Zinc in PDB 4cqf: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor, PDB code: 4cqf was solved by M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.89 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.778, 70.815, 98.024, 77.79, 75.45, 85.40
R / Rfree (%)	19 / 23.23

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor (pdb code 4cqf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor, PDB code: 4cqf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor


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 Complexed with A Mercaptoacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:28.1 occ:1.00 OD2 A:ASP285 1.9 20.6 1.0 OD1 A:ASP186 2.0 18.2 1.0 ND1 A:HIS188 2.1 15.6 1.0 S04 A:9Z8700 2.2 27.3 1.0 CG A:ASP186 2.9 17.0 1.0 CG A:ASP285 2.9 20.9 1.0 CE1 A:HIS188 3.0 14.6 1.0 OD2 A:ASP186 3.1 16.3 1.0 CG A:HIS188 3.2 14.1 1.0 OD1 A:ASP285 3.3 20.4 1.0 C03 A:9Z8700 3.3 27.2 1.0 O01 A:9Z8700 3.5 29.1 1.0 C02 A:9Z8700 3.5 28.4 1.0 CB A:HIS188 3.6 12.0 1.0 N A:HIS188 3.8 14.2 1.0 CA A:GLY339 4.2 17.7 1.0 NE2 A:HIS188 4.2 15.3 1.0 CB A:ASP285 4.3 16.8 1.0 NE2 A:HIS141 4.3 17.5 1.0 N A:LEU187 4.3 15.1 1.0 CB A:ASP186 4.3 13.1 1.0 CD2 A:HIS188 4.3 15.0 1.0 CA A:HIS188 4.4 13.2 1.0 OH A:TYR341 4.5 25.8 1.0 N A:GLY339 4.5 17.3 1.0 N05 A:9Z8700 4.5 30.3 1.0 CB A:LEU187 4.6 14.8 1.0 CE1 A:HIS141 4.6 17.5 1.0 NE2 A:HIS142 4.7 22.2 1.0 C A:LEU187 4.7 18.6 1.0 CE2 A:TYR341 4.8 24.1 1.0 CA A:LEU187 4.8 14.7 1.0 C A:ASP186 5.0 19.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:24.7 occ:1.00 OD2 B:ASP285 2.0 17.0 1.0 OD1 B:ASP186 2.0 18.0 1.0 ND1 B:HIS188 2.1 14.0 1.0 S04 B:9Z8700 2.3 21.9 1.0 CG B:ASP285 2.9 17.2 1.0 CG B:ASP186 2.9 17.6 1.0 CE1 B:HIS188 3.0 13.5 1.0 OD2 B:ASP186 3.1 19.6 1.0 OD1 B:ASP285 3.1 16.8 1.0 CG B:HIS188 3.2 12.6 1.0 C03 B:9Z8700 3.4 24.8 1.0 C02 B:9Z8700 3.6 27.0 1.0 O01 B:9Z8700 3.6 28.2 1.0 CB B:HIS188 3.7 9.8 1.0 N B:HIS188 3.8 10.0 1.0 CA B:GLY339 4.1 14.2 1.0 NE2 B:HIS188 4.2 14.1 1.0 N B:LEU187 4.2 14.2 1.0 CB B:ASP285 4.2 14.6 1.0 CB B:ASP186 4.3 13.9 1.0 CD2 B:HIS188 4.3 14.3 1.0 NE2 B:HIS141 4.3 14.2 1.0 CA B:HIS188 4.4 9.5 1.0 CB B:LEU187 4.4 13.5 1.0 N05 B:9Z8700 4.5 28.8 1.0 N B:GLY339 4.6 13.9 1.0 CE1 B:HIS141 4.6 13.6 1.0 OH B:TYR341 4.6 28.4 1.0 CA B:LEU187 4.7 13.6 1.0 C B:LEU187 4.7 15.3 1.0 CE2 B:TYR341 4.7 22.6 1.0 NE2 B:HIS142 4.8 22.1 1.0 C B:ASP186 4.9 17.