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Zinc in PDB 6htt: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7, PDB code: 6htt 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) 47.82 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.400, 70.500, 98.330, 75.80, 77.71, 85.53
R / Rfree (%) 15 / 18.3

Other elements in 6htt:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7 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 7 (pdb code 6htt). 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 7, PDB code: 6htt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6htt

Go back to Zinc Binding Sites List in 6htt
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7


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

b:21.1
occ:1.00
 OD1 A:ASP186 2.0 15.7 1.0
OD2 A:ASP285 2.0 16.2 1.0
ND1 A:HIS188 2.1 12.8 1.0
O19 A:GQZ504 2.2 20.3 1.0
O17 A:GQZ504 2.2 22.7 1.0
C15 A:GQZ504 2.7 28.9 1.0
N16 A:GQZ504 2.7 31.4 1.0
CG A:ASP186 2.8 19.7 1.0
CE1 A:HIS188 3.0 17.5 1.0
CG A:ASP285 3.0 21.2 1.0
OD2 A:ASP186 3.1 16.6 1.0
CG A:HIS188 3.2 16.7 1.0
OD1 A:ASP285 3.4 19.4 1.0
CB A:HIS188 3.6 12.2 1.0
N A:HIS188 3.8 13.6 1.0
C10 A:GQZ504 4.0 26.1 1.0
CA A:GLY339 4.1 19.4 1.0
NE2 A:HIS188 4.1 16.1 1.0
O A:HOH716 4.2 32.4 1.0
CD2 A:HIS188 4.3 13.0 1.0
CB A:ASP186 4.3 13.7 1.0
N A:LEU187 4.3 13.2 1.0
CB A:ASP285 4.3 16.7 1.0
CA A:HIS188 4.4 11.6 1.0
OH A:TYR341 4.4 21.0 1.0
NE2 A:HIS141 4.4 19.3 1.0
N A:GLY339 4.5 18.2 1.0
CB A:LEU187 4.5 15.0 1.0
CE2 A:TYR341 4.6 18.5 1.0
C11 A:GQZ504 4.7 22.6 1.0
C A:LEU187 4.7 13.5 1.0
CA A:LEU187 4.7 16.4 1.0
CE1 A:HIS141 4.8 16.3 1.0
NE2 A:HIS142 4.9 16.1 1.0
C A:ASP186 5.0 16.2 1.0

Zinc binding site 2 out of 4 in 6htt

Go back to Zinc Binding Sites List in 6htt
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7


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

b:19.7
occ:1.00
 OD1 B:ASP186 1.9 10.6 1.0
OD2 B:ASP285 2.0 12.9 1.0
O19 B:GQZ504 2.2 18.3 1.0
ND1 B:HIS188 2.2 13.7 1.0
O17 B:GQZ504 2.2 21.1 1.0
C15 B:GQZ504 2.7 24.9 1.0
N16 B:GQZ504 2.7 27.3 1.0
CG B:ASP186 2.8 12.9 1.0
OD2 B:ASP186 3.0 14.7 1.0
CE1 B:HIS188 3.0 17.3 1.0
CG B:ASP285 3.0 16.0 1.0
CG B:HIS188 3.2 12.3 1.0
OD1 B:ASP285 3.4 14.2 1.0
CB B:HIS188 3.6 10.3 1.0
N B:HIS188 3.9 12.8 1.0
C10 B:GQZ504 4.1 23.1 1.0
CA B:GLY339 4.1 9.4 1.0
NE2 B:HIS188 4.2 14.7 1.0
CB B:ASP186 4.2 11.1 1.0
O B:HOH777 4.3 41.1 1.0
CD2 B:HIS188 4.3 13.6 1.0
N B:LEU187 4.3 11.3 1.0
CB B:ASP285 4.4 12.0 1.0
NE2 B:HIS141 4.4 16.4 1.0
CA B:HIS188 4.4 11.1 1.0
N B:GLY339 4.5 12.8 1.0
OH B:TYR341 4.5 18.2 1.0
CB B:LEU187 4.5 11.3 1.0
CE2 B:TYR341 4.7 14.6 1.0
C11 B:GQZ504 4.7 22.6 1.0
CE1 B:HIS141 4.7 12.2 1.0
C B:LEU187 4.7 14.5 1.0
CA B:LEU187 4.8 10.4 1.0
NE2 B:HIS142 4.9 18.1 1.0
C B:ASP186 5.0 12.3 1.0
CA B:ASP186 5.0 10.4 1.0

