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Zinc in PDB 6hu3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

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

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3 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) 48.95 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.640, 70.430, 97.920, 75.48, 78.20, 86.17
R / Rfree (%) 16.2 / 19.4

Other elements in 6hu3:

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

Fluorine (F) 4 atoms
Potassium (K) 8 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor (pdb code 6hu3). 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 Triazole Hydroxamate Inhibitor, PDB code: 6hu3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hu3

Go back to Zinc Binding Sites List in 6hu3
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


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

b:49.2
occ:1.00
 OD1 A:ASP186 2.0 29.6 1.0
OD2 A:ASP285 2.0 27.5 1.0
ND1 A:HIS188 2.2 26.8 1.0
O30 A:GRZ504 2.4 43.2 1.0
N29 A:GRZ504 2.7 58.1 1.0
O31 A:GRZ504 2.8 58.4 1.0
CG A:ASP186 2.8 31.3 1.0
C28 A:GRZ504 2.9 58.1 1.0
OD2 A:ASP186 3.1 26.7 1.0
CG A:ASP285 3.1 31.6 1.0
CE1 A:HIS188 3.1 31.6 1.0
CG A:HIS188 3.3 26.5 1.0
OD1 A:ASP285 3.4 27.4 1.0
CB A:HIS188 3.7 23.4 1.0
N A:HIS188 3.9 23.3 1.0
CA A:GLY339 4.0 28.2 1.0
C26 A:GRZ504 4.1 59.1 1.0
CB A:ASP186 4.2 24.3 1.0
NE2 A:HIS188 4.2 29.7 1.0
N A:LEU187 4.4 22.0 1.0
CD2 A:HIS188 4.4 27.7 1.0
CB A:ASP285 4.4 23.6 1.0
NE2 A:HIS141 4.4 27.9 1.0
N A:GLY339 4.4 26.5 1.0
CA A:HIS188 4.5 20.3 1.0
CB A:LEU187 4.5 21.1 1.0
OH A:TYR341 4.7 55.2 1.0
C27 A:GRZ504 4.7 56.3 1.0
NE2 A:HIS142 4.7 26.5 1.0
C A:LEU187 4.8 21.7 1.0
CA A:LEU187 4.8 21.2 1.0
CE1 A:HIS141 4.8 27.2 1.0
CE2 A:TYR341 4.9 53.4 1.0
CA A:ASP186 5.0 27.1 1.0

Zinc binding site 2 out of 4 in 6hu3

Go back to Zinc Binding Sites List in 6hu3
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


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 Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:43.9
occ:1.00
 OD1 B:ASP186 2.0 22.4 1.0
OD2 B:ASP285 2.0 22.2 1.0
O30 B:GRZ504 2.2 31.7 1.0
ND1 B:HIS188 2.2 24.5 1.0
O31 B:GRZ504 2.6 52.9 1.0
N29 B:GRZ504 2.7 51.3 1.0
CG B:ASP186 2.8 22.5 1.0
C28 B:GRZ504 2.8 53.0 1.0
CE1 B:HIS188 3.0 27.4 1.0
OD2 B:ASP186 3.0 22.0 1.0
CG B:ASP285 3.0 28.0 1.0
CG B:HIS188 3.3 24.5 1.0
OD1 B:ASP285 3.4 23.9 1.0
CB B:HIS188 3.7 23.2 1.0
N B:HIS188 3.9 20.5 1.0
CA B:GLY339 4.0 22.8 1.0
C26 B:GRZ504 4.1 51.6 1.0
NE2 B:HIS188 4.2 27.8 1.0
CB B:ASP186 4.2 18.9 1.0
CB B:ASP285 4.3 20.8 1.0
CD2 B:HIS188 4.3 25.9 1.0
NE2 B:HIS141 4.4 23.5 1.0
N B:LEU187 4.4 20.0 1.0
N B:GLY339 4.4 23.7 1.0
CA B:HIS188 4.5 18.7 1.0
O B:HOH737 4.5 46.9 1.0
CB B:LEU187 4.6 19.9 1.0
OH B:TYR341 4.7 58.9 1.0
C27 B:GRZ504 4.7 51.2 1.0
NE2 B:HIS142 4.7 25.6 1.0
C B:LEU187 4.8 20.7 1.0
CE1 B:HIS141 4.8 20.9 1.0
CA B:LEU187 4.8 18.4 1.0
CE2 B:TYR341 4.9 44.0 1.0
CA B:ASP186 5.0 20.1 1.0
C B:ASP186 5.0 21.0 1.0

