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Chlorine in PDB 4bz9: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075, PDB code: 4bz9 was solved by M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.16 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.280, 70.316, 98.130, 77.93, 75.59, 85.54
R / Rfree (%) 19.08 / 22.12

Other elements in 4bz9:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075 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 J1075 (pdb code 4bz9). 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 J1075, PDB code: 4bz9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4bz9

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Chlorine binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl700

b:46.8
occ:1.00
 CL A:KMY700 0.0 46.8 1.0
C13 A:KMY700 1.7 41.8 1.0
C12 A:KMY700 2.8 39.0 1.0
C05 A:KMY700 2.8 38.9 1.0
OH A:TYR341 3.1 52.1 1.0
NZ A:LYS20 3.2 82.9 1.0
C11 A:KMY700 3.2 39.4 1.0
C02 A:KMY700 3.4 36.2 1.0
O01 A:KMY700 3.4 34.8 1.0
CZ A:PHE21 3.5 21.2 1.0
O A:GLY150 3.6 21.3 1.0
CZ A:TYR341 3.8 48.9 1.0
CE1 A:TYR341 3.8 40.9 1.0
O A:HOH2122 3.9 37.4 1.0
CE2 A:PHE21 3.9 22.9 1.0
C07 A:KMY700 4.0 39.1 1.0
CB A:PHE151 4.0 19.2 1.0
S06 A:KMY700 4.2 39.4 1.0
C A:GLY150 4.4 21.5 1.0
CE1 A:PHE21 4.5 23.2 1.0
C10 A:KMY700 4.6 41.0 1.0
N03 A:KMY700 4.6 32.1 1.0
CE A:LYS20 4.6 73.4 1.0
CG A:LYS20 4.9 43.2 1.0
CE2 A:TYR341 5.0 39.0 1.0
N A:PHE151 5.0 17.4 1.0

Chlorine binding site 2 out of 8 in 4bz9

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Chlorine binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:65.1
occ:1.00
 CL A:KMY701 0.0 65.1 1.0
C13 A:KMY701 1.7 60.3 1.0
C05 A:KMY701 2.7 60.6 1.0
C12 A:KMY701 2.8 54.9 1.0
O01 A:KMY701 3.1 62.4 1.0
C11 A:KMY701 3.2 52.0 1.0
C02 A:KMY701 3.3 62.9 1.0
O A:LYS330 3.4 24.4 1.0
CD A:PRO332 3.7 23.6 1.0
N A:PRO332 3.7 20.8 1.0
CG A:PRO332 3.8 28.0 1.0
C07 A:KMY701 4.0 55.0 1.0
C A:LYS330 4.0 24.9 1.0
CG A:GLU131 4.0 34.3 1.0
C A:VAL331 4.1 22.9 1.0
CA A:PRO332 4.1 19.9 1.0
S06 A:KMY701 4.2 58.9 1.0
CB A:GLU131 4.2 19.5 1.0
O A:GLU131 4.4 20.9 1.0
CA A:GLU131 4.4 17.3 1.0
CA A:VAL331 4.5 19.3 1.0
CB A:PRO332 4.5 22.1 1.0
N A:VAL331 4.5 20.3 1.0
C10 A:KMY701 4.6 51.5 1.0
N03 A:KMY701 4.6 65.1 1.0
O A:VAL331 4.7 21.6 1.0
CA A:LYS330 4.9 23.1 1.0
C A:GLU131 4.9 20.9 1.0

Chlorine binding site 3 out of 8 in 4bz9

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Chlorine binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl700

b:48.9
occ:1.00
 CL B:KMY700 0.0 48.9 1.0
C13 B:KMY700 1.7 45.6 1.0
C05 B:KMY700 2.7 43.5 1.0
C12 B:KMY700 2.8 40.9 1.0
C11 B:KMY700 3.2 40.0 1.0
O01 B:KMY700 3.2 44.7 1.0
OH B:TYR341 3.2 51.5 1.0
CZ B:PHE21 3.3 23.6 1.0
C02 B:KMY700 3.3 44.8 1.0
CE1 B:TYR341 3.6 37.9 1.0
CE2 B:PHE21 3.6 24.2 1.0
O B:GLY150 3.7 17.8 1.0
CZ B:TYR341 3.8 47.8 1.0
CB B:PHE151 4.0 19.6 1.0
C07 B:KMY700 4.0 39.3 1.0
CD B:LYS20 4.1 59.1 1.0
O B:HOH2120 4.1 27.9 1.0
S06 B:KMY700 4.2 40.2 1.0
CE1 B:PHE21 4.4 25.1 1.0
C B:GLY150 4.5 19.0 1.0
N03 B:KMY700 4.6 42.3 1.0
C10 B:KMY700 4.6 40.5 1.0
CG B:LYS20 4.7 45.9 1.0
CD1 B:TYR341 4.8 36.0 1.0
O B:HOH2124 4.8 42.5 1.0
CD2 B:PHE21 4.9 20.7 1.0
CA B:PHE151 5.0 17.3 1.0
N B:PHE151 5.0 15.8 1.0

