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Chlorine in PDB 6hu0: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9, PDB code: 6hu0 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) 47.99 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.690, 70.730, 98.120, 75.51, 78.08, 85.55
R / Rfree (%) 18.9 / 22.6

Other elements in 6hu0:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 also contains other interesting chemical elements:

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 Benzohydroxamate Inhibitor 9 (pdb code 6hu0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9, PDB code: 6hu0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6hu0

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Chlorine binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:39.3
occ:1.00
 CL1 A:T86504 0.0 39.3 1.0
C4 A:T86504 1.7 38.2 1.0
C3 A:T86504 2.7 32.1 1.0
C5 A:T86504 2.7 39.6 1.0
O A:HOH916 3.0 38.0 1.0
CB A:PRO291 3.6 22.7 1.0
O A:PRO291 3.9 18.7 1.0
C2 A:T86504 4.0 34.9 1.0
C6 A:T86504 4.0 35.5 1.0
C A:PRO291 4.2 18.5 1.0
O A:HOH747 4.2 37.1 1.0
O A:HOH858 4.2 36.6 1.0
C1 A:T86504 4.5 30.6 1.0
CA A:PRO291 4.5 17.7 1.0
O A:HOH925 4.7 37.9 1.0
CG A:PRO291 4.8 23.7 1.0
N A:HIS292 4.9 11.9 1.0

Chlorine binding site 2 out of 8 in 6hu0

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Chlorine binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:35.0
occ:1.00
 CL2 A:T86504 0.0 35.0 1.0
C2 A:T86504 1.7 34.9 1.0
C3 A:T86504 2.7 32.1 1.0
C1 A:T86504 2.7 30.6 1.0
O23 A:T86504 3.0 27.0 1.0
C12 A:T86504 3.2 26.7 1.0
CD1 A:TYR341 3.4 18.2 1.0
O A:HOH792 3.5 20.5 1.0
CG A:TYR341 3.7 16.8 1.0
CE A:LYS20 3.9 28.2 1.0
CE1 A:TYR341 3.9 20.3 1.0
C4 A:T86504 4.0 38.2 1.0
C6 A:T86504 4.0 35.5 1.0
CB A:TYR341 4.0 13.8 1.0
O A:HOH925 4.4 37.9 1.0
CD2 A:TYR341 4.4 15.6 1.0
N13 A:T86504 4.5 24.2 1.0
C5 A:T86504 4.5 39.6 1.0
O A:HOH652 4.5 27.0 1.0
NZ A:LYS20 4.6 27.6 1.0
CZ A:TYR341 4.6 14.4 1.0
CE2 A:TYR341 4.9 16.3 1.0
CE1 A:HIS292 4.9 19.0 1.0

Chlorine binding site 3 out of 8 in 6hu0

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Chlorine binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:34.0
occ:1.00
 CL1 B:T86504 0.0 34.0 1.0
C4 B:T86504 1.7 39.6 1.0
C5 B:T86504 2.7 33.4 1.0
C3 B:T86504 2.7 37.7 1.0
CB B:PRO291 3.8 13.7 1.0
O A:HOH632 3.8 43.1 1.0
C2 B:T86504 4.0 35.2 1.0
C6 B:T86504 4.0 28.7 1.0
O B:PRO291 4.0 11.9 1.0
O B:HOH1022 4.0 52.1 1.0
O A:HOH957 4.0 32.9 1.0
C B:PRO291 4.3 14.9 1.0
C1 B:T86504 4.5 24.2 1.0
O B:HOH888 4.5 47.8 1.0
CG B:PRO291 4.5 14.0 1.0
OD2 A:ASP50 4.6 41.2 1.0
O A:HOH887 4.6 50.5 1.0
CA B:PRO291 4.6 15.0 1.0
O B:HOH861 4.7 37.7 1.0
N B:HIS292 4.9 9.9 1.0

Chlorine binding site 4 out of 8 in 6hu0

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Chlorine binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


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 Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:39.8
occ:1.00
 CL2 B:T86504 0.0 39.8 1.0
C2 B:T86504 1.7 35.2 1.0
C3 B:T86504 2.7 37.7 1.0
C1 B:T86504 2.7 24.2 1.0
O23 B:T86504 3.2 25.7 1.0
C12 B:T86504 3.2 21.1 1.0
CD1 B:TYR341 3.3 16.6 1.0
O B:HOH1005 3.4 36.5 1.0
O B:HOH827 3.5 25.1 1.0
CG B:TYR341 3.6 9.9 1.0
CE B:LYS20 3.9 36.0 1.0
CB B:TYR341 3.9 17.6 1.0
CE1 B:TYR341 3.9 16.0 1.0
C4 B:T86504 4.0 39.6 1.0
C6 B:T86504 4.0 28.7 1.0
CD2 B:TYR341 4.3 8.3 1.0
N13 B:T86504 4.4 20.2 1.0
C5 B:T86504 4.5 33.4 1.0
CZ B:TYR341 4.6 15.5 1.0
O B:HOH740 4.6 21.9 1.0
NZ B:LYS20 4.7 29.8 1.0
CE2 B:TYR341 4.8 11.1 1.0
CG B:LYS20 4.9 13.0 1.0
CD B:LYS20 5.0 33.0 1.0

