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Zinc in PDB 6hth: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5, PDB code: 6hth 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) 46.76 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.520, 70.555, 98.232, 78.36, 75.84, 85.74
R / Rfree (%) 21 / 25.7

Other elements in 6hth:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5 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 5 (pdb code 6hth). 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 5, PDB code: 6hth:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hth

Go back to Zinc Binding Sites List in 6hth
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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

b:24.1
occ:1.00
 OD2 A:ASP285 2.0 13.4 1.0
OD1 A:ASP186 2.1 16.6 1.0
ND1 A:HIS188 2.3 15.4 1.0
O10 A:GQN504 2.6 34.2 1.0
O08 A:GQN504 2.6 53.7 1.0
N09 A:GQN504 2.8 49.5 1.0
C07 A:GQN504 2.9 53.2 1.0
CG A:ASP186 2.9 16.2 1.0
CG A:ASP285 3.0 19.7 1.0
OD2 A:ASP186 3.0 18.3 1.0
CG A:HIS188 3.2 11.4 1.0
OD1 A:ASP285 3.2 18.6 1.0
CE1 A:HIS188 3.3 12.8 1.0
CB A:HIS188 3.5 9.3 1.0
N A:HIS188 3.9 12.3 1.0
C06 A:GQN504 4.1 49.6 1.0
CA A:GLY339 4.1 17.3 1.0
CB A:ASP186 4.3 9.7 1.0
CA A:HIS188 4.3 9.5 1.0
CB A:ASP285 4.3 7.0 1.0
N A:LEU187 4.3 14.9 1.0
CB A:LEU187 4.4 4.9 1.0
CD2 A:HIS188 4.4 8.3 1.0
NE2 A:HIS188 4.4 11.7 1.0
N A:GLY339 4.5 15.1 1.0
NE2 A:HIS141 4.5 21.5 1.0
C11 A:GQN504 4.6 55.2 1.0
OH A:TYR341 4.6 31.2 1.0
C A:LEU187 4.7 10.6 1.0
CA A:LEU187 4.7 8.5 1.0
CE1 A:TYR341 4.8 31.7 1.0
CE1 A:HIS141 4.9 14.7 1.0
NE2 A:HIS142 4.9 11.6 1.0
C A:ASP186 5.0 23.0 1.0

Zinc binding site 2 out of 4 in 6hth

Go back to Zinc Binding Sites List in 6hth
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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

b:24.3
occ:1.00
 OD2 B:ASP285 1.9 7.2 1.0
OD1 B:ASP186 2.0 9.4 1.0
ND1 B:HIS188 2.2 7.5 1.0
O10 B:GQN504 2.4 15.9 1.0
O08 B:GQN504 2.5 34.5 1.0
N09 B:GQN504 2.6 34.6 1.0
C07 B:GQN504 2.8 37.5 1.0
CG B:ASP186 2.8 7.2 1.0
OD2 B:ASP186 3.0 12.1 1.0
CG B:ASP285 3.0 18.4 1.0
CE1 B:HIS188 3.1 8.3 1.0
CG B:HIS188 3.3 10.5 1.0
OD1 B:ASP285 3.5 13.2 1.0
CB B:HIS188 3.7 15.8 1.0
N B:HIS188 3.8 13.0 1.0
CA B:GLY339 4.1 15.5 1.0
C06 B:GQN504 4.1 38.6 1.0
N B:LEU187 4.2 9.8 1.0
CB B:ASP186 4.2 5.6 1.0
NE2 B:HIS188 4.2 11.2 1.0
CB B:ASP285 4.3 1.4 1.0
CD2 B:HIS188 4.3 14.1 1.0
NE2 B:HIS141 4.4 14.4 1.0
CA B:HIS188 4.4 11.0 1.0
N B:GLY339 4.5 16.8 1.0
CB B:LEU187 4.5 7.1 1.0
C B:LEU187 4.6 11.5 1.0
CE1 B:HIS141 4.7 16.3 1.0
CA B:LEU187 4.7 7.7 1.0
OH B:TYR341 4.7 29.4 1.0
C11 B:GQN504 4.7 44.5 1.0
CE1 B:TYR341 4.7 23.0 1.0
C B:ASP186 4.8 7.7 1.0
NE2 B:HIS142 4.9 17.0 1.0
CA B:ASP186 4.9 5.2 1.0

