Zinc in PDB 5fue: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate, PDB code: 5fue 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)	42.145 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.955, 70.669, 98.656, 77.99, 75.41, 85.40
R / Rfree (%)	14.76 / 19.57

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate 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 3-Benzamido-Benzohydroxamate (pdb code 5fue). 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 3-Benzamido-Benzohydroxamate, PDB code: 5fue:
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 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:24.4 occ:1.00 OD2 A:ASP285 2.0 25.0 1.0 OD1 A:ASP186 2.0 19.1 1.0 ND1 A:HIS188 2.0 19.9 1.0 O06 A:UV4700 2.4 40.7 1.0 O08 A:UV4700 2.5 36.1 1.0 C05 A:UV4700 2.8 49.0 1.0 CG A:ASP186 2.8 19.8 1.0 CE1 A:HIS188 2.9 13.8 1.0 N07 A:UV4700 2.9 50.9 1.0 OD2 A:ASP186 3.0 18.9 1.0 CG A:ASP285 3.0 26.4 1.0 CG A:HIS188 3.1 14.4 1.0 OD1 A:ASP285 3.4 22.7 1.0 CB A:HIS188 3.6 13.8 1.0 N A:HIS188 3.8 13.1 1.0 C04 A:UV4700 4.0 48.4 1.0 NE2 A:HIS188 4.0 14.7 1.0 CA A:GLY339 4.1 18.2 1.0 CD2 A:HIS188 4.2 19.2 1.0 N A:LEU187 4.2 17.2 1.0 CB A:ASP186 4.2 15.8 1.0 CB A:ASP285 4.3 14.5 1.0 CA A:HIS188 4.3 15.8 1.0 C09 A:UV4700 4.4 44.2 1.0 CB A:LEU187 4.4 17.5 1.0 OH A:TYR341 4.4 33.1 1.0 N A:GLY339 4.5 20.0 1.0 NE2 A:HIS141 4.6 22.6 1.0 C A:LEU187 4.6 17.9 1.0 CE2 A:TYR341 4.6 29.3 1.0 CA A:LEU187 4.7 16.7 1.0 C A:ASP186 4.9 18.3 1.0 NE2 A:HIS142 5.0 19.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:20.7 occ:1.00 OD1 B:ASP186 1.9 15.8 1.0 OD2 B:ASP285 2.0 19.1 1.0 ND1 B:HIS188 2.1 17.8 1.0 O06 B:UV4700 2.2 37.9 1.0 O08 B:UV4700 2.4 31.6 1.0 C05 B:UV4700 2.6 44.1 1.0 N07 B:UV4700 2.7 46.4 1.0 CG B:ASP186 2.8 15.8 1.0 CG B:ASP285 3.0 21.4 1.0 CE1 B:HIS188 3.0 18.3 1.0 OD2 B:ASP186 3.0 18.0 1.0 CG B:HIS188 3.2 18.4 1.0 OD1 B:ASP285 3.3 20.4 1.0 CB B:HIS188 3.6 12.7 1.0 N B:HIS188 3.8 12.8 1.0 C04 B:UV4700 3.8 38.1 1.0 NE2 B:HIS188 4.1 22.4 1.0 CA B:GLY339 4.2 11.2 1.0 CB B:ASP186 4.2 13.2 1.0 N B:LEU187 4.3 14.8 1.0 CD2 B:HIS188 4.3 18.4 1.0 C09 B:UV4700 4.3 38.8 1.0 CB B:ASP285 4.3 8.5 1.0 CB B:LEU187 4.3 11.6 1.0 CA B:HIS188 4.4 14.6 1.0 OH B:TYR341 4.5 31.5 1.0 NE2 B:HIS141 4.5 14.7 1.0 N B:GLY339 4.5 19.5 1.0 CE2 B:TYR341 4.6 21.1 1.0 CA B:LEU187 4.6 17.6 1.0 C B:LEU187 4.6 18.8 1.0 CE1 B:HIS141 4.9 13.8 1.0 C B:ASP186 4.9 18.9 1.0 C03 B:UV4700 4.9 30.5 1.0 CA B:ASP186 5.0 17.3 1.0 NE2 B:HIS142 5.0 26.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:21.3 occ:1.00 OD1 C:ASP186 2.0 15.2 1.0 OD2 C:ASP285 2.0 20.5 1.0 O06 C:UV4700 2.2 39.1 1.0 ND1 C:HIS188 2.2 19.9 1.0 O08 C:UV4700 2.4 27.3 1.0 C05 C:UV4700 2.6 42.2 1.0 N07 C:UV4700 2.6 40.9 1.0 CG C:ASP186 2.8 12.2 1.0 OD2 C:ASP186 3.0 19.0 1.0 CG C:ASP285 3.0 21.8 1.0 CE1 C:HIS188 3.0 20.7 1.0 CG C:HIS188 3.2 20.3 1.0 OD1 C:ASP285 3.4 18.4 1.0 CB C:HIS188 3.6 18.0 1.0 C04 C:UV4700 3.8 36.9 1.0 N C:HIS188 3.8 14.7 1.0 CA C:GLY339 4.1 16.0 1.0 NE2 C:HIS188 4.2 24.3 1.0 CB C:ASP186 4.3 10.2 1.0 C09 C:UV4700 4.3 34.3 1.0 N C:LEU187 4.3 17.9 1.0 CD2 C:HIS188 4.3 19.8 1.0 CA C:HIS188 4.4 17.9 1.0 CB C:ASP285 4.4 12.0 1.0 CB C:LEU187 4.5 11.3 1.0 NE2 C:HIS141 4.5 16.0 1.0 N C:GLY339 4.5 20.0 1.0 OH C:TYR341 4.6 30.1 1.0 CE2 C:TYR341 4.6 27.7 1.0 C C:LEU187 4.7 22.0 1.0 CA C:LEU187 4.7 15.7 1.0 CE1 C:HIS141 4.8 14.4 1.0 C03 C:UV4700 4.9 30.4 1.0 C C:ASP186 4.9 19.1 1.0 NE2 C:HIS142 5.0 30.7 1.0 CA C:ASP186 5.0 16.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with 3-Benzamido-Benzohydroxamate


