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Zinc in PDB 6hu0: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9, PDB code: 6hu0 was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.690, 70.730, 98.120, 75.51, 78.08, 85.55
R / Rfree (%) 18.9 / 22.6

Other elements in 6hu0:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 (pdb code 6hu0). 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 Benzohydroxamate Inhibitor 9, PDB code: 6hu0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hu0

Go back to Zinc Binding Sites List in 6hu0
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.4
occ:1.00
 OD2 A:ASP285 2.0 12.6 1.0
OD1 A:ASP186 2.0 8.1 1.0
O29 A:T86504 2.2 20.8 1.0
O28 A:T86504 2.2 22.0 1.0
ND1 A:HIS188 2.2 12.0 1.0
C26 A:T86504 2.7 30.4 1.0
N27 A:T86504 2.8 41.4 1.0
CG A:ASP186 2.9 10.2 1.0
OD2 A:ASP186 3.0 6.2 1.0
CE1 A:HIS188 3.0 14.2 1.0
CG A:ASP285 3.1 16.2 1.0
CG A:HIS188 3.2 11.4 1.0
OD1 A:ASP285 3.5 11.0 1.0
CB A:HIS188 3.7 9.1 1.0
N A:HIS188 3.9 8.6 1.0
C15 A:T86504 4.0 24.4 1.0
CA A:GLY339 4.1 9.9 1.0
NE2 A:HIS188 4.2 10.8 1.0
O A:HOH831 4.2 30.5 1.0
CB A:ASP186 4.3 5.8 1.0
CD2 A:HIS188 4.3 10.9 1.0
CB A:ASP285 4.3 7.9 1.0
N A:LEU187 4.4 9.4 1.0
CA A:HIS188 4.4 10.9 1.0
NE2 A:HIS141 4.4 13.4 1.0
OH A:TYR341 4.4 17.4 1.0
N A:GLY339 4.5 10.4 1.0
C16 A:T86504 4.5 19.4 1.0
CB A:LEU187 4.6 14.5 1.0
CE2 A:TYR341 4.6 16.3 1.0
C A:LEU187 4.8 11.0 1.0
CA A:LEU187 4.8 14.8 1.0
NE2 A:HIS142 4.8 8.6 1.0
CE1 A:HIS141 4.9 8.9 1.0

Zinc binding site 2 out of 4 in 6hu0

Go back to Zinc Binding Sites List in 6hu0
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.5
occ:1.00
 OD2 B:ASP285 2.0 11.0 1.0
OD1 B:ASP186 2.0 7.0 1.0
O28 B:T86504 2.1 17.7 1.0
O29 B:T86504 2.2 16.3 1.0
ND1 B:HIS188 2.3 10.1 1.0
N27 B:T86504 2.7 29.8 1.0
C26 B:T86504 2.8 25.2 1.0
CG B:ASP186 2.8 7.3 1.0
OD2 B:ASP186 2.9 9.5 1.0
CG B:ASP285 3.0 15.5 1.0
CE1 B:HIS188 3.1 7.5 1.0
CG B:HIS188 3.3 7.3 1.0
OD1 B:ASP285 3.4 10.6 1.0
CB B:HIS188 3.8 7.7 1.0
N B:HIS188 3.9 7.6 1.0
CA B:GLY339 4.0 11.7 1.0
C15 B:T86504 4.1 17.6 1.0
O B:HOH814 4.2 32.2 1.0
CB B:ASP186 4.2 6.1 1.0
NE2 B:HIS188 4.3 9.2 1.0
N B:LEU187 4.3 8.0 1.0
CB B:ASP285 4.3 11.8 1.0
NE2 B:HIS141 4.4 14.1 1.0
CD2 B:HIS188 4.4 6.6 1.0
N B:GLY339 4.4 9.9 1.0
CA B:HIS188 4.5 10.1 1.0
CB B:LEU187 4.5 4.8 1.0
OH B:TYR341 4.5 15.6 1.0
C16 B:T86504 4.6 15.9 1.0
CE2 B:TYR341 4.6 11.1 1.0
CE1 B:HIS141 4.7 9.1 1.0
C B:LEU187 4.8 9.4 1.0
CA B:LEU187 4.8 9.4 1.0
C B:ASP186 4.9 5.5 1.0
NE2 B:HIS142 5.0 9.0 1.0
CA B:ASP186 5.0 5.4 1.0

