Zinc in PDB 7p2v: Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site, PDB code: 7p2v was solved by F.Saccoccia, S.Gemma, G.Campiani, G.Ruberti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.14 / 2.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.14, 71.14, 186.911, 90, 90, 90
R / Rfree (%)	21.2 / 25.2

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site (pdb code 7p2v). 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 Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site, PDB code: 7p2v:

Zinc binding site 1 out of 1 in the Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site


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 Schistosoma Mansoni HDAC8 in Complex with A 4- Chlorophenyl-Spiroindoline Capped Hydroxamate-Based Inhibitor, Bound to A Novel Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.2 occ:1.00 OD1 A:ASP186 1.9 30.9 1.0 OD2 A:ASP285 2.0 36.3 1.0 ND1 A:HIS188 2.3 36.8 1.0 O2 A:TLA504 2.3 41.9 0.8 O1 A:TLA504 2.3 35.4 0.8 CG A:ASP186 2.8 36.7 1.0 OD2 A:ASP186 3.0 29.4 1.0 CG A:ASP285 3.0 34.1 1.0 C1 A:TLA504 3.1 35.8 0.8 C2 A:TLA504 3.2 42.8 0.8 CE1 A:HIS188 3.2 41.5 1.0 CG A:HIS188 3.3 40.1 1.0 O3 A:TLA504 3.4 45.8 0.8 OD1 A:ASP285 3.4 35.2 1.0 CB A:HIS188 3.6 36.8 1.0 N A:HIS188 3.8 32.7 1.0 C3 A:TLA504 3.9 44.9 0.8 CA A:GLY339 4.1 34.7 1.0 O11 A:TLA504 4.2 40.2 0.8 CB A:ASP186 4.2 37.5 1.0 N A:LEU187 4.3 34.5 1.0 CB A:ASP285 4.3 38.6 1.0 CA A:HIS188 4.3 34.7 1.0 NE2 A:HIS188 4.4 44.4 1.0 CD2 A:HIS188 4.4 36.9 1.0 NE2 A:HIS141 4.5 30.1 1.0 N A:GLY339 4.6 34.2 1.0 O4 A:TLA504 4.6 50.9 0.8 C A:LEU187 4.7 37.5 1.0 CB A:LEU187 4.7 34.6 1.0 C4 A:TLA504 4.7 52.1 0.8 CA A:LEU187 4.8 35.7 1.0 NE2 A:HIS142 4.8 31.3 1.0 CE1 A:HIS141 4.9 31.1 1.0 C A:ASP186 5.0 33.2 1.0

F.Saccoccia, L.Pozzetti, R.Gimmelli, S.Butini, A.Guidi, G.Papoff, M.Giannaccari, S.Brogi, V.Scognamiglio, S.Gemma, G.Ruberti, G.Campiani. Crystal Structures of Schistosoma Mansoni Histone Deacetylase 8 Reveal A Novel Binding Site For Allosteric Inhibitors. J.Biol.Chem. V. 298 02375 2022.
ISSN: ESSN 1083-351X
PubMed: 35970392
DOI: 10.1016/J.JBC.2022.102375