Zinc in PDB 7p2t: Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative

The structure of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative, PDB code: 7p2t 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)	48.06 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.205, 99.003, 178.585, 90, 91.3, 90
R / Rfree (%)	n/a / 29.4

The structure of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Bromine	(Br)	4 atoms
Potassium	(K)	10 atoms

The binding sites of Zinc atom in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative (pdb code 7p2t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative, PDB code: 7p2t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:41.2 occ:1.00 OD2 A:ASP285 2.1 42.8 1.0 OD1 A:ASP186 2.1 39.3 1.0 ND1 A:HIS188 2.3 39.9 1.0 OD2 A:ASP186 2.7 40.3 1.0 CG A:ASP186 2.7 40.0 1.0 O2 A:4VX504 2.9 63.5 0.9 CE1 A:HIS188 3.1 40.0 1.0 N2 A:4VX504 3.1 63.8 0.9 CG A:ASP285 3.2 43.1 1.0 CG A:HIS188 3.4 39.9 1.0 CB A:ASP285 3.7 43.1 1.0 CB A:HIS188 3.8 39.4 1.0 N A:HIS188 3.9 39.8 1.0 CA A:GLY339 4.1 45.9 1.0 CB A:ASP186 4.2 40.1 1.0 OD1 A:ASP285 4.3 43.5 1.0 NE2 A:HIS188 4.3 39.9 1.0 N A:LEU187 4.3 40.2 1.0 C16 A:4VX504 4.4 63.7 0.9 CD2 A:HIS188 4.4 39.6 1.0 CA A:HIS188 4.5 39.3 1.0 NE2 A:HIS141 4.6 39.5 1.0 NE2 A:HIS142 4.7 39.5 1.0 CB A:LEU187 4.7 40.4 1.0 N A:GLY339 4.7 45.8 1.0 C A:LEU187 4.8 40.0 1.0 CA A:LEU187 4.9 40.2 1.0 C A:ASP186 5.0 40.3 1.0

Zinc binding site 2 out of 4 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:46.3 occ:1.00 O2 B:4VX505 2.0 64.0 0.9 OD2 B:ASP285 2.1 43.0 1.0 OD1 B:ASP186 2.1 38.7 1.0 ND1 B:HIS188 2.3 44.3 1.0 N2 B:4VX505 2.4 63.8 0.9 CG B:ASP186 2.8 39.0 1.0 OD2 B:ASP186 2.8 39.6 1.0 CE1 B:HIS188 3.2 44.4 1.0 CG B:ASP285 3.2 42.8 1.0 CG B:HIS188 3.3 43.6 1.0 C16 B:4VX505 3.6 63.9 0.9 N B:HIS188 3.7 41.8 1.0 CB B:HIS188 3.7 42.8 1.0 OD1 B:ASP285 3.7 42.7 1.0 N B:LEU187 4.2 39.7 1.0 CB B:ASP186 4.2 39.0 1.0 O1 B:4VX505 4.3 63.5 0.9 NE2 B:HIS188 4.3 44.1 1.0 CA B:HIS188 4.3 42.3 1.0 CB B:ASP285 4.4 42.8 1.0 CE1 B:HIS142 4.4 36.0 1.0 CE1 B:HIS141 4.4 35.3 1.0 CD2 B:HIS188 4.4 43.9 1.0 CA B:GLY339 4.4 46.0 1.0 CB B:LEU187 4.5 40.1 1.0 C13 B:4VX505 4.5 63.9 0.9 C B:LEU187 4.6 40.9 1.0 CA B:LEU187 4.7 40.3 1.0 C14 B:4VX505 4.7 63.8 0.9 NE2 B:HIS142 4.7 36.0 1.0 NE2 B:HIS141 4.8 35.2 1.0 C B:ASP186 4.9 39.3 1.0

Zinc binding site 3 out of 4 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:48.8 occ:1.00 OD2 C:ASP285 1.9 52.5 1.0 O2 C:4VX504 2.0 77.7 0.9 OD1 C:ASP186 2.0 46.8 1.0 ND1 C:HIS188 2.3 47.6 1.0 CG C:ASP186 2.7 46.9 1.0 OD2 C:ASP186 2.8 47.4 1.0 N2 C:4VX504 2.9 78.0 0.9 CG C:ASP285 3.1 52.3 1.0 CG C:HIS188 3.2 47.7 1.0 CE1 C:HIS188 3.3 47.9 1.0 CB C:HIS188 3.4 47.4 1.0 N C:HIS188 3.5 47.5 1.0 C16 C:4VX504 3.6 78.1 0.9 OD1 C:ASP285 3.6 52.6 1.0 O1 C:4VX504 3.7 78.0 0.9 CA C:HIS188 4.1 47.1 1.0 CB C:ASP186 4.2 46.9 1.0 N C:LEU187 4.2 47.2 1.0 CB C:ASP285 4.3 52.1 1.0 NE2 C:HIS142 4.3 49.4 1.0 CD2 C:HIS188 4.3 47.7 1.0 NE2 C:HIS188 4.4 47.5 1.0 CB C:LEU187 4.5 47.2 1.0 C C:LEU187 4.5 47.3 1.0 NE2 C:HIS141 4.6 49.7 1.0 CA C:LEU187 4.6 47.3 1.0 C13 C:4VX504 4.8 78.1 0.9 C C:ASP186 4.9 47.2 1.0 CA C:GLY339 4.9 49.8 1.0 O C:HIS188 4.9 47.0 1.0 C C:HIS188 4.9 47.0 1.0

Zinc binding site 4 out of 4 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:54.1 occ:1.00 ND1 D:HIS188 1.9 52.2 1.0 OD1 D:ASP186 2.1 51.8 1.0 OD2 D:ASP285 2.3 59.6 1.0 CE1 D:HIS188 2.4 52.1 1.0 OD2 D:ASP186 2.6 51.4 1.0 CG D:ASP186 2.6 51.5 1.0 O2 D:4VX505 2.9 60.4 0.9 CG D:HIS188 3.2 51.8 1.0 CG D:ASP285 3.5 59.8 1.0 NE2 D:HIS188 3.6 52.0 1.0 N2 D:4VX505 3.8 60.8 0.9 CB D:HIS188 3.9 51.3 1.0 N D:HIS188 4.0 51.1 1.0 NE2 D:HIS142 4.0 51.0 1.0 CD2 D:HIS188 4.0 51.7 1.0 O1 D:4VX505 4.0 61.2 0.9 OD1 D:ASP285 4.1 60.3 1.0 CE1 D:HIS141 4.1 47.5 1.0 CB D:ASP186 4.1 51.4 1.0 CA D:GLY339 4.1 52.3 1.0 C16 D:4VX505 4.2 61.2 0.9 N D:LEU187 4.4 51.7 1.0 CA D:HIS188 4.6 50.8 1.0 CB D:ASP285 4.6 59.8 1.0 NE2 D:HIS141 4.6 47.4 1.0 N D:GLY339 4.6 52.3 1.0 CE1 D:HIS142 4.8 50.9 1.0 CB D:LEU187 4.8 51.7 1.0 C D:LEU187 4.9 51.5 1.0 CD2 D:HIS142 4.9 50.5 1.0 CA D:LEU187 4.9 51.7 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