Zinc in PDB 6hqy: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051:
3.5.1.98;

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051, PDB code: 6hqy was solved by M.Marek, T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.76 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.877, 71.053, 98.198, 78.06, 75.61, 85.45
R / Rfree (%)	18 / 25.4

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051 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 Pci- 34051 (pdb code 6hqy). 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 Pci- 34051, PDB code: 6hqy:
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 Pci- 34051


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 Pci- 34051 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.3 occ:1.00 OD2 A:ASP285 2.1 16.9 1.0 ND1 A:HIS188 2.1 17.2 1.0 OD1 A:ASP186 2.1 22.5 1.0 O18 A:GKW504 2.3 51.3 1.0 O16 A:GKW504 2.4 72.8 1.0 N17 A:GKW504 2.7 60.6 1.0 C15 A:GKW504 2.7 68.7 1.0 CE1 A:HIS188 2.9 14.9 1.0 CG A:ASP186 2.9 15.0 1.0 OD2 A:ASP186 3.0 12.6 1.0 CG A:ASP285 3.1 16.8 1.0 CG A:HIS188 3.2 19.8 1.0 OD1 A:ASP285 3.6 15.4 1.0 CB A:HIS188 3.7 14.8 1.0 N A:HIS188 3.9 24.0 1.0 NE2 A:HIS188 4.0 19.9 1.0 CA A:GLY339 4.0 28.1 1.0 C14 A:GKW504 4.1 71.5 1.0 CD2 A:HIS188 4.2 19.5 1.0 CB A:ASP186 4.3 9.9 1.0 N A:LEU187 4.4 18.6 1.0 CB A:ASP285 4.4 17.0 1.0 N A:GLY339 4.4 27.5 1.0 CA A:HIS188 4.4 19.0 1.0 NE2 A:HIS141 4.5 28.4 1.0 CB A:LEU187 4.6 14.2 1.0 OH A:TYR341 4.6 38.5 1.0 C A:LEU187 4.8 17.0 1.0 C13 A:GKW504 4.8 69.8 1.0 CE2 A:TYR341 4.8 31.1 1.0 CA A:LEU187 4.8 11.6 1.0 NE2 A:HIS142 4.9 28.2 1.0 C19 A:GKW504 4.9 77.1 1.0 CE1 A:HIS141 4.9 28.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:21.5 occ:1.00 OD2 B:ASP285 1.9 23.9 1.0 OD1 B:ASP186 2.2 6.1 1.0 O18 B:GKW504 2.3 30.5 1.0 ND1 B:HIS188 2.3 10.9 1.0 N17 B:GKW504 2.6 48.0 1.0 O16 B:GKW504 2.8 43.6 1.0 CG B:ASP285 2.9 27.0 1.0 C15 B:GKW504 2.9 50.4 1.0 CG B:ASP186 3.0 29.7 1.0 CE1 B:HIS188 3.1 19.3 1.0 OD2 B:ASP186 3.1 17.9 1.0 OD1 B:ASP285 3.3 28.3 1.0 CG B:HIS188 3.4 19.0 1.0 N B:HIS188 3.8 11.3 1.0 CB B:HIS188 3.8 17.6 1.0 CA B:GLY339 4.0 27.1 1.0 N B:LEU187 4.1 14.6 1.0 CB B:ASP285 4.2 17.8 1.0 C14 B:GKW504 4.2 48.0 1.0 NE2 B:HIS188 4.2 26.8 1.0 CB B:LEU187 4.4 22.0 1.0 CB B:ASP186 4.4 5.8 1.0 CD2 B:HIS188 4.4 24.6 1.0 CA B:HIS188 4.5 13.7 1.0 N B:GLY339 4.5 26.9 1.0 NE2 B:HIS141 4.5 23.0 1.0 CA B:LEU187 4.6 7.7 1.0 C B:LEU187 4.6 8.9 1.0 CE1 B:HIS141 4.7 17.4 1.0 CE2 B:TYR341 4.8 28.1 1.0 C13 B:GKW504 4.8 46.6 1.0 NE2 B:HIS142 4.8 34.0 1.0 C B:ASP186 4.9 18.