.Hansen. Multicomponent Synthesis and Binding Mode of Imidazo[1,2- A]Pyridine-Capped Selective HDAC6 Inhibitors. Org. Lett. V. 20 3255 2018.
ISSN: ISSN 1523-7052
PubMed: 29790770
DOI: 10.1021/ACS.ORGLETT.8B01118