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Zinc in PDB 6htz: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8, PDB code: 6htz 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) 48.32 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.260, 71.260, 99.070, 77.90, 75.53, 85.44
R / Rfree (%) 17.7 / 21.8

Other elements in 6htz:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8 also contains other interesting chemical elements:

Potassium (K) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8 (pdb code 6htz). 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 8, PDB code: 6htz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6htz

Go back to Zinc Binding Sites List in 6htz
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:29.1
occ:1.00
 OD2 A:ASP285 2.1 16.3 1.0
OD1 A:ASP186 2.1 18.0 1.0
ND1 A:HIS188 2.2 12.7 1.0
O1 A:GRK504 2.3 25.4 1.0
O4 A:GRK504 2.4 27.6 1.0
C3 A:GRK504 2.8 33.8 1.0
N2 A:GRK504 2.8 38.3 1.0
CG A:ASP186 2.9 14.1 1.0
OD2 A:ASP186 3.0 13.5 1.0
CE1 A:HIS188 3.1 16.0 1.0
CG A:ASP285 3.1 20.5 1.0
CG A:HIS188 3.3 12.8 1.0
OD1 A:ASP285 3.5 18.3 1.0
CB A:HIS188 3.7 13.3 1.0
N A:HIS188 3.9 13.2 1.0
CA A:GLY339 4.1 17.1 1.0
C5 A:GRK504 4.1 27.5 1.0
NE2 A:HIS188 4.2 11.9 1.0
CB A:ASP186 4.4 8.1 1.0
CD2 A:HIS188 4.4 11.3 1.0
N A:LEU187 4.4 12.3 1.0
CB A:ASP285 4.4 12.6 1.0
CA A:HIS188 4.5 13.8 1.0
OH A:TYR341 4.5 18.6 1.0
NE2 A:HIS141 4.5 18.9 1.0
N A:GLY339 4.5 17.0 1.0
CB A:LEU187 4.5 9.1 1.0
CE2 A:TYR341 4.7 17.8 1.0
C10 A:GRK504 4.7 19.9 1.0
C A:LEU187 4.8 9.2 1.0
CA A:LEU187 4.8 8.1 1.0
NE2 A:HIS142 4.9 14.7 1.0
CE1 A:HIS141 4.9 14.7 1.0

Zinc binding site 2 out of 4 in 6htz

Go back to Zinc Binding Sites List in 6htz
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:26.4
occ:1.00
 OD2 B:ASP285 2.0 14.9 1.0
OD1 B:ASP186 2.0 11.8 1.0
O4 B:GRK504 2.1 21.1 1.0
ND1 B:HIS188 2.2 15.5 1.0
O1 B:GRK504 2.3 17.5 1.0
C3 B:GRK504 2.7 30.7 1.0
N2 B:GRK504 2.8 34.0 1.0
CG B:ASP186 2.9 12.5 1.0
CG B:ASP285 3.1 20.8 1.0
CE1 B:HIS188 3.1 17.7 1.0
OD2 B:ASP186 3.1 9.6 1.0
CG B:HIS188 3.3 12.6 1.0
OD1 B:ASP285 3.5 16.6 1.0
CB B:HIS188 3.7 9.9 1.0
N B:HIS188 4.0 13.4 1.0
C5 B:GRK504 4.0 23.4 1.0
CA B:GLY339 4.1 12.5 1.0
NE2 B:HIS188 4.2 21.6 1.0
CB B:ASP186 4.3 12.5 1.0
CD2 B:HIS188 4.4 15.3 1.0
CB B:ASP285 4.4 12.7 1.0
O B:HOH710 4.4 33.5 1.0
N B:LEU187 4.4 9.8 1.0
OH B:TYR341 4.5 21.4 1.0
CA B:HIS188 4.5 13.2 1.0
NE2 B:HIS141 4.5 12.1 1.0
N B:GLY339 4.5 16.9 1.0
C10 B:GRK504 4.5 20.9 1.0
CB B:LEU187 4.6 15.8 1.0
CE2 B:TYR341 4.7 16.5 1.0
C B:LEU187 4.8 16.0 1.0
CA B:LEU187 4.8 11.4 1.0
NE2 B:HIS142 4.9 13.7 1.0
CE1 B:HIS141 4.9 13.1 1.0

