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Zinc in PDB 6hsf: Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051, PDB code: 6hsf 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) 43.37 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.600, 70.670, 98.170, 75.83, 78.25, 86.05
R / Rfree (%) 21.1 / 26.5

Other elements in 6hsf:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051 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 Mutant H292M Complexed with Pci-34051 (pdb code 6hsf). 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 Mutant H292M Complexed with Pci-34051, PDB code: 6hsf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hsf

Go back to Zinc Binding Sites List in 6hsf
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051


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 Mutant H292M Complexed with Pci-34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.3
occ:1.00
 OD2 A:ASP285 1.9 26.1 1.0
OD1 A:ASP186 2.0 24.1 1.0
ND1 A:HIS188 2.1 16.2 1.0
O18 A:GKW504 2.2 38.2 1.0
O16 A:GKW504 2.4 54.0 1.0
N17 A:GKW504 2.7 42.5 1.0
C15 A:GKW504 2.8 57.3 1.0
CG A:ASP186 2.8 19.4 1.0
CE1 A:HIS188 2.9 12.8 1.0
CG A:ASP285 3.0 26.2 1.0
OD2 A:ASP186 3.0 23.7 1.0
CG A:HIS188 3.1 20.5 1.0
OD1 A:ASP285 3.3 21.2 1.0
CB A:HIS188 3.6 12.6 1.0
N A:HIS188 3.8 26.9 1.0
NE2 A:HIS188 4.1 16.6 1.0
C14 A:GKW504 4.1 69.7 1.0
CA A:GLY339 4.2 27.3 1.0
CB A:ASP186 4.2 10.9 1.0
CD2 A:HIS188 4.2 18.5 1.0
CB A:ASP285 4.3 9.9 1.0
N A:LEU187 4.3 16.4 1.0
CA A:HIS188 4.3 16.8 1.0
N A:GLY339 4.4 22.9 1.0
OH A:TYR341 4.5 36.1 1.0
NE2 A:HIS141 4.6 29.1 1.0
CB A:LEU187 4.7 6.8 1.0
C A:LEU187 4.7 20.9 1.0
C19 A:GKW504 4.8 73.5 1.0
CA A:LEU187 4.8 17.1 1.0
CE2 A:TYR341 4.8 37.4 1.0
NE2 A:HIS142 4.8 24.5 1.0
C A:ASP186 4.9 13.9 1.0
CA A:ASP186 5.0 14.9 1.0
CE1 A:HIS141 5.0 25.2 1.0

Zinc binding site 2 out of 4 in 6hsf

Go back to Zinc Binding Sites List in 6hsf
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051


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 Mutant H292M Complexed with Pci-34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:24.5
occ:1.00
 OD2 B:ASP285 1.9 15.6 1.0
OD1 B:ASP186 2.0 15.8 1.0
ND1 B:HIS188 2.3 20.0 1.0
O18 B:GKW504 2.5 33.3 1.0
O16 B:GKW504 2.6 37.0 1.0
N17 B:GKW504 2.7 41.7 1.0
C15 B:GKW504 2.8 51.5 1.0
CG B:ASP186 2.9 15.2 1.0
CG B:ASP285 3.0 25.0 1.0
CE1 B:HIS188 3.1 22.1 1.0
OD2 B:ASP186 3.2 17.1 1.0
CG B:HIS188 3.3 19.3 1.0
OD1 B:ASP285 3.3 18.1 1.0
CB B:HIS188 3.7 25.2 1.0
N B:HIS188 3.7 16.6 1.0
C14 B:GKW504 4.0 67.8 1.0
CA B:GLY339 4.2 25.1 1.0
N B:LEU187 4.2 17.2 1.0
NE2 B:HIS188 4.3 29.2 1.0
CB B:ASP285 4.3 11.8 1.0
CB B:ASP186 4.3 15.4 1.0
CB B:LEU187 4.3 17.0 1.0
CA B:HIS188 4.4 14.9 1.0
CD2 B:HIS188 4.4 24.9 1.0
OH B:TYR341 4.4 43.5 1.0
NE2 B:HIS141 4.5 18.7 1.0
C19 B:GKW504 4.5 75.7 1.0
C B:LEU187 4.6 19.0 1.0
N B:GLY339 4.6 27.4 1.0
CA B:LEU187 4.6 18.0 1.0
CE1 B:HIS141 4.7 17.9 1.0
CE1 B:TYR341 4.8 41.3 1.0
C B:ASP186 4.9 13.4 1.0
NE2 B:HIS142 4.9 20.1 1.0
C13 B:GKW504 5.0 76.6 1.0