Zinc binding site 3 out of 4 in 6hu0

Go back to Zinc Binding Sites List in 6hu0
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:23.2
occ:1.00
 OD1 C:ASP186 2.0 11.1 1.0
OD2 C:ASP285 2.0 9.4 1.0
O28 C:T86504 2.2 20.6 1.0
ND1 C:HIS188 2.2 12.0 1.0
O29 C:T86504 2.3 15.6 1.0
CG C:ASP186 2.8 11.6 1.0
C26 C:T86504 2.8 23.7 1.0
N27 C:T86504 2.8 29.2 1.0
OD2 C:ASP186 2.9 10.1 1.0
CG C:ASP285 3.0 16.8 1.0
CE1 C:HIS188 3.1 11.6 1.0
CG C:HIS188 3.3 11.2 1.0
OD1 C:ASP285 3.4 12.0 1.0
CB C:HIS188 3.7 8.8 1.0
N C:HIS188 3.8 8.6 1.0
O C:HOH698 4.1 35.0 1.0
CA C:GLY339 4.1 8.9 1.0
C15 C:T86504 4.1 17.8 1.0
CB C:ASP186 4.2 5.6 1.0
NE2 C:HIS188 4.2 7.9 1.0
N C:LEU187 4.3 9.0 1.0
CB C:ASP285 4.3 12.2 1.0
CD2 C:HIS188 4.3 11.5 1.0
NE2 C:HIS141 4.4 12.9 1.0
CA C:HIS188 4.4 8.8 1.0
CB C:LEU187 4.4 8.0 1.0
N C:GLY339 4.5 10.9 1.0
OH C:TYR341 4.5 14.9 1.0
C16 C:T86504 4.6 16.5 1.0
CE2 C:TYR341 4.6 11.6 1.0
CE1 C:HIS141 4.7 10.3 1.0
C C:LEU187 4.7 10.8 1.0
CA C:LEU187 4.7 7.8 1.0
NE2 C:HIS142 4.9 11.2 1.0
C C:ASP186 4.9 8.4 1.0
CA C:ASP186 5.0 8.1 1.0

Zinc binding site 4 out of 4 in 6hu0

Go back to Zinc Binding Sites List in 6hu0
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:22.8
occ:1.00
 OD1 D:ASP186 2.0 10.6 1.0
OD2 D:ASP285 2.1 9.6 1.0
ND1 D:HIS188 2.2 14.4 1.0
O28 D:T86504 2.2 17.9 1.0
O29 D:T86504 2.2 27.2 1.0
N27 D:T86504 2.6 31.4 1.0
C26 D:T86504 2.6 29.1 1.0
CG D:ASP186 2.9 16.5 1.0
CG D:ASP285 3.0 19.9 1.0
CE1 D:HIS188 3.0 18.2 1.0
OD2 D:ASP186 3.1 11.8 1.0
CG D:HIS188 3.2 15.1 1.0
OD1 D:ASP285 3.3 10.8 1.0
CB D:HIS188 3.6 9.1 1.0
N D:HIS188 3.9 6.1 1.0
C15 D:T86504 4.0 26.9 1.0
CA D:GLY339 4.1 14.8 1.0
NE2 D:HIS188 4.2 13.6 1.0
O D:HOH788 4.2 34.9 1.0
CB D:ASP186 4.3 9.5 1.0
CD2 D:HIS188 4.3 14.8 1.0
CB D:ASP285 4.4 10.5 1.0
NE2 D:HIS141 4.4 12.4 1.0
N D:LEU187 4.4 7.9 1.0
CA D:HIS188 4.4 11.8 1.0
OH D:TYR341 4.5 16.7 1.0
C16 D:T86504 4.5 24.8 1.0
N D:GLY339 4.5 11.8 1.0
CB D:LEU187 4.6 11.8 1.0
CE2 D:TYR341 4.6 13.3 1.0
CE1 D:HIS141 4.8 14.9 1.0
C D:LEU187 4.8 6.9 1.0
O D:HOH742 4.8 43.9 1.0
CA D:LEU187 4.9 10.0 1.0
NE2 D:HIS142 4.9 9.8 1.0
C14 D:T86504 5.0 22.8 1.0

Reference:

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
Page generated: Mon Oct 28 23:19:18 2024

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