Zinc binding site 3 out of 4 in 6htt

Go back to Zinc Binding Sites List in 6htt
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7


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

b:20.7
occ:1.00
 OD1 C:ASP186 1.9 14.0 1.0
OD2 C:ASP285 2.0 14.9 1.0
O19 C:GQZ504 2.1 19.0 1.0
ND1 C:HIS188 2.1 14.6 1.0
O17 C:GQZ504 2.2 20.4 1.0
C15 C:GQZ504 2.7 25.9 1.0
N16 C:GQZ504 2.8 30.9 1.0
CG C:ASP186 2.8 14.0 1.0
CE1 C:HIS188 3.0 18.8 1.0
CG C:ASP285 3.0 16.6 1.0
OD2 C:ASP186 3.1 13.5 1.0
CG C:HIS188 3.2 13.0 1.0
OD1 C:ASP285 3.4 14.2 1.0
CB C:HIS188 3.7 13.3 1.0
N C:HIS188 3.8 13.2 1.0
C10 C:GQZ504 4.0 28.3 1.0
CA C:GLY339 4.1 15.0 1.0
NE2 C:HIS188 4.1 13.4 1.0
CB C:ASP186 4.3 11.7 1.0
CD2 C:HIS188 4.3 12.6 1.0
CB C:ASP285 4.3 15.0 1.0
N C:LEU187 4.3 10.3 1.0
O C:HOH727 4.4 35.1 1.0
CA C:HIS188 4.4 11.4 1.0
NE2 C:HIS141 4.4 18.3 1.0
OH C:TYR341 4.4 18.0 1.0
N C:GLY339 4.4 13.5 1.0
CB C:LEU187 4.5 11.6 1.0
CE2 C:TYR341 4.6 16.5 1.0
C11 C:GQZ504 4.7 21.8 1.0
C C:LEU187 4.7 16.9 1.0
CA C:LEU187 4.7 13.5 1.0
CE1 C:HIS141 4.8 16.5 1.0
NE2 C:HIS142 4.9 18.7 1.0
C C:ASP186 5.0 10.1 1.0

Zinc binding site 4 out of 4 in 6htt

Go back to Zinc Binding Sites List in 6htt
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:20.6
occ:1.00
 OD2 D:ASP285 2.0 17.5 1.0
OD1 D:ASP186 2.0 13.4 1.0
ND1 D:HIS188 2.1 12.8 1.0
O17 D:GQZ505 2.1 19.8 1.0
O19 D:GQZ505 2.2 26.2 1.0
C15 D:GQZ505 2.7 32.1 1.0
N16 D:GQZ505 2.7 29.9 1.0
CG D:ASP186 2.9 16.1 1.0
CE1 D:HIS188 2.9 21.8 1.0
CG D:ASP285 3.0 14.0 1.0
OD2 D:ASP186 3.1 13.8 1.0
CG D:HIS188 3.2 15.6 1.0
OD1 D:ASP285 3.4 16.6 1.0
CB D:HIS188 3.6 15.6 1.0
N D:HIS188 3.8 12.4 1.0
C10 D:GQZ505 4.1 26.9 1.0
NE2 D:HIS188 4.1 16.7 1.0
CA D:GLY339 4.2 13.2 1.0
O D:HOH779 4.2 37.2 1.0
CD2 D:HIS188 4.2 15.6 1.0
CB D:ASP186 4.3 14.1 1.0
CB D:ASP285 4.3 12.2 1.0
N D:LEU187 4.3 11.5 1.0
CA D:HIS188 4.4 12.8 1.0
OH D:TYR341 4.4 17.3 1.0
NE2 D:HIS141 4.4 21.7 1.0
CB D:LEU187 4.5 11.9 1.0
N D:GLY339 4.5 16.5 1.0
CE2 D:TYR341 4.6 18.5 1.0
C D:LEU187 4.7 15.2 1.0
C11 D:GQZ505 4.7 24.1 1.0
CA D:LEU187 4.8 10.8 1.0
CE1 D:HIS141 4.8 17.3 1.0
NE2 D:HIS142 4.9 15.9 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

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