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Zinc in PDB 6htg: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 4

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 4

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 4:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 4, PDB code: 6htg 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) 49.25 / 1.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.660, 70.640, 98.330, 77.73, 75.86, 85.63
R / Rfree (%) 16.9 / 21.5

Other elements in 6htg:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 4 also contains other interesting chemical elements:

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 Benzohydroxamate Inhibitor 4 (pdb code 6htg). 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 4, PDB code: 6htg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6htg

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


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

b:22.6
occ:1.00
 OD2 A:ASP285 1.9 21.4 1.0
OD2 A:ASP186 2.0 16.3 1.0
ND1 A:HIS188 2.1 16.4 1.0
O1 A:T61504 2.4 38.5 1.0
O A:T61504 2.4 43.3 1.0
CG A:ASP186 2.9 20.6 1.0
C A:T61504 2.9 46.5 1.0
N A:T61504 2.9 50.8 1.0
CG A:ASP285 2.9 17.5 1.0
CE1 A:HIS188 3.0 19.9 1.0
OD1 A:ASP186 3.1 21.8 1.0
CG A:HIS188 3.2 16.1 1.0
OD1 A:ASP285 3.3 19.7 1.0
CB A:HIS188 3.6 17.8 1.0
N A:HIS188 3.8 13.8 1.0
CA A:GLY339 4.0 17.7 1.0
C1 A:T61504 4.1 39.4 1.0
NE2 A:HIS188 4.1 16.4 1.0
N A:LEU187 4.2 17.2 1.0
CB A:ASP285 4.3 16.4 1.0
CB A:ASP186 4.3 15.5 1.0
CD2 A:HIS188 4.3 16.0 1.0
CA A:HIS188 4.3 15.0 1.0
CB A:LEU187 4.4 14.7 1.0
N A:GLY339 4.5 16.5 1.0
NE2 A:HIS141 4.5 22.9 1.0
C A:LEU187 4.6 17.9 1.0
CA A:LEU187 4.7 18.7 1.0
OH A:TYR341 4.7 29.4 1.0
CE2 A:TYR341 4.7 26.1 1.0
C13 A:T61504 4.8 35.4 1.0
NE2 A:HIS142 4.9 20.2 1.0
C A:ASP186 4.9 24.9 1.0
CE1 A:HIS141 4.9 18.4 1.0
CA A:ASP186 5.0 17.1 1.0
C2 A:T61504 5.0 40.1 1.0

Zinc binding site 2 out of 4 in 6htg

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


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn614

b:20.8
occ:1.00
 OD1 B:ASP186 1.9 17.6 1.0
OD2 B:ASP285 1.9 20.0 1.0
O B:T61603 2.2 32.0 1.0
ND1 B:HIS188 2.2 20.7 1.0
O1 B:T61603 2.4 30.4 1.0
C B:T61603 2.7 44.2 1.0
CG B:ASP186 2.8 18.5 1.0
N B:T61603 2.8 45.5 1.0
CG B:ASP285 2.9 19.9 1.0
OD2 B:ASP186 3.0 16.1 1.0
CE1 B:HIS188 3.1 17.9 1.0
CG B:HIS188 3.2 16.1 1.0
OD1 B:ASP285 3.3 17.4 1.0
CB B:HIS188 3.6 13.4 1.0
N B:HIS188 3.8 18.2 1.0
C1 B:T61603 4.0 39.0 1.0
CA B:GLY339 4.1 12.8 1.0
CB B:ASP186 4.2 13.4 1.0
NE2 B:HIS188 4.2 17.0 1.0
N B:LEU187 4.3 13.8 1.0
CB B:ASP285 4.3 14.5 1.0
CD2 B:HIS188 4.3 13.2 1.0
CA B:HIS188 4.4 15.3 1.0
CB B:LEU187 4.4 13.2 1.0
C13 B:T61603 4.4 37.8 1.0
N B:GLY339 4.5 16.8 1.0
NE2 B:HIS141 4.5 17.5 1.0
OH B:TYR341 4.5 25.3 1.0
CE2 B:TYR341 4.6 25.5 1.0
C B:LEU187 4.7 22.3 1.0
CA B:LEU187 4.7 17.2 1.0
CE1 B:HIS141 4.8 17.1 1.0
C B:ASP186 4.9 16.1 1.0
CA B:ASP186 4.9 18.2 1.0
NE2 B:HIS142 4.9 20.0 1.0