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 3-Benzamido-Benzohydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:24.6 occ:1.00 OD2 D:ASP285 1.9 19.3 1.0 OD1 D:ASP186 2.0 20.2 1.0 ND1 D:HIS188 2.2 22.5 1.0 O06 D:UV4700 2.4 40.4 1.0 O08 D:UV4700 2.5 33.2 1.0 C05 D:UV4700 2.8 49.8 1.0 CG D:ASP186 2.8 17.5 1.0 N07 D:UV4700 2.9 52.5 1.0 CG D:ASP285 3.0 24.8 1.0 OD2 D:ASP186 3.0 16.1 1.0 CE1 D:HIS188 3.1 17.1 1.0 CG D:HIS188 3.2 20.1 1.0 OD1 D:ASP285 3.4 22.4 1.0 CB D:HIS188 3.6 18.2 1.0 N D:HIS188 3.8 20.8 1.0 C04 D:UV4700 4.0 46.3 1.0 CA D:GLY339 4.1 20.6 1.0 NE2 D:HIS188 4.2 21.9 1.0 CB D:ASP186 4.3 15.2 1.0 N D:LEU187 4.3 18.5 1.0 CD2 D:HIS188 4.3 17.9 1.0 CB D:ASP285 4.3 17.3 1.0 CA D:HIS188 4.3 19.6 1.0 C09 D:UV4700 4.5 36.7 1.0 NE2 D:HIS141 4.5 20.9 1.0 N D:GLY339 4.5 21.0 1.0 CB D:LEU187 4.5 10.7 1.0 OH D:TYR341 4.6 37.7 1.0 C D:LEU187 4.7 22.9 1.0 CE2 D:TYR341 4.7 31.4 1.0 CA D:LEU187 4.7 20.7 1.0 NE2 D:HIS142 4.9 23.4 1.0 CE1 D:HIS141 4.9 19.6 1.0 C D:ASP186 4.9 23.4 1.0 C03 D:UV4700 5.0 41.1 1.0

T.Heimburg, A.Chakrabarti, J.Lancelot, M.Marek, J.Melesina, A.T.Hauser, T.B.Shaik, S.Duclaud, D.Robaa, F.Erdmann, M.Schmidt, C.Romier, R.J.Pierce, M.Jung, W.Sippl. Structure-Based Design and Synthesis of Novel Inhibitors Targeting HDAC8 From Schistosoma Mansoni For the Treatment of Schistosomiasis. J.Med.Chem. V. 59 2423 2016.
ISSN: ISSN 0022-2623
PubMed: 26937828
DOI: 10.1021/ACS.JMEDCHEM.5B01478