Zinc binding site 3 out of 4 in 6htz

Go back to Zinc Binding Sites List in 6htz
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:27.1
occ:1.00
 OD2 C:ASP285 2.1 14.4 1.0
OD1 C:ASP186 2.1 12.4 1.0
O4 C:GRK504 2.2 26.5 1.0
O1 C:GRK504 2.3 21.1 1.0
ND1 C:HIS188 2.3 13.8 1.0
C3 C:GRK504 2.7 33.9 1.0
N2 C:GRK504 2.7 29.5 1.0
CG C:ASP186 3.0 12.7 1.0
CG C:ASP285 3.1 19.7 1.0
CE1 C:HIS188 3.1 14.8 1.0
OD2 C:ASP186 3.2 11.6 1.0
CG C:HIS188 3.3 12.3 1.0
OD1 C:ASP285 3.5 15.7 1.0
CB C:HIS188 3.7 12.2 1.0
N C:HIS188 4.0 13.3 1.0
C5 C:GRK504 4.0 26.9 1.0
CA C:GLY339 4.2 9.7 1.0
NE2 C:HIS188 4.3 16.3 1.0
CB C:ASP186 4.4 16.4 1.0
CD2 C:HIS188 4.4 15.2 1.0
CB C:ASP285 4.4 12.3 1.0
OH C:TYR341 4.4 20.3 1.0
N C:LEU187 4.4 12.6 1.0
CA C:HIS188 4.5 12.6 1.0
C10 C:GRK504 4.5 26.0 1.0
N C:GLY339 4.6 12.7 1.0
NE2 C:HIS141 4.6 14.6 1.0
CB C:LEU187 4.6 8.3 1.0
CE2 C:TYR341 4.7 17.6 1.0
C C:LEU187 4.8 15.0 1.0
CA C:LEU187 4.9 10.4 1.0
NE2 C:HIS142 5.0 13.7 1.0
CE1 C:HIS141 5.0 13.5 1.0

Zinc binding site 4 out of 4 in 6htz

Go back to Zinc Binding Sites List in 6htz
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:29.0
occ:1.00
 OD2 D:ASP285 2.0 13.0 1.0
OD1 D:ASP186 2.1 16.5 1.0
ND1 D:HIS188 2.2 17.5 1.0
O1 D:GRK504 2.3 23.0 1.0
O4 D:GRK504 2.4 27.6 1.0
N2 D:GRK504 2.7 35.7 1.0
C3 D:GRK504 2.8 32.6 1.0
CG D:ASP186 2.9 16.8 1.0
CE1 D:HIS188 2.9 16.9 1.0
CG D:ASP285 3.0 18.2 1.0
OD2 D:ASP186 3.1 14.7 1.0
CG D:HIS188 3.3 12.1 1.0
OD1 D:ASP285 3.4 16.9 1.0
CB D:HIS188 3.8 10.6 1.0
N D:HIS188 4.0 16.3 1.0
C5 D:GRK504 4.0 26.3 1.0
NE2 D:HIS188 4.1 15.2 1.0
CA D:GLY339 4.2 18.8 1.0
O D:HOH663 4.2 39.0 1.0
CD2 D:HIS188 4.3 16.1 1.0
CB D:ASP186 4.3 12.3 1.0
CB D:ASP285 4.3 16.8 1.0
N D:LEU187 4.4 15.1 1.0
CB D:LEU187 4.5 12.1 1.0
NE2 D:HIS141 4.5 22.2 1.0
CA D:HIS188 4.5 15.6 1.0
OH D:TYR341 4.6 25.6 1.0
C10 D:GRK504 4.6 21.9 1.0
N D:GLY339 4.6 18.1 1.0
CE2 D:TYR341 4.8 19.1 1.0
CA D:LEU187 4.8 16.8 1.0
C D:LEU187 4.8 15.2 1.0
CE1 D:HIS141 4.8 16.4 1.0
NE2 D:HIS142 4.9 12.3 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 23:18:19 2024

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