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Zinc in PDB 6hsz: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2, PDB code: 6hsz 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) 34.97 / 2.37
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.774, 70.802, 98.343, 77.85, 75.48, 85.28
R / Rfree (%) 15.9 / 22

Other elements in 6hsz:

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

Zinc binding site 1 out of 4 in 6hsz

Go back to Zinc Binding Sites List in 6hsz
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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

b:35.8
occ:1.00
 OD2 A:ASP285 2.1 32.3 1.0
OD1 A:ASP186 2.1 29.2 1.0
ND1 A:HIS188 2.2 32.7 1.0
O07 A:GOW504 2.4 45.6 1.0
O09 A:GOW504 2.5 44.3 1.0
N08 A:GOW504 2.8 56.5 1.0
C06 A:GOW504 2.8 52.4 1.0
CG A:ASP186 2.9 19.6 1.0
OD2 A:ASP186 3.0 19.1 1.0
CE1 A:HIS188 3.0 29.2 1.0
CG A:ASP285 3.1 31.2 1.0
CG A:HIS188 3.3 27.7 1.0
OD1 A:ASP285 3.4 27.6 1.0
CB A:HIS188 3.7 19.4 1.0
N A:HIS188 3.9 27.6 1.0
CA A:GLY339 4.0 28.3 1.0
C05 A:GOW504 4.0 53.6 1.0
NE2 A:HIS188 4.2 32.2 1.0
CB A:ASP186 4.3 22.3 1.0
CD2 A:HIS188 4.3 30.5 1.0
N A:LEU187 4.3 23.6 1.0
CB A:ASP285 4.4 21.8 1.0
N A:GLY339 4.4 26.2 1.0
CA A:HIS188 4.4 26.2 1.0
C10 A:GOW504 4.4 52.5 1.0
CB A:LEU187 4.5 24.3 1.0
OH A:TYR341 4.5 35.5 1.0
NE2 A:HIS141 4.5 31.7 1.0
CE2 A:TYR341 4.6 37.5 1.0
C A:LEU187 4.7 27.1 1.0
CA A:LEU187 4.8 18.2 1.0
C A:ASP186 5.0 24.9 1.0
NE2 A:HIS142 5.0 26.6 1.0

Zinc binding site 2 out of 4 in 6hsz

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


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

b:34.5
occ:1.00
 OD1 B:ASP186 1.9 19.8 1.0
OD2 B:ASP285 2.1 23.2 1.0
ND1 B:HIS188 2.2 24.9 1.0
O07 B:GOW504 2.5 51.9 1.0
O09 B:GOW504 2.5 36.5 1.0
N08 B:GOW504 2.9 54.0 1.0
CG B:ASP186 2.9 22.4 1.0
C06 B:GOW504 2.9 50.7 1.0
CE1 B:HIS188 3.0 19.1 1.0
CG B:ASP285 3.0 25.9 1.0
OD2 B:ASP186 3.2 25.4 1.0
OD1 B:ASP285 3.2 23.6 1.0
CG B:HIS188 3.3 20.0 1.0
CB B:HIS188 3.7 23.1 1.0
N B:HIS188 3.9 23.5 1.0
CA B:GLY339 4.1 21.5 1.0
C05 B:GOW504 4.1 43.9 1.0
NE2 B:HIS188 4.2 28.4 1.0
N B:LEU187 4.2 26.2 1.0
CB B:ASP186 4.2 16.0 1.0
CD2 B:HIS188 4.3 26.4 1.0
CB B:ASP285 4.4 18.5 1.0
CB B:LEU187 4.4 26.6 1.0
CA B:HIS188 4.5 24.9 1.0
N B:GLY339 4.5 25.7 1.0
C10 B:GOW504 4.5 44.3 1.0
NE2 B:HIS141 4.6 23.3 1.0
CA B:LEU187 4.6 23.9 1.0
C B:LEU187 4.7 24.6 1.0
OH B:TYR341 4.7 40.4 1.0
CE2 B:TYR341 4.7 41.9 1.0
C B:ASP186 4.9 22.1 1.0
CE1 B:HIS141 5.0 25.6 1.0