Zinc binding site 3 out of 4 in 6hu3

Go back to Zinc Binding Sites List in 6hu3
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


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

b:44.8
occ:1.00
 OD1 C:ASP186 2.0 23.4 1.0
OD2 C:ASP285 2.0 22.8 1.0
ND1 C:HIS188 2.2 22.3 1.0
O30 C:GRZ504 2.3 33.2 1.0
O31 C:GRZ504 2.5 52.2 1.0
CG C:ASP186 2.8 25.8 1.0
N29 C:GRZ504 2.9 56.1 1.0
C28 C:GRZ504 2.9 55.1 1.0
OD2 C:ASP186 3.0 23.7 1.0
CE1 C:HIS188 3.0 27.2 1.0
CG C:ASP285 3.0 25.2 1.0
CG C:HIS188 3.3 21.8 1.0
OD1 C:ASP285 3.4 26.3 1.0
CB C:HIS188 3.7 22.9 1.0
N C:HIS188 4.0 21.2 1.0
CA C:GLY339 4.0 25.9 1.0
C26 C:GRZ504 4.2 49.7 1.0
NE2 C:HIS188 4.2 26.8 1.0
CB C:ASP186 4.2 21.0 1.0
O C:HOH618 4.3 45.7 1.0
CD2 C:HIS188 4.3 25.6 1.0
N C:GLY339 4.3 26.3 1.0
NE2 C:HIS141 4.3 24.0 1.0
CB C:ASP285 4.3 22.0 1.0
N C:LEU187 4.4 19.8 1.0
CA C:HIS188 4.5 21.6 1.0
CB C:LEU187 4.6 20.5 1.0
OH C:TYR341 4.7 57.4 1.0
C27 C:GRZ504 4.8 44.4 1.0
NE2 C:HIS142 4.8 24.6 1.0
CE2 C:TYR341 4.8 45.0 1.0
CE1 C:HIS141 4.8 24.5 1.0
C C:LEU187 4.8 22.7 1.0
CA C:LEU187 4.9 18.5 1.0
C C:GLY339 5.0 23.3 1.0

Zinc binding site 4 out of 4 in 6hu3

Go back to Zinc Binding Sites List in 6hu3
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


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

b:47.8
occ:1.00
 OD2 D:ASP285 2.0 27.1 1.0
OD1 D:ASP186 2.1 26.5 1.0
ND1 D:HIS188 2.2 27.0 1.0
O30 D:GRZ504 2.5 53.9 1.0
O31 D:GRZ504 2.7 63.1 1.0
N29 D:GRZ504 2.7 66.8 1.0
C28 D:GRZ504 2.9 66.7 1.0
CG D:ASP186 2.9 30.7 1.0
CE1 D:HIS188 3.0 30.6 1.0
CG D:ASP285 3.1 33.6 1.0
OD2 D:ASP186 3.1 27.4 1.0
CG D:HIS188 3.3 24.4 1.0
OD1 D:ASP285 3.4 29.2 1.0
CB D:HIS188 3.8 22.4 1.0
N D:HIS188 3.9 23.7 1.0
CA D:GLY339 4.0 26.5 1.0
C26 D:GRZ504 4.0 65.9 1.0
NE2 D:HIS188 4.1 29.4 1.0
CB D:ASP186 4.3 28.5 1.0
CD2 D:HIS188 4.3 28.1 1.0
CB D:ASP285 4.4 25.7 1.0
NE2 D:HIS141 4.4 26.1 1.0
N D:GLY339 4.4 24.0 1.0
N D:LEU187 4.4 22.8 1.0
CA D:HIS188 4.5 21.9 1.0
CB D:LEU187 4.6 22.9 1.0
OH D:TYR341 4.6 56.3 1.0
C27 D:GRZ504 4.6 63.7 1.0
NE2 D:HIS142 4.7 24.8 1.0
CE2 D:TYR341 4.8 51.9 1.0
C D:LEU187 4.8 21.2 1.0
CE1 D:HIS141 4.8 25.9 1.0
CA D:LEU187 4.9 20.3 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 23:21:03 2024

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