Zinc in PDB 4bz5: Crystal Structure of Schistosoma Mansoni HDAC8

The structure of Crystal Structure of Schistosoma Mansoni HDAC8, PDB code: 4bz5 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)	31.370 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.649, 70.734, 98.295, 75.90, 78.32, 85.59
R / Rfree (%)	15.44 / 18.83

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 (pdb code 4bz5). 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, PDB code: 4bz5:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:19.1 occ:1.00 OD1 A:ASP186 2.0 12.3 1.0 OD2 A:ASP285 2.0 11.7 1.0 ND1 A:HIS188 2.1 14.0 1.0 O1 A:TLA700 2.2 20.5 1.0 O2 A:TLA700 2.3 24.4 1.0 CG A:ASP186 2.8 12.7 1.0 CE1 A:HIS188 3.0 18.0 1.0 OD2 A:ASP186 3.0 11.9 1.0 C1 A:TLA700 3.0 29.3 1.0 HA A:TLA700 3.1 29.3 1.0 CG A:ASP285 3.1 14.2 1.0 C2 A:TLA700 3.2 28.3 1.0 CG A:HIS188 3.2 12.2 1.0 OD1 A:ASP285 3.5 14.4 1.0 CB A:HIS188 3.7 10.0 1.0 O3 A:TLA700 3.7 23.2 1.0 N A:HIS188 3.8 11.1 1.0 C3 A:TLA700 4.0 23.8 1.0 H2 A:TLA700 4.1 33.9 1.0 CA A:GLY339 4.1 11.8 1.0 NE2 A:HIS188 4.1 16.9 1.0 N A:LEU187 4.2 12.7 1.0 O11 A:TLA700 4.2 25.8 1.0 CB A:ASP186 4.2 10.8 1.0 CD2 A:HIS188 4.3 14.1 1.0 CB A:ASP285 4.4 11.9 1.0 NE2 A:HIS141 4.4 13.6 1.0 CA A:HIS188 4.4 11.9 1.0 CB A:LEU187 4.5 11.5 1.0 HB A:TLA700 4.5 27.9 1.0 N A:GLY339 4.5 11.8 1.0 C4 A:TLA700 4.7 35.7 1.0 NE2 A:HIS142 4.7 14.7 1.0 CA A:LEU187 4.7 11.1 1.0 C A:LEU187 4.7 12.0 1.0 O A:HOH2046 4.7 16.8 1.0 CE1 A:HIS141 4.8 16.5 1.0 C A:ASP186 4.9 12.8 1.0 O41 A:TLA700 4.9 32.9 1.0 H3 A:TLA700 4.9 28.5 1.0 CA A:ASP186 5.0 11.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:18.5 occ:1.00 OD1 B:ASP186 2.0 9.5 1.0 OD2 B:ASP285 2.0 10.6 1.0 HB B:TLA700 2.1 28.1 1.0 ND1 B:HIS188 2.2 14.7 1.0 O41 B:TLA700 2.2 16.4 1.0 O3 B:TLA700 2.3 23.4 1.0 CG B:ASP186 2.8 9.4 1.0 CE1 B:HIS188 3.0 20.9 1.0 OD2 B:ASP186 3.0 11.3 1.0 C4 B:TLA700 3.0 28.8 1.0 CG B:ASP285 3.0 12.0 1.0 C3 B:TLA700 3.2 28.9 1.0 CG B:HIS188 3.3 15.4 1.0 OD1 B:ASP285 3.4 12.2 1.0 CB B:HIS188 3.7 13.7 1.0 O2 B:TLA700 3.8 25.9 1.0 HA B:TLA700 3.9 31.0 1.0 N B:HIS188 3.9 9.5 1.0 CA B:GLY339 4.0 11.5 1.0 H3 B:TLA700 4.1 34.6 1.0 C2 B:TLA700 4.1 29.6 1.0 NE2 B:HIS188 4.2 18.4 1.0 O4 B:TLA700 4.2 24.1 1.0 N B:LEU187 4.2 8.6 1.0 CB B:ASP186 4.2 11.0 1.0 CD2 B:HIS188 4.3 15.2 1.0 CB B:ASP285 4.3 10.4 1.0 NE2 B:HIS141 4.4 13.4 1.0 CA B:HIS188 4.4 11.1 1.0 N B:GLY339 4.5 9.8 1.0 CB B:LEU187 4.5 8.5 1.0 C1 B:TLA700 4.7 42.1 1.0 CA B:LEU187 4.7 10.4 1.0 CE1 B:HIS141 4.7 11.4 1.0 O B:HOH2040 4.7 16.9 1.0 C B:LEU187 4.7 11.7 1.0 NE2 B:HIS142 4.8 14.0 1.0 C B:ASP186 4.9 10.8 1.0 C B:GLY339 5.0 12.8 1.0 CA B:ASP186 5.0 10.