Atomistry » Zinc » PDB 6hqy-6hyh » 6htz
Atomistry »
  Zinc »
    PDB 6hqy-6hyh »
      6htz »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy