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Chlorine in PDB 6gxw: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4, PDB code: 6gxw 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) 48.13 / 2.07
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.800, 70.990, 98.200, 75.58, 77.93, 85.56
R / Rfree (%) 18.9 / 24.7

Other elements in 6gxw:

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

Chlorine binding site 1 out of 8 in 6gxw

Go back to Chlorine Binding Sites List in 6gxw
Chlorine binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:90.0
occ:1.00
 CL A:FGN504 0.0 90.0 1.0
C11 A:FGN504 1.7 98.5 1.0
C12 A:FGN504 2.7 0.1 1.0
C10 A:FGN504 2.7 0.4 1.0
ND1 A:HIS292 3.1 49.1 1.0
C9 A:FGN504 3.1 97.2 1.0
CE1 A:HIS292 3.2 50.4 1.0
CG A:HIS292 3.7 54.2 1.0
NE2 A:HIS292 3.8 62.2 1.0
C13 A:FGN504 4.0 0.8 1.0
N A:HIS292 4.0 41.5 1.0
C15 A:FGN504 4.0 0.9 1.0
O1 A:FGN504 4.1 95.8 1.0
CD2 A:HIS292 4.2 59.7 1.0
CA A:HIS292 4.2 50.1 1.0
C A:PRO291 4.3 32.2 1.0
CB A:PRO291 4.4 27.2 1.0
C14 A:FGN504 4.5 0.2 1.0
CB A:HIS292 4.5 46.7 1.0
O A:PRO291 4.5 34.7 1.0
OD1 A:ASP290 4.7 28.9 1.0
CD2 A:TYR341 4.8 24.4 1.0
CG A:TYR341 4.9 27.0 1.0
CA A:PRO291 5.0 26.8 1.0

Chlorine binding site 2 out of 8 in 6gxw

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Chlorine binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:0.5
occ:1.00
 CL1 A:FGN504 0.0 0.5 1.0
C15 A:FGN504 1.7 0.9 1.0
NZ A:LYS20 2.5 64.8 1.0
C14 A:FGN504 2.7 0.2 1.0
C10 A:FGN504 2.7 0.4 1.0
O1 A:FGN504 2.9 95.8 1.0
C9 A:FGN504 3.1 97.2 1.0
C8 A:FGN504 3.2 97.4 1.0
C7 A:FGN504 3.4 99.3 1.0
CE A:LYS20 3.5 57.0 1.0
C13 A:FGN504 4.0 0.8 1.0
C11 A:FGN504 4.0 98.5 1.0
C3 A:FGN504 4.1 91.9 1.0
C6 A:FGN504 4.4 94.6 1.0
C12 A:FGN504 4.5 0.1 1.0
C2 A:FGN504 4.7 83.5 1.0
CD A:LYS20 4.8 45.2 1.0
C4 A:FGN504 4.9 89.8 1.0

Chlorine binding site 3 out of 8 in 6gxw

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Chlorine binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:84.0
occ:1.00
 CL B:FGN504 0.0 84.0 1.0
C11 B:FGN504 1.7 89.8 1.0
C12 B:FGN504 2.7 92.3 1.0
C10 B:FGN504 2.7 92.6 1.0
C9 B:FGN504 3.0 85.3 1.0
OD2 A:ASP50 3.2 56.4 1.0
CE1 B:HIS292 3.3 49.5 1.0
ND1 B:HIS292 3.4 40.8 1.0
NE2 B:HIS292 3.8 53.3 1.0
CG A:ASP50 3.8 48.2 1.0
CB A:ASP50 3.9 43.0 1.0
C13 B:FGN504 4.0 95.2 1.0
CG B:HIS292 4.0 44.0 1.0
C15 B:FGN504 4.0 0.9 1.0
O1 B:FGN504 4.1 84.9 1.0
CD2 B:HIS292 4.2 48.0 1.0
N B:HIS292 4.3 29.2 1.0
C B:PRO291 4.4 33.2 1.0
O B:PRO291 4.5 34.7 1.0
CA B:HIS292 4.5 29.9 1.0
C14 B:FGN504 4.5 0.5 1.0
CB B:PRO291 4.6 26.2 1.0
OD1 A:ASP50 4.8 49.7 1.0
CB B:HIS292 4.8 26.2 1.0

Chlorine binding site 4 out of 8 in 6gxw

Go back to Chlorine Binding Sites List in 6gxw
Chlorine binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:0.8
occ:1.00
 CL1 B:FGN504 0.0 0.8 1.0
C15 B:FGN504 1.7 0.9 1.0
C14 B:FGN504 2.7 0.5 1.0
C10 B:FGN504 2.7 92.6 1.0
O1 B:FGN504 3.0 84.9 1.0
C9 B:FGN504 3.1 85.3 1.0
CD B:LYS20 3.3 60.2 1.0
CE B:LYS20 3.6 60.2 1.0
C8 B:FGN504 3.6 83.9 1.0
CG B:LYS20 3.7 50.8 1.0
C7 B:FGN504 3.9 81.2 1.0
CE1 B:TYR341 3.9 37.9 1.0
C13 B:FGN504 4.0 95.2 1.0
C11 B:FGN504 4.0 89.8 1.0
CD1 B:TYR341 4.1 32.5 1.0
NZ B:LYS20 4.3 58.0 1.0
C12 B:FGN504 4.5 92.3 1.0
C3 B:FGN504 4.5 76.1 1.0
CZ B:TYR341 4.7 40.2 1.0
CG B:TYR341 4.9 31.6 1.0
C2 B:FGN504 4.9 64.9 1.0