Zinc binding site 3 out of 4 in 6hsf

Go back to Zinc Binding Sites List in 6hsf
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051


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 Mutant H292M Complexed with Pci-34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:21.9
occ:1.00
 OD2 C:ASP285 1.9 13.8 1.0
OD1 C:ASP186 2.0 17.2 1.0
ND1 C:HIS188 2.1 18.4 1.0
O18 C:GKW504 2.4 41.5 1.0
O16 C:GKW504 2.5 31.5 1.0
N17 C:GKW504 2.7 40.3 1.0
C15 C:GKW504 2.7 46.8 1.0
CG C:ASP186 2.8 16.6 1.0
CG C:ASP285 2.9 25.6 1.0
CE1 C:HIS188 2.9 21.9 1.0
OD2 C:ASP186 3.0 16.2 1.0
CG C:HIS188 3.3 22.8 1.0
OD1 C:ASP285 3.3 22.9 1.0
CB C:HIS188 3.7 23.1 1.0
N C:HIS188 3.8 19.2 1.0
C14 C:GKW504 4.0 58.6 1.0
CA C:GLY339 4.0 32.4 1.0
NE2 C:HIS188 4.1 25.8 1.0
CB C:ASP186 4.3 9.8 1.0
N C:LEU187 4.3 17.6 1.0
CB C:ASP285 4.3 9.5 1.0
CD2 C:HIS188 4.3 18.5 1.0
CB C:LEU187 4.4 13.4 1.0
CA C:HIS188 4.4 19.0 1.0
OH C:TYR341 4.5 31.2 1.0
NE2 C:HIS141 4.6 20.6 1.0
N C:GLY339 4.6 26.3 1.0
C C:LEU187 4.6 19.4 1.0
C19 C:GKW504 4.6 68.0 1.0
CA C:LEU187 4.6 16.3 1.0
CE2 C:TYR341 4.7 31.7 1.0
CE1 C:HIS141 4.8 19.4 1.0
C C:ASP186 4.9 10.6 1.0
CA C:ASP186 5.0 12.7 1.0
C13 C:GKW504 5.0 64.6 1.0

Zinc binding site 4 out of 4 in 6hsf

Go back to Zinc Binding Sites List in 6hsf
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Mutant H292M Complexed with Pci-34051


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 Mutant H292M Complexed with Pci-34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:23.7
occ:1.00
 OD2 D:ASP285 2.0 26.8 1.0
OD1 D:ASP186 2.1 18.4 1.0
ND1 D:HIS188 2.1 20.2 1.0
O18 D:GKW504 2.3 37.8 1.0
O16 D:GKW504 2.5 57.1 1.0
N17 D:GKW504 2.7 45.4 1.0
C15 D:GKW504 2.8 55.4 1.0
CG D:ASP186 2.8 14.3 1.0
CE1 D:HIS188 2.9 16.6 1.0
CG D:ASP285 3.0 22.3 1.0
OD2 D:ASP186 3.0 22.2 1.0
CG D:HIS188 3.2 21.4 1.0
OD1 D:ASP285 3.3 21.0 1.0
CB D:HIS188 3.6 14.7 1.0
N D:HIS188 3.9 22.6 1.0
NE2 D:HIS188 4.1 28.0 1.0
C14 D:GKW504 4.1 65.0 1.0
CA D:GLY339 4.1 26.6 1.0
CD2 D:HIS188 4.2 28.8 1.0
CB D:ASP186 4.3 10.7 1.0
CB D:ASP285 4.3 10.3 1.0
N D:LEU187 4.3 18.4 1.0
CA D:HIS188 4.4 15.2 1.0
N D:GLY339 4.4 28.6 1.0
OH D:TYR341 4.5 48.7 1.0
CB D:LEU187 4.6 13.7 1.0
NE2 D:HIS141 4.6 28.1 1.0
C19 D:GKW504 4.7 72.0 1.0
C D:LEU187 4.7 22.7 1.0
CE2 D:TYR341 4.8 41.0 1.0
CA D:LEU187 4.8 20.1 1.0
NE2 D:HIS142 4.9 20.6 1.0
C D:ASP186 5.0 25.2 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 23:13:25 2024

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