Chlorine binding site 4 out of 8 in 4bz9

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Chlorine binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:55.8
occ:1.00
 CL B:KMY701 0.0 55.8 1.0
C13 B:KMY701 1.7 49.6 1.0
C12 B:KMY701 2.7 41.7 1.0
C05 B:KMY701 2.7 52.6 1.0
C11 B:KMY701 3.1 37.5 1.0
O01 B:KMY701 3.2 58.4 1.0
C02 B:KMY701 3.2 58.3 1.0
O B:LYS330 3.6 21.1 1.0
CD B:PRO332 3.7 16.8 1.0
N B:PRO332 3.7 14.1 1.0
CG B:GLU131 3.7 34.6 1.0
CG B:PRO332 3.9 20.4 1.0
CB B:GLU131 3.9 19.2 1.0
C07 B:KMY701 4.0 42.5 1.0
C B:LYS330 4.1 21.3 1.0
C B:VAL331 4.1 16.2 1.0
CA B:PRO332 4.2 13.8 1.0
S06 B:KMY701 4.2 50.5 1.0
CA B:GLU131 4.4 17.4 1.0
N03 B:KMY701 4.4 63.6 1.0
O B:GLU131 4.5 18.6 1.0
C10 B:KMY701 4.5 33.6 1.0
N B:VAL331 4.5 17.5 1.0
CB B:PRO332 4.6 15.7 1.0
CA B:VAL331 4.6 16.2 1.0
O B:VAL331 4.7 11.5 1.0
CA B:LYS330 4.9 17.4 1.0
C B:GLU131 4.9 18.3 1.0

Chlorine binding site 5 out of 8 in 4bz9

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Chlorine binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl700

b:53.2
occ:1.00
 CL C:KMY700 0.0 53.2 1.0
C13 C:KMY700 1.7 46.8 1.0
C05 C:KMY700 2.7 43.7 1.0
C12 C:KMY700 2.8 43.1 1.0
C11 C:KMY700 3.2 40.6 1.0
O01 C:KMY700 3.3 42.5 1.0
OH C:TYR341 3.3 56.6 1.0
C02 C:KMY700 3.3 42.6 1.0
CZ C:PHE21 3.5 22.3 1.0
O C:GLY150 3.6 17.6 1.0
CE2 C:PHE21 3.7 23.1 1.0
CE1 C:TYR341 3.8 38.8 1.0
CB C:PHE151 3.9 16.5 1.0
CZ C:TYR341 3.9 49.4 1.0
C07 C:KMY700 4.0 40.9 1.0
S06 C:KMY700 4.2 41.2 1.0
C C:GLY150 4.3 19.2 1.0
O C:HOH2137 4.3 30.9 1.0
NZ C:LYS20 4.4 85.3 1.0
N03 C:KMY700 4.6 37.5 1.0
C10 C:KMY700 4.6 39.9 1.0
CG C:LYS20 4.6 36.0 1.0
CE1 C:PHE21 4.7 22.6 1.0
CD C:LYS20 4.8 47.2 1.0
CA C:PHE151 4.9 15.1 1.0
N C:PHE151 4.9 14.9 1.0
O C:HOH2139 4.9 41.3 1.0
CG C:PHE151 4.9 17.7 1.0
CD1 C:TYR341 5.0 36.0 1.0
CD2 C:PHE21 5.0 20.2 1.0

Chlorine binding site 6 out of 8 in 4bz9

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Chlorine binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl701

