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Zinc in PDB 6hu1: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10, PDB code: 6hu1 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) 47.08 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.220, 71.190, 99.030, 78.27, 75.65, 85.73
R / Rfree (%) 16 / 20.5

Other elements in 6hu1:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 (pdb code 6hu1). 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 10, PDB code: 6hu1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hu1

Go back to Zinc Binding Sites List in 6hu1
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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

b:38.9
occ:1.00
 OD1 A:ASP186 2.1 21.1 1.0
OD2 A:ASP285 2.1 22.8 1.0
ND1 A:HIS188 2.3 20.8 1.0
O27 A:GT2504 2.4 32.8 1.0
O28 A:GT2504 2.6 47.7 1.0
N26 A:GT2504 2.7 50.4 1.0
C25 A:GT2504 2.8 54.3 1.0
CG A:ASP186 2.9 15.1 1.0
OD2 A:ASP186 3.0 18.1 1.0
CG A:ASP285 3.2 28.3 1.0
CE1 A:HIS188 3.2 20.4 1.0
CG A:HIS188 3.3 19.4 1.0
OD1 A:ASP285 3.5 27.5 1.0
CB A:HIS188 3.7 16.6 1.0
N A:HIS188 4.0 14.5 1.0
C17 A:GT2504 4.0 57.7 1.0
CA A:GLY339 4.0 24.1 1.0
CB A:ASP186 4.3 13.0 1.0
NE2 A:HIS188 4.3 23.4 1.0
NE2 A:HIS141 4.4 24.8 1.0
CD2 A:HIS188 4.4 23.4 1.0
N A:GLY339 4.5 23.9 1.0
N A:LEU187 4.5 11.8 1.0
CB A:ASP285 4.5 20.9 1.0
CA A:HIS188 4.5 15.9 1.0
OH A:TYR341 4.6 38.0 1.0
CB A:LEU187 4.6 12.6 1.0
C18 A:GT2504 4.6 60.9 1.0
CE2 A:TYR341 4.7 31.8 1.0
O A:HOH748 4.8 56.8 1.0
C A:LEU187 4.8 20.0 1.0
CE1 A:HIS141 4.9 18.4 1.0
CA A:LEU187 4.9 13.4 1.0
NE2 A:HIS142 4.9 21.3 1.0
C16 A:GT2504 5.0 60.2 1.0

Zinc binding site 2 out of 4 in 6hu1

Go back to Zinc Binding Sites List in 6hu1
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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

b:38.9
occ:1.00
 OD1 B:ASP186 2.0 18.1 1.0
OD2 B:ASP285 2.0 20.5 1.0
ND1 B:HIS188 2.3 29.6 1.0
O27 B:GT2504 2.4 36.2 1.0
O28 B:GT2504 2.4 46.3 1.0
C25 B:GT2504 2.8 53.8 1.0
N26 B:GT2504 2.8 55.5 1.0
CG B:ASP186 2.9 16.9 1.0
CG B:ASP285 3.0 25.0 1.0
OD2 B:ASP186 3.0 16.5 1.0
CE1 B:HIS188 3.1 27.7 1.0
CG B:HIS188 3.3 23.2 1.0
OD1 B:ASP285 3.3 22.4 1.0
CB B:HIS188 3.8 18.2 1.0
N B:HIS188 4.0 17.7 1.0
C17 B:GT2504 4.1 53.1 1.0
CA B:GLY339 4.1 15.2 1.0
NE2 B:HIS188 4.2 23.7 1.0
CB B:ASP186 4.3 14.2 1.0
N B:LEU187 4.3 14.8 1.0
CB B:ASP285 4.3 12.8 1.0
CD2 B:HIS188 4.4 17.1 1.0
NE2 B:HIS141 4.5 17.6 1.0
CA B:HIS188 4.5 22.3 1.0
CB B:LEU187 4.5 16.9 1.0
OH B:TYR341 4.6 40.7 1.0
N B:GLY339 4.6 21.4 1.0
O B:HOH670 4.6 40.2 1.0
C18 B:GT2504 4.7 54.9 1.0
CE2 B:TYR341 4.7 35.3 1.0
CA B:LEU187 4.8 19.3 1.0
C B:LEU187 4.8 17.7 1.0
CE1 B:HIS141 4.8 17.3 1.0
NE2 B:HIS142 4.9 20.2 1.0
C B:ASP186 5.0 23.9 1.0