Zinc binding site 3 out of 4 in 6hth

Go back to Zinc Binding Sites List in 6hth
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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

b:25.8
occ:1.00
 OD2 C:ASP285 1.9 10.6 1.0
OD1 C:ASP186 2.0 11.7 1.0
ND1 C:HIS188 2.3 7.6 1.0
O10 C:GQN504 2.5 29.4 1.0
O08 C:GQN504 2.7 40.5 1.0
CG C:ASP186 2.8 6.2 1.0
N09 C:GQN504 2.9 42.9 1.0
OD2 C:ASP186 2.9 8.7 1.0
C07 C:GQN504 3.0 44.0 1.0
CG C:ASP285 3.0 18.1 1.0
CE1 C:HIS188 3.2 6.4 1.0
CG C:HIS188 3.2 11.6 1.0
OD1 C:ASP285 3.4 15.4 1.0
CB C:HIS188 3.6 10.1 1.0
N C:HIS188 3.8 13.5 1.0
CA C:GLY339 4.1 17.6 1.0
CB C:ASP186 4.2 11.3 1.0
C06 C:GQN504 4.2 42.3 1.0
N C:LEU187 4.3 13.6 1.0
NE2 C:HIS188 4.3 7.1 1.0
CB C:ASP285 4.3 4.8 1.0
CB C:LEU187 4.3 11.7 1.0
CD2 C:HIS188 4.3 12.7 1.0
CA C:HIS188 4.4 8.4 1.0
NE2 C:HIS141 4.4 17.5 1.0
N C:GLY339 4.5 22.9 1.0
CE1 C:HIS141 4.6 15.5 1.0
CA C:LEU187 4.6 11.5 1.0
C C:LEU187 4.6 10.9 1.0
CE1 C:TYR341 4.7 13.6 1.0
OH C:TYR341 4.8 29.8 1.0
C11 C:GQN504 4.8 50.2 1.0
C C:ASP186 4.9 15.0 1.0
CA C:ASP186 5.0 11.7 1.0
NE2 C:HIS142 5.0 10.4 1.0

Zinc binding site 4 out of 4 in 6hth

Go back to Zinc Binding Sites List in 6hth
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 5


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

b:24.2
occ:1.00
 OD2 D:ASP186 2.0 13.1 1.0
OD2 D:ASP285 2.1 10.9 1.0
O10 D:GQN504 2.3 33.8 1.0
ND1 D:HIS188 2.3 10.7 1.0
O08 D:GQN504 2.5 47.7 1.0
CG D:ASP186 2.8 12.3 1.0
C07 D:GQN504 2.9 48.7 1.0
N09 D:GQN504 2.9 46.4 1.0
OD1 D:ASP186 3.0 16.2 1.0
CG D:ASP285 3.0 18.5 1.0
CE1 D:HIS188 3.2 11.2 1.0
CG D:HIS188 3.3 10.3 1.0
OD1 D:ASP285 3.4 18.9 1.0
CB D:HIS188 3.6 7.3 1.0
N D:HIS188 3.8 11.2 1.0
CA D:GLY339 4.1 14.9 1.0
C06 D:GQN504 4.1 45.3 1.0
CB D:ASP186 4.2 11.7 1.0
CA D:HIS188 4.3 9.2 1.0
NE2 D:HIS188 4.4 11.0 1.0
CB D:ASP285 4.4 7.4 1.0
N D:LEU187 4.4 12.2 1.0
CD2 D:HIS188 4.4 4.5 1.0
NE2 D:HIS141 4.4 13.4 1.0
N D:GLY339 4.5 16.9 1.0
CB D:LEU187 4.5 7.7 1.0
C D:LEU187 4.7 15.1 1.0
C11 D:GQN504 4.7 51.2 1.0
CA D:LEU187 4.8 3.5 1.0
OH D:TYR341 4.8 31.3 1.0
CE1 D:HIS141 4.8 15.9 1.0
CE2 D:TYR341 4.9 30.1 1.0
NE2 D:HIS142 5.0 16.8 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 23:17:18 2024

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