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:18.1 occ:1.00 OD1 C:ASP186 1.9 9.8 1.0 OD2 C:ASP285 2.0 10.3 1.0 ND1 C:HIS188 2.1 14.2 1.0 O1 C:TLA700 2.2 17.6 1.0 O2 C:TLA700 2.3 22.6 1.0 CG C:ASP186 2.8 12.5 1.0 CE1 C:HIS188 2.9 19.1 1.0 OD2 C:ASP186 3.0 11.1 1.0 CG C:ASP285 3.0 13.7 1.0 C1 C:TLA700 3.0 26.3 1.0 HA C:TLA700 3.1 27.1 1.0 C2 C:TLA700 3.2 27.1 1.0 CG C:HIS188 3.2 14.6 1.0 OD1 C:ASP285 3.4 14.3 1.0 CB C:HIS188 3.7 11.9 1.0 O3 C:TLA700 3.7 23.8 1.0 N C:HIS188 3.9 8.1 1.0 C3 C:TLA700 4.0 25.7 1.0 CA C:GLY339 4.1 10.3 1.0 H2 C:TLA700 4.1 32.5 1.0 NE2 C:HIS188 4.1 18.2 1.0 CB C:ASP186 4.2 10.3 1.0 O11 C:TLA700 4.2 21.9 1.0 N C:LEU187 4.2 8.2 1.0 CD2 C:HIS188 4.3 14.8 1.0 CB C:ASP285 4.3 12.1 1.0 NE2 C:HIS141 4.4 12.5 1.0 CA C:HIS188 4.4 12.2 1.0 N C:GLY339 4.5 10.2 1.0 CB C:LEU187 4.5 8.7 1.0 HB C:TLA700 4.6 28.6 1.0 C4 C:TLA700 4.7 38.1 1.0 CE1 C:HIS141 4.7 12.1 1.0 NE2 C:HIS142 4.7 12.9 1.0 C C:LEU187 4.7 9.9 1.0 CA C:LEU187 4.7 7.7 1.0 O C:HOH2227 4.8 34.9 1.0 C C:ASP186 4.9 8.2 1.0 O C:HOH2059 4.9 17.6 1.0 H3 C:TLA700 5.0 30.8 1.0 O41 C:TLA700 5.0 33.7 1.0 CA C:ASP186 5.0 8.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:19.8 occ:1.00 OD1 D:ASP186 2.0 12.1 1.0 OD2 D:ASP285 2.0 12.8 1.0 ND1 D:HIS188 2.1 13.8 1.0 O2 D:TLA700 2.2 22.3 1.0 O1 D:TLA700 2.2 20.8 1.0 CG D:ASP186 2.8 13.8 1.0 CE1 D:HIS188 2.9 21.5 1.0 HA D:TLA700 3.0 26.8 1.0 OD2 D:ASP186 3.0 12.6 1.0 CG D:ASP285 3.0 16.6 1.0 C1 D:TLA700 3.0 30.9 1.0 C2 D:TLA700 3.1 30.9 1.0 CG D:HIS188 3.2 13.9 1.0 OD1 D:ASP285 3.4 17.3 1.0 O3 D:TLA700 3.7 29.1 1.0 CB D:HIS188 3.7 12.1 1.0 N D:HIS188 3.9 12.0 1.0 C3 D:TLA700 4.0 28.3 1.0 H2 D:TLA700 4.0 37.0 1.0 CA D:GLY339 4.1 12.5 1.0 NE2 D:HIS188 4.1 19.3 1.0 N D:LEU187 4.2 10.3 1.0 O11 D:TLA700 4.2 27.1 1.0 CB D:ASP186 4.2 12.2 1.0 CD2 D:HIS188 4.3 16.6 1.0 CB D:ASP285 4.3 11.3 1.0 NE2 D:HIS141 4.4 15.6 1.0 N D:GLY339 4.4 10.9 1.0 CB D:LEU187 4.4 11.5 1.0 CA D:HIS188 4.4 9.8 1.0 HB D:TLA700 4.5 34.8 1.0 C4 D:TLA700 4.6 38.1 1.0 CA D:LEU187 4.7 11.2 1.0 C D:LEU187 4.7 13.8 1.0 NE2 D:HIS142 4.7 14.1 1.0 O D:HOH2030 4.7 17.5 1.0 CE1 D:HIS141 4.8 15.0 1.0 O41 D:TLA700 4.9 35.3 1.0 C D:ASP186 4.9 14.5 1.0 H3 D:TLA700 4.9 33.9 1.0 CA D:ASP186 5.0 11.0 1.0

M.Marek, S.Kannan, A.Hauser, M.Moraes Mourao, S.Caby, V.Cura, D.A.Stolfa, K.Schmidtkunz, J.Lancelot, L.Andrade, J.Renaud, G.Oliveira, W.Sippl, M.Jung, J.Cavarelli, R.J.Pierce, C.Romier. Structural Basis For the Inhibition of Histone Deacetylase 8 (HDAC8), A Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni. Plos Pathog. V. 9 03645 2013.
ISSN: ISSN 1553-7366
PubMed: 24086136
DOI: 10.1371/JOURNAL.PPAT.1003645