b:58.4
occ:1.00
 CL C:KMY701 0.0 58.4 1.0
C13 C:KMY701 1.7 57.3 1.0
C12 C:KMY701 2.7 52.4 1.0
C05 C:KMY701 2.7 61.7 1.0
O01 C:KMY701 2.9 66.2 1.0
C11 C:KMY701 3.1 48.4 1.0
C02 C:KMY701 3.2 66.7 1.0
N C:PRO332 3.2 16.4 1.0
O C:LYS330 3.4 19.3 1.0
CD C:PRO332 3.5 19.0 1.0
C C:VAL331 3.6 17.7 1.0
CA C:PRO332 3.6 15.9 1.0
CG C:PRO332 3.7 22.9 1.0
C C:LYS330 3.8 18.9 1.0
CB C:GLU131 3.9 19.2 1.0
O C:GLU131 3.9 17.4 1.0
C07 C:KMY701 3.9 54.4 1.0
CG C:GLU131 4.0 35.1 1.0
O C:VAL331 4.0 15.9 1.0
N C:VAL331 4.1 13.5 1.0
CB C:PRO332 4.1 18.1 1.0
S06 C:KMY701 4.2 59.2 1.0
CA C:VAL331 4.2 13.9 1.0
CA C:GLU131 4.2 17.3 1.0
C C:GLU131 4.4 18.1 1.0
C10 C:KMY701 4.5 47.9 1.0
N03 C:KMY701 4.6 71.9 1.0
CA C:LYS330 4.6 14.2 1.0
C C:PRO332 4.9 17.3 1.0

Chlorine binding site 7 out of 8 in 4bz9

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Chlorine binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl700

b:46.9
occ:1.00
 CL D:KMY700 0.0 46.9 1.0
C13 D:KMY700 1.7 45.0 1.0
C05 D:KMY700 2.8 44.0 1.0
C12 D:KMY700 2.8 44.1 1.0
OH D:TYR341 2.9 47.6 1.0
C11 D:KMY700 3.2 42.9 1.0
C02 D:KMY700 3.3 43.8 1.0
CZ D:PHE21 3.4 20.6 1.0
O01 D:KMY700 3.4 43.2 1.0
CZ D:TYR341 3.7 45.0 1.0
O D:GLY150 3.7 19.4 1.0
CE2 D:PHE21 3.7 22.3 1.0
CE1 D:TYR341 3.8 36.9 1.0
CB D:PHE151 3.8 20.2 1.0
CD D:LYS20 3.9 56.2 1.0
C07 D:KMY700 4.0 44.8 1.0
S06 D:KMY700 4.2 43.7 1.0
C D:GLY150 4.3 20.1 1.0
O D:HOH2112 4.4 43.2 1.0
CE1 D:PHE21 4.5 22.1 1.0
N03 D:KMY700 4.5 41.3 1.0
C10 D:KMY700 4.6 45.5 1.0
CG D:LYS20 4.8 41.7 1.0
CE2 D:TYR341 4.8 36.7 1.0
CA D:PHE151 4.8 18.1 1.0
CE D:LYS20 4.8 69.8 1.0
N D:PHE151 4.8 16.9 1.0
CG D:PHE151 4.9 22.2 1.0

Chlorine binding site 8 out of 8 in 4bz9

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Chlorine binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with J1075


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 J1075 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl701

b:66.6
occ:1.00
 CL D:KMY701 0.0 66.6 1.0
C13 D:KMY701 1.7 61.6 1.0
C05 D:KMY701 2.8 61.7 1.0
C12 D:KMY701 2.8 55.5 1.0
O D:HOH2030 3.0 37.4 1.0
C11 D:KMY701 3.2 50.7 1.0
O01 D:KMY701 3.2 65.2 1.0
C02 D:KMY701 3.3 65.3 1.0
CG D:PRO332 3.7 25.5 1.0
O D:LYS330 3.8 22.9 1.0
CD D:PRO332 3.9 21.0 1.0
CG D:GLU131 3.9 33.0 1.0
C07 D:KMY701 4.0 54.8 1.0
N D:PRO332 4.1 19.1 1.0
CB D:GLU131 4.2 21.1 1.0
S06 D:KMY701 4.2 58.1 1.0
N03 D:KMY701 4.5 69.0 1.0
CA D:PRO332 4.5 18.4 1.0
CA D:GLU131 4.5 19.0 1.0
C D:LYS330 4.5 23.2 1.0
C10 D:KMY701 4.6 47.9 1.0
CB D:PRO332 4.6 19.6 1.0
C D:VAL331 4.7 23.3 1.0
O D:GLU131 4.9 22.1 1.0

Reference:

M.Marek, S.Kannan, A.Hauser, M.Moraes Mourao, S.Caby, V.Cura, D.A.Stolfa, K.Schmidtkunz, J.Lancelot, L.Andrade, J.Renaud, G.Oliveira, W.Sippl, M.Jung, J.Cavarelli, R.J.Pierce, C.Romier. Structural Basis For the Inhibition of Histone Deacetylase 8 (HDAC8), A Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni. Plos Pathog. V. 9 03645 2013.
ISSN: ISSN 1553-7366
PubMed: 24086136
DOI: 10.1371/JOURNAL.PPAT.1003645
Page generated: Fri Jul 11 13:39:21 2025

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