Chlorine binding site 5 out of 8 in 6gxw

Go back to Chlorine Binding Sites List in 6gxw
Chlorine binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl805

b:78.3
occ:1.00
 CL C:FGN805 0.0 78.3 1.0
C11 C:FGN805 1.7 86.9 1.0
C12 C:FGN805 2.7 86.6 1.0
C10 C:FGN805 2.7 93.1 1.0
C9 C:FGN805 3.0 91.8 1.0
CE1 C:HIS292 3.6 38.3 1.0
ND1 C:HIS292 3.7 38.0 1.0
CB C:PRO291 3.9 37.9 1.0
C13 C:FGN805 4.0 86.1 1.0
C15 C:FGN805 4.0 94.7 1.0
NE2 C:HIS292 4.1 42.3 1.0
O1 C:FGN805 4.2 89.0 1.0
CG C:HIS292 4.2 40.3 1.0
C C:PRO291 4.3 26.3 1.0
N C:HIS292 4.3 29.0 1.0
O C:PRO291 4.4 30.9 1.0
OD2 D:ASP50 4.4 53.1 1.0
CD2 C:HIS292 4.4 43.1 1.0
CB D:ASP50 4.4 32.9 1.0
C14 C:FGN805 4.5 88.3 1.0
CG D:ASP50 4.5 46.0 1.0
CA C:HIS292 4.6 25.8 1.0
CA C:PRO291 4.8 36.2 1.0
CG C:PRO291 4.9 41.8 1.0
CB C:HIS292 5.0 29.5 1.0

Chlorine binding site 6 out of 8 in 6gxw

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Chlorine binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl805

b:0.2
occ:1.00
 CL1 C:FGN805 0.0 0.2 1.0
C15 C:FGN805 1.7 94.7 1.0
C14 C:FGN805 2.7 88.3 1.0
C10 C:FGN805 2.7 93.1 1.0
O1 C:FGN805 2.9 89.0 1.0
C9 C:FGN805 3.2 91.8 1.0
CE C:LYS20 3.4 64.9 1.0
CD C:LYS20 3.4 59.6 1.0
NZ C:LYS20 3.4 65.1 1.0
CG C:LYS20 3.5 50.1 1.0
C8 C:FGN805 3.6 86.6 1.0
C13 C:FGN805 4.0 86.1 1.0
CE1 C:TYR341 4.0 36.7 1.0
C11 C:FGN805 4.0 86.9 1.0
C7 C:FGN805 4.0 82.7 1.0
CD1 C:TYR341 4.1 29.7 1.0
C3 C:FGN805 4.5 84.0 1.0
C12 C:FGN805 4.5 86.6 1.0
CZ C:TYR341 4.6 37.5 1.0
CG C:TYR341 4.8 29.5 1.0
C2 C:FGN805 4.9 77.8 1.0
CB C:LYS20 5.0 31.7 1.0

Chlorine binding site 7 out of 8 in 6gxw

Go back to Chlorine Binding Sites List in 6gxw
Chlorine binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:0.1
occ:1.00
 CL D:FGN504 0.0 0.1 1.0
C11 D:FGN504 1.7 0.4 1.0
NZ D:LYS20 2.4 74.6 1.0
C12 D:FGN504 2.7 0.1 1.0
C10 D:FGN504 2.7 0.3 1.0
O1 D:FGN504 2.9 93.5 1.0
C9 D:FGN504 3.0 95.9 1.0
CD D:LYS20 3.2 49.3 1.0
CE D:LYS20 3.3 68.1 1.0
C8 D:FGN504 3.5 93.5 1.0
C7 D:FGN504 3.7 96.3 1.0
C13 D:FGN504 4.0 1.0 1.0
C15 D:FGN504 4.0 94.0 1.0
C14 D:FGN504 4.5 0.1 1.0
C3 D:FGN504 4.5 83.2 1.0
CG D:LYS20 4.7 32.4 1.0
C6 D:FGN504 4.8 92.0 1.0
CE1 D:TYR341 4.8 27.1 1.0

Chlorine binding site 8 out of 8 in 6gxw

Go back to Chlorine Binding Sites List in 6gxw
Chlorine binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:79.5
occ:1.00
 CL1 D:FGN504 0.0 79.5 1.0
C15 D:FGN504 1.7 94.0 1.0
C14 D:FGN504 2.7 0.1 1.0
C10 D:FGN504 2.7 0.3 1.0
ND1 D:HIS292 3.0 86.0 1.0
C9 D:FGN504 3.1 95.9 1.0
CE1 D:HIS292 3.2 89.2 1.0
C13 D:FGN504 4.0 1.0 1.0
C11 D:FGN504 4.0 0.4 1.0
CG D:HIS292 4.2 82.1 1.0
O1 D:FGN504 4.3 93.5 1.0
NE2 D:HIS292 4.4 89.7 1.0
N D:HIS292 4.4 57.1 1.0
C D:PRO291 4.5 45.5 1.0
C12 D:FGN504 4.5 0.1 1.0
O D:PRO291 4.5 42.7 1.0
CB D:PRO291 4.6 32.8 1.0
CA D:HIS292 4.7 64.8 1.0
CD2 D:HIS292 4.9 85.5 1.0
CB D:HIS292 4.9 70.6 1.0

Reference:

T.Bayer, A.Chakrabarti, J.Lancelot, T.B.Shaik, K.Hausmann, J.Melesina, K.Schmidtkunz, M.Marek, F.Erdmann, M.Schmidt, D.Robaa, C.Romier, R.J.Pierce, M.Jung, W.Sippl. Synthesis, Crystallization Studies, and in Vitro Characterization of Cinnamic Acid Derivatives As SMHDAC8 Inhibitors For the Treatment of Schistosomiasis. Chemmedchem V. 13 1517 