Zinc binding site 3 out of 4 in 6hu1

Go back to Zinc Binding Sites List in 6hu1
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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

b:39.7
occ:1.00
 OD1 C:ASP186 2.0 19.5 1.0
OD2 C:ASP285 2.1 19.0 1.0
ND1 C:HIS188 2.2 24.8 1.0
O27 C:GT2504 2.4 28.1 1.0
O28 C:GT2504 2.5 51.4 1.0
C25 C:GT2504 2.9 54.9 1.0
N26 C:GT2504 2.9 50.1 1.0
CG C:ASP186 2.9 18.8 1.0
CE1 C:HIS188 3.0 20.6 1.0
CG C:ASP285 3.1 22.0 1.0
OD2 C:ASP186 3.2 14.4 1.0
CG C:HIS188 3.2 17.6 1.0
OD1 C:ASP285 3.4 22.4 1.0
CB C:HIS188 3.7 13.7 1.0
N C:HIS188 3.9 17.0 1.0
CA C:GLY339 4.1 16.8 1.0
C17 C:GT2504 4.1 56.0 1.0
NE2 C:HIS188 4.2 22.3 1.0
CD2 C:HIS188 4.3 16.4 1.0
CB C:ASP186 4.3 15.3 1.0
NE2 C:HIS141 4.4 18.7 1.0
CB C:ASP285 4.4 12.5 1.0
CA C:HIS188 4.4 18.3 1.0
N C:LEU187 4.5 14.6 1.0
N C:GLY339 4.5 22.9 1.0
OH C:TYR341 4.5 49.4 1.0
CB C:LEU187 4.5 14.4 1.0
C18 C:GT2504 4.6 60.9 1.0
CE2 C:TYR341 4.7 26.6 1.0
CE1 C:HIS141 4.8 13.8 1.0
C C:LEU187 4.8 15.8 1.0
CA C:LEU187 4.9 15.6 1.0
NE2 C:HIS142 4.9 20.9 1.0

Zinc binding site 4 out of 4 in 6hu1

Go back to Zinc Binding Sites List in 6hu1
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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

b:38.7
occ:1.00
 OD2 D:ASP285 2.0 19.1 1.0
OD1 D:ASP186 2.1 18.0 1.0
O27 D:GT2504 2.4 26.4 0.8
ND1 D:HIS188 2.4 20.4 1.0
O28 D:GT2504 2.6 40.8 0.8
N26 D:GT2504 2.8 46.9 0.8
C25 D:GT2504 2.9 44.0 0.8
CG D:ASP186 2.9 16.5 1.0
OD2 D:ASP186 3.0 15.2 1.0
CG D:ASP285 3.1 25.8 1.0
CE1 D:HIS188 3.2 23.1 1.0
CG D:HIS188 3.4 21.0 1.0
OD1 D:ASP285 3.5 21.8 1.0
CB D:HIS188 3.8 20.0 1.0
CA D:GLY339 4.0 20.2 1.0
N D:HIS188 4.1 19.0 1.0
C17 D:GT2504 4.1 41.5 0.8
NE2 D:HIS188 4.4 23.2 1.0
CB D:ASP186 4.4 11.6 1.0
CB D:ASP285 4.4 18.8 1.0
N D:GLY339 4.5 19.5 1.0
CD2 D:HIS188 4.5 17.9 1.0
NE2 D:HIS141 4.5 20.9 1.0
OH D:TYR341 4.5 42.5 1.0
N D:LEU187 4.5 15.9 1.0
CA D:HIS188 4.6 22.6 1.0
CB D:LEU187 4.7 16.1 1.0
CE2 D:TYR341 4.7 37.2 1.0
C18 D:GT2504 4.7 39.3 0.8
NE2 D:HIS142 4.9 25.4 1.0
C D:LEU187 4.9 21.7 1.0
CE1 D:HIS141 4.9 15.7 1.0
CA D:LEU187 5.0 20.2 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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