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:24.3 occ:1.00 OD1 C:ASP186 2.0 18.3 1.0 OD2 C:ASP285 2.1 13.9 1.0 ND1 C:HIS188 2.2 16.2 1.0 S04 C:9Z8700 2.3 20.8 1.0 CG C:ASP186 2.9 18.8 1.0 CG C:ASP285 3.0 12.7 1.0 CE1 C:HIS188 3.1 15.9 1.0 OD2 C:ASP186 3.2 19.5 1.0 OD1 C:ASP285 3.3 11.4 1.0 CG C:HIS188 3.3 14.9 1.0 C03 C:9Z8700 3.4 23.6 1.0 O01 C:9Z8700 3.5 25.8 1.0 C02 C:9Z8700 3.5 25.3 1.0 CB C:HIS188 3.7 11.9 1.0 N C:HIS188 3.8 12.5 1.0 CA C:GLY339 4.1 12.1 1.0 NE2 C:HIS188 4.3 16.7 1.0 NE2 C:HIS141 4.3 12.7 1.0 N C:LEU187 4.3 15.3 1.0 CB C:ASP186 4.3 16.8 1.0 CB C:ASP285 4.4 13.0 1.0 CD2 C:HIS188 4.4 16.8 1.0 CA C:HIS188 4.4 11.6 1.0 N05 C:9Z8700 4.4 27.4 1.0 CB C:LEU187 4.5 14.6 1.0 N C:GLY339 4.6 12.3 1.0 CE1 C:HIS141 4.6 12.2 1.0 CE2 C:TYR341 4.7 21.2 1.0 C C:LEU187 4.7 17.8 1.0 OH C:TYR341 4.7 29.9 1.0 CA C:LEU187 4.7 14.6 1.0 NE2 C:HIS142 4.8 21.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Mercaptoacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:25.2 occ:1.00 OD1 D:ASP186 2.0 20.4 1.0 OD2 D:ASP285 2.0 18.0 1.0 ND1 D:HIS188 2.1 18.8 1.0 S04 D:9Z8700 2.3 26.6 1.0 CG D:ASP186 2.9 19.5 1.0 CG D:ASP285 2.9 17.8 1.0 CE1 D:HIS188 3.0 18.6 1.0 OD2 D:ASP186 3.2 18.1 1.0 OD1 D:ASP285 3.2 19.1 1.0 CG D:HIS188 3.2 17.6 1.0 C03 D:9Z8700 3.4 28.6 1.0 C02 D:9Z8700 3.6 31.4 1.0 CB D:HIS188 3.7 14.8 1.0 O01 D:9Z8700 3.7 31.3 1.0 N D:HIS188 3.9 16.2 1.0 CA D:GLY339 4.1 16.4 1.0 NE2 D:HIS141 4.2 15.9 1.0 NE2 D:HIS188 4.2 19.6 1.0 CB D:ASP186 4.3 15.5 1.0 N D:LEU187 4.3 16.6 1.0 CB D:ASP285 4.3 17.9 1.0 CD2 D:HIS188 4.3 19.2 1.0 N D:GLY339 4.4 17.0 1.0 CA D:HIS188 4.4 15.1 1.0 N05 D:9Z8700 4.5 32.7 1.0 CB D:LEU187 4.5 17.1 1.0 CE1 D:HIS141 4.5 15.5 1.0 OH D:TYR341 4.7 28.2 1.0 CA D:LEU187 4.8 16.9 1.0 C D:LEU187 4.8 20.8 1.0 NE2 D:HIS142 4.8 18.7 1.0 CE2 D:TYR341 4.9 20.5 1.0 C D:ASP186 4.9 21.3 1.0 CA D:ASP186 5.0 15.5 1.0

D.A.Stolfa, M.Marek, J.Lancelot, A.T.Hauser, A.Walter, E.Leproult, J.Melesina, T.Rumpf, J.M.Wurtz, J.Cavarelli, W.Sippl, R.J.Pierce, C.Romier, M.Jung. Molecular Basis For the Anti-Parasitic Activity of A Mercaptoacetamide Derivative That Inhibits Histone Deacetylase 8 (HDAC8) From the Human Pathogen Schistosoma Mansoni J.Mol.Biol. V. 426 3442 2014.
ISSN: ISSN 0022-2836
PubMed: 24657767
DOI: 10.1016/J.JMB.2014.03.007