Chlorine binding site 5 out of 8 in 6hu0

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Chlorine binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:30.9
occ:1.00
 CL1 C:T86504 0.0 30.9 1.0
C4 C:T86504 1.7 31.9 1.0
C3 C:T86504 2.7 30.5 1.0
C5 C:T86504 2.7 31.6 1.0
CB C:PRO291 3.7 17.4 1.0
C2 C:T86504 4.0 32.9 1.0
C6 C:T86504 4.0 24.3 1.0
O C:PRO291 4.0 9.8 1.0
O D:HOH609 4.1 32.3 1.0
C C:PRO291 4.3 6.6 1.0
O C:HOH710 4.4 34.4 1.0
O C:HOH902 4.5 35.8 1.0
C1 C:T86504 4.5 31.4 1.0
O C:HOH982 4.5 42.7 1.0
CA C:PRO291 4.6 11.9 1.0
OD2 D:ASP50 4.7 42.4 1.0
CG C:PRO291 4.8 24.9 1.0
N C:HIS292 4.8 9.9 1.0

Chlorine binding site 6 out of 8 in 6hu0

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Chlorine binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:35.2
occ:1.00
 CL2 C:T86504 0.0 35.2 1.0
C2 C:T86504 1.7 32.9 1.0
C3 C:T86504 2.7 30.5 1.0
C1 C:T86504 2.7 31.4 1.0
O23 C:T86504 3.2 24.8 1.0
C12 C:T86504 3.2 25.8 1.0
CD1 C:TYR341 3.2 11.4 1.0
O C:HOH996 3.4 35.3 1.0
CG C:TYR341 3.5 13.2 1.0
O C:HOH801 3.6 15.2 1.0
O C:HOH982 3.7 42.7 1.0
CE1 C:TYR341 3.8 12.9 1.0
CB C:TYR341 3.9 10.9 1.0
CE C:LYS20 3.9 32.1 1.0
C4 C:T86504 4.0 31.9 1.0
C6 C:T86504 4.0 24.3 1.0
CD2 C:TYR341 4.3 13.1 1.0
N13 C:T86504 4.4 24.2 1.0
C5 C:T86504 4.5 31.6 1.0
O C:HOH693 4.6 21.8 1.0
CZ C:TYR341 4.6 15.1 1.0
NZ C:LYS20 4.7 30.8 1.0
CE2 C:TYR341 4.8 11.6 1.0
CE1 C:HIS292 4.8 18.9 1.0

Chlorine binding site 7 out of 8 in 6hu0

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Chlorine binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:37.9
occ:1.00
 CL1 D:T86504 0.0 37.9 1.0
C4 D:T86504 1.7 39.0 1.0
C5 D:T86504 2.7 36.0 1.0
C3 D:T86504 2.7 36.1 1.0
CB D:PRO291 3.6 18.9 1.0
O D:PRO291 3.8 19.8 1.0
C2 D:T86504 4.0 39.4 1.0
C6 D:T86504 4.0 31.1 1.0
C D:PRO291 4.0 18.1 1.0
CG D:PRO291 4.3 19.0 1.0
CA D:PRO291 4.4 14.3 1.0
C1 D:T86504 4.5 28.8 1.0
N D:HIS292 4.6 14.5 1.0
O D:HOH937 4.8 44.2 1.0

Chlorine binding site 8 out of 8 in 6hu0

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Chlorine binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:45.9
occ:1.00
 CL2 D:T86504 0.0 45.9 1.0
C2 D:T86504 1.7 39.4 1.0
C3 D:T86504 2.7 36.1 1.0
C1 D:T86504 2.7 28.8 1.0
O23 D:T86504 3.0 29.6 1.0
C12 D:T86504 3.2 24.3 1.0
O D:HOH943 3.3 30.4 1.0
CD1 D:TYR341 3.3 15.6 1.0
CG D:TYR341 3.5 11.8 1.0
O D:HOH773 3.6 25.4 1.0
CB D:TYR341 3.9 14.8 1.0
CE1 D:TYR341 3.9 18.1 1.0
CE D:LYS20 3.9 34.9 1.0
C4 D:T86504 4.0 39.0 1.0
C6 D:T86504 4.0 31.1 1.0
CD2 D:TYR341 4.3 12.9 1.0
O D:HOH937 4.3 44.2 1.0
N13 D:T86504 4.3 24.6 1.0
C5 D:T86504 4.5 36.0 1.0
CZ D:TYR341 4.6 11.2 1.0
NZ D:LYS20 4.6 32.5 1.0
CE2 D:TYR341 4.7 13.3 1.0
CE1 D:HIS292 4.7 20.3 1.0
O D:HOH945 4.9 40.6 1.0
O D:HOH671 4.9 21.8 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: Sun Jul 28 01:10:20 2024

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