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:24.4 occ:1.00 OD2 C:ASP285 2.1 13.5 1.0 O18 C:GKW504 2.1 42.9 1.0 OD1 C:ASP186 2.2 10.5 1.0 ND1 C:HIS188 2.3 10.6 1.0 N17 C:GKW504 2.6 52.8 1.0 O16 C:GKW504 2.9 53.2 1.0 CG C:ASP186 3.0 20.4 1.0 C15 C:GKW504 3.0 55.9 1.0 CG C:ASP285 3.0 19.1 1.0 OD2 C:ASP186 3.1 11.0 1.0 CE1 C:HIS188 3.1 16.6 1.0 OD1 C:ASP285 3.3 25.9 1.0 CG C:HIS188 3.4 16.0 1.0 CB C:HIS188 3.8 9.0 1.0 N C:HIS188 3.9 14.1 1.0 CA C:GLY339 4.1 13.7 1.0 N C:LEU187 4.2 10.9 1.0 NE2 C:HIS188 4.3 23.0 1.0 CB C:LEU187 4.3 18.1 1.0 C14 C:GKW504 4.4 55.8 1.0 CB C:ASP285 4.4 8.6 1.0 CD2 C:HIS188 4.5 18.9 1.0 CB C:ASP186 4.5 3.4 1.0 NE2 C:HIS141 4.5 21.0 1.0 CA C:HIS188 4.5 9.2 1.0 N C:GLY339 4.5 23.7 1.0 CA C:LEU187 4.6 5.2 1.0 C C:LEU187 4.7 13.8 1.0 NE2 C:HIS142 4.7 41.7 1.0 CE1 C:HIS141 4.8 23.2 1.0 CE1 C:TYR341 4.9 32.6 1.0 C C:ASP186 5.0 13.3 1.0 C13 C:GKW504 5.0 50.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:24.1 occ:1.00 OD2 D:ASP285 2.0 20.6 1.0 OD1 D:ASP186 2.1 24.1 1.0 ND1 D:HIS188 2.1 16.0 1.0 O18 D:GKW504 2.1 38.6 1.0 O16 D:GKW504 2.5 66.5 1.0 N17 D:GKW504 2.5 54.1 1.0 C15 D:GKW504 2.7 63.8 1.0 CE1 D:HIS188 2.9 7.5 1.0 CG D:ASP186 2.9 10.8 1.0 OD2 D:ASP186 3.1 12.3 1.0 CG D:ASP285 3.1 21.4 1.0 CG D:HIS188 3.2 14.0 1.0 OD1 D:ASP285 3.6 23.6 1.0 CB D:HIS188 3.7 14.2 1.0 N D:HIS188 3.9 26.2 1.0 C14 D:GKW504 4.0 68.0 1.0 CA D:GLY339 4.1 32.9 1.0 NE2 D:HIS188 4.1 14.8 1.0 CD2 D:HIS188 4.3 11.4 1.0 CB D:ASP186 4.3 10.8 1.0 CB D:ASP285 4.4 22.6 1.0 CA D:HIS188 4.4 22.4 1.0 N D:LEU187 4.5 18.9 1.0 N D:GLY339 4.5 23.2 1.0 NE2 D:HIS141 4.5 29.4 1.0 C13 D:GKW504 4.7 66.6 1.0 CB D:LEU187 4.8 7.7 1.0 C D:LEU187 4.8 24.3 1.0 NE2 D:HIS142 4.8 34.4 1.0 CA D:LEU187 4.9 14.8 1.0 CE1 D:HIS141 4.9 25.6 1.0 OH D:TYR341 4.9 35.7 1.0 C19 D:GKW504 5.0 74.7 1.0 CE2 D:TYR341 5.0 31.1 1.0

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087