Zinc binding site 3 out of 4 in 6hsz

Go back to Zinc Binding Sites List in 6hsz
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 2


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

b:34.5
occ:1.00
 OD1 C:ASP186 2.1 20.3 1.0
OD2 C:ASP285 2.2 18.6 1.0
ND1 C:HIS188 2.2 21.0 1.0
O07 C:GOW504 2.5 55.7 1.0
O09 C:GOW504 2.5 32.1 1.0
N08 C:GOW504 2.8 50.0 1.0
C06 C:GOW504 2.8 49.7 1.0
CG C:ASP186 3.0 18.1 1.0
CG C:ASP285 3.1 27.9 1.0
CE1 C:HIS188 3.1 21.3 1.0
OD2 C:ASP186 3.3 22.5 1.0
CG C:HIS188 3.3 23.1 1.0
OD1 C:ASP285 3.3 27.7 1.0
CB C:HIS188 3.6 24.5 1.0
N C:HIS188 3.9 29.4 1.0
C05 C:GOW504 4.1 38.1 1.0
CA C:GLY339 4.1 27.7 1.0
NE2 C:HIS188 4.3 28.2 1.0
CB C:ASP186 4.4 22.1 1.0
N C:LEU187 4.4 26.3 1.0
CD2 C:HIS188 4.4 25.9 1.0
CA C:HIS188 4.4 25.0 1.0
CB C:ASP285 4.4 23.1 1.0
CB C:LEU187 4.5 26.7 1.0
C10 C:GOW504 4.5 38.7 1.0
NE2 C:HIS141 4.6 22.5 1.0
N C:GLY339 4.6 34.1 1.0
OH C:TYR341 4.6 40.7 1.0
C C:LEU187 4.7 30.5 1.0
CE2 C:TYR341 4.7 28.6 1.0
CA C:LEU187 4.7 21.4 1.0
CE1 C:HIS141 5.0 24.1 1.0
NE2 C:HIS142 5.0 30.2 1.0
C C:ASP186 5.0 27.0 1.0

Zinc binding site 4 out of 4 in 6hsz

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


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

b:35.1
occ:1.00
 OD2 D:ASP285 2.1 36.4 1.0
OD1 D:ASP186 2.1 25.2 1.0
ND1 D:HIS188 2.2 27.0 1.0
O07 D:GOW504 2.4 54.2 1.0
O09 D:GOW504 2.5 38.9 1.0
C06 D:GOW504 2.8 55.4 1.0
N08 D:GOW504 2.8 56.6 1.0
CG D:ASP186 2.9 28.8 1.0
CG D:ASP285 3.0 35.8 1.0
OD2 D:ASP186 3.1 23.7 1.0
CE1 D:HIS188 3.1 14.1 1.0
CG D:HIS188 3.3 25.4 1.0
OD1 D:ASP285 3.4 34.9 1.0
CB D:HIS188 3.6 21.3 1.0
N D:HIS188 3.8 31.1 1.0
C05 D:GOW504 4.0 50.6 1.0
CA D:GLY339 4.0 26.6 1.0
NE2 D:HIS188 4.3 27.4 1.0
N D:LEU187 4.3 28.9 1.0
CB D:ASP186 4.3 23.3 1.0
CA D:HIS188 4.4 28.3 1.0
CD2 D:HIS188 4.4 20.0 1.0
CB D:ASP285 4.4 29.9 1.0
N D:GLY339 4.5 27.9 1.0
C10 D:GOW504 4.5 49.1 1.0
NE2 D:HIS141 4.5 30.4 1.0
OH D:TYR341 4.5 34.5 1.0
CB D:LEU187 4.6 19.6 1.0
C D:LEU187 4.7 26.9 1.0
CE2 D:TYR341 4.7 37.5 1.0
CA D:LEU187 4.8 22.9 1.0
NE2 D:HIS142 4.9 31.8 1.0
C D:ASP186 5.0 28.0 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 23:14:17 2024

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