Zinc binding site 3 out of 4 in 6htg

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


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

b:21.6
occ:1.00
 OD1 C:ASP186 1.9 19.0 1.0
OD2 C:ASP285 2.0 20.1 1.0
ND1 C:HIS188 2.1 18.2 1.0
O C:T61504 2.2 33.3 1.0
O1 C:T61504 2.5 31.1 1.0
C C:T61504 2.7 45.0 1.0
CG C:ASP186 2.8 17.4 1.0
N C:T61504 2.8 41.8 1.0
CE1 C:HIS188 2.9 21.3 1.0
CG C:ASP285 3.0 24.4 1.0
OD2 C:ASP186 3.0 17.4 1.0
CG C:HIS188 3.2 16.1 1.0
OD1 C:ASP285 3.2 17.0 1.0
CB C:HIS188 3.6 12.9 1.0
N C:HIS188 3.7 18.8 1.0
C1 C:T61504 4.0 43.3 1.0
NE2 C:HIS188 4.1 16.8 1.0
CA C:GLY339 4.2 10.3 1.0
CB C:ASP186 4.2 13.3 1.0
CD2 C:HIS188 4.2 16.3 1.0
N C:LEU187 4.3 12.0 1.0
CA C:HIS188 4.3 16.2 1.0
CB C:ASP285 4.4 17.1 1.0
CB C:LEU187 4.4 13.7 1.0
C13 C:T61504 4.4 42.1 1.0
NE2 C:HIS141 4.5 19.8 1.0
N C:GLY339 4.5 16.1 1.0
OH C:TYR341 4.5 24.5 1.0
C C:LEU187 4.6 21.0 1.0
CA C:LEU187 4.6 16.5 1.0
CE2 C:TYR341 4.7 24.4 1.0
CE1 C:HIS141 4.8 17.9 1.0
C C:ASP186 4.9 13.3 1.0
CA C:ASP186 5.0 13.6 1.0
NE2 C:HIS142 5.0 21.1 1.0

Zinc binding site 4 out of 4 in 6htg

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


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

b:24.3
occ:1.00
 OD2 D:ASP285 1.9 20.1 1.0
OD1 D:ASP186 2.0 18.4 1.0
ND1 D:HIS188 2.2 17.3 1.0
O1 D:T61504 2.4 35.9 1.0
O D:T61504 2.5 46.6 1.0
N D:T61504 2.8 49.7 1.0
C D:T61504 2.8 50.7 1.0
CG D:ASP186 2.8 18.4 1.0
CG D:ASP285 2.9 21.2 1.0
OD2 D:ASP186 3.0 20.6 1.0
CE1 D:HIS188 3.1 22.0 1.0
CG D:HIS188 3.2 19.1 1.0
OD1 D:ASP285 3.3 23.6 1.0
CB D:HIS188 3.6 16.6 1.0
N D:HIS188 3.8 15.1 1.0
C1 D:T61504 4.0 45.0 1.0
CA D:GLY339 4.2 24.0 1.0
NE2 D:HIS188 4.2 19.1 1.0
CB D:ASP285 4.2 17.7 1.0
N D:LEU187 4.3 21.6 1.0
CB D:ASP186 4.3 17.5 1.0
CD2 D:HIS188 4.3 18.8 1.0
CA D:HIS188 4.3 18.7 1.0
C13 D:T61504 4.4 37.6 1.0
CB D:LEU187 4.4 16.6 1.0
NE2 D:HIS141 4.5 24.1 1.0
N D:GLY339 4.5 17.9 1.0
OH D:TYR341 4.5 32.8 1.0
CE2 D:TYR341 4.6 29.9 1.0
C D:LEU187 4.6 18.9 1.0
CA D:LEU187 4.7 21.2 1.0
CE1 D:HIS141 4.9 18.2 1.0
C D:ASP186 4.9 21.9 1.0
NE2 D:HIS142 5.0 20.8 1.0
CA D:ASP186 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 23:17:18 2024

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