Atomistry » Zinc » PDB 6hrg-6i0l » 6hu0
Atomistry »
  Zinc »
    PDB 6hrg-6i0l »
      6hu0 »

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

Last articles

Mn in 5H62
Mn in 5H6H
Mn in 5H1W
Mn in 5H60
Mn in 5H0O
Mn in 5GTI
Mn in 5GVW
Mn in 5GXO
Mn in 5GTH
Mn in 5GVV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy