Zinc in PDB 6uhu: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid, PDB code: 6uhu was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.61 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.550, 80.550, 244.817, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 25.4

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid 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 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid (pdb code 6uhu). 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 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid, PDB code: 6uhu:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid


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 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:34.7 occ:1.00 O13 A:Q7V701 1.9 34.7 1.0 OD2 A:ASP174 2.0 26.1 1.0 OD2 A:ASP267 2.0 23.1 1.0 ND1 A:HIS176 2.1 29.8 1.0 OD1 A:ASP174 2.4 24.4 1.0 O14 A:Q7V701 2.4 26.3 1.0 CG A:ASP174 2.5 23.4 1.0 B11 A:Q7V701 2.7 30.9 1.0 CE1 A:HIS176 3.0 33.4 1.0 CG A:ASP267 3.1 25.9 1.0 CG A:HIS176 3.1 28.2 1.0 CB A:HIS176 3.5 20.9 1.0 OD1 A:ASP267 3.5 23.5 1.0 O12 A:Q7V701 3.7 37.2 1.0 N A:HIS176 3.7 26.1 1.0 C10 A:Q7V701 3.8 40.0 1.0 C09 A:Q7V701 3.9 33.9 1.0 CB A:ASP174 4.0 19.0 1.0 NE2 A:HIS176 4.1 35.1 1.0 NE2 A:HIS136 4.2 24.6 1.0 CD2 A:HIS176 4.2 25.8 1.0 N A:VAL175 4.2 23.2 1.0 CG1 A:VAL175 4.2 24.4 1.0 CA A:GLY305 4.2 28.4 1.0 CA A:HIS176 4.2 20.3 1.0 OH A:TYR307 4.3 37.3 1.0 CE1 A:HIS136 4.4 21.4 1.0 CB A:ASP267 4.4 27.2 1.0 N A:GLY305 4.6 35.7 1.0 CE2 A:TYR307 4.6 32.0 1.0 C A:VAL175 4.6 26.2 1.0 NE2 A:HIS137 4.7 25.1 1.0 C A:ASP174 4.8 23.9 1.0 CA A:VAL175 4.8 26.8 1.0 CA A:ASP174 4.8 22.6 1.0 CZ A:TYR307 5.0 34.7 1.0

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906