Chlorine in PDB 6hu3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

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

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3 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) 48.95 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.640, 70.430, 97.920, 75.48, 78.20, 86.17
R / Rfree (%) 16.2 / 19.4

Other elements in 6hu3:

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

Fluorine (F) 4 atoms
Potassium (K) 8 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor (pdb code 6hu3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6hu3

Go back to Chlorine Binding Sites List in 6hu3
Chlorine binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:60.5
occ:1.00
 CL1 A:GRZ504 0.0 60.5 1.0
C16 A:GRZ504 1.7 65.0 1.0
C15 A:GRZ504 2.7 60.5 1.0
C17 A:GRZ504 2.7 64.7 1.0
C18 A:GRZ504 4.0 64.4 1.0
C14 A:GRZ504 4.0 62.0 1.0
O A:HOH760 4.1 60.2 1.0
OD2 A:ASP100 4.4 59.3 1.0
C13 A:GRZ504 4.5 60.0 1.0
CB A:PHE216 4.5 35.3 1.0
O A:HOH634 4.9 47.0 1.0

Chlorine binding site 2 out of 4 in 6hu3

Go back to Chlorine Binding Sites List in 6hu3
Chlorine binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:61.3
occ:1.00
 CL1 B:GRZ504 0.0 61.3 1.0
C16 B:GRZ504 1.7 62.8 1.0
C15 B:GRZ504 2.7 58.6 1.0
C17 B:GRZ504 2.7 64.9 1.0
O A:GLN48 2.9 35.0 1.0
C A:GLN48 3.3 34.6 1.0
N A:TRP49 3.8 29.8 1.0
C A:TRP49 3.8 32.4 1.0
O A:HOH624 3.8 38.4 1.0
CA A:TRP49 3.9 27.0 1.0
O A:TRP49 4.0 29.4 1.0
C14 B:GRZ504 4.0 58.2 1.0
C18 B:GRZ504 4.0 63.5 1.0
O A:HOH710 4.1 35.3 1.0
CB A:GLN48 4.1 28.7 1.0
N A:ASP50 4.2 30.1 1.0
CA A:GLN48 4.2 26.6 1.0
CB B:PHE216 4.3 28.1 1.0
OD2 B:ASP100 4.3 72.9 1.0
C13 B:GRZ504 4.5 57.9 1.0
N A:GLN48 4.7 28.0 1.0
CA A:ASP50 4.8 30.9 1.0
CG B:PHE216 4.8 26.9 1.0
O A:HOH732 4.8 37.9 1.0
CD1 B:PHE216 4.9 32.0 1.0
CB A:ASP50 4.9 42.0 1.0

Chlorine binding site 3 out of 4 in 6hu3

Go back to Chlorine Binding Sites List in 6hu3
Chlorine binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:54.6
occ:1.00
 CL1 C:GRZ504 0.0 54.6 1.0
C16 C:GRZ504 1.7 57.9 1.0
C15 C:GRZ504 2.7 50.7 1.0
C17 C:GRZ504 2.7 58.9 1.0
O D:GLN48 2.9 33.0 1.0
C D:GLN48 3.3 33.6 1.0
N D:TRP49 3.6 25.8 1.0
C D:TRP49 3.7 29.2 1.0
CA D:TRP49 3.8 27.7 1.0
O D:HOH634 3.9 36.4 1.0
O D:TRP49 3.9 27.3 1.0
C18 C:GRZ504 4.0 55.7 1.0
C14 C:GRZ504 4.0 50.2 1.0
CB D:GLN48 4.1 30.6 1.0
N D:ASP50 4.1 27.2 1.0
O D:HOH737 4.1 39.0 1.0
CA D:GLN48 4.2 29.9 1.0
CB C:PHE216 4.3 28.8 1.0
OD2 C:ASP100 4.4 69.0 1.0
C13 C:GRZ504 4.5 53.3 1.0
N D:GLN48 4.6 27.4 1.0
CA D:ASP50 4.7 28.1 1.0
O D:HOH712 4.8 39.5 1.0
CB D:ASP50 4.9 43.0 1.0
CG C:PHE216 4.9 29.6 1.0

Chlorine binding site 4 out of 4 in 6hu3

Go back to Chlorine Binding Sites List in 6hu3
Chlorine binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:74.5
occ:1.00
 CL1 D:GRZ504 0.0 74.5 1.0
C16 D:GRZ504 1.7 77.2 1.0
C15 D:GRZ504 2.7 77.3 1.0
C17 D:GRZ504 2.7 74.9 1.0
C14 D:GRZ504 4.0 72.7 1.0
C18 D:GRZ504 4.0 74.1 1.0
OD2 D:ASP100 4.3 69.3 1.0
C13 D:GRZ504 4.5 72.8 1.0
CB D:PHE216 4.7 29.4 1.0
O D:HOH665 4.8 50.7 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: Sat Dec 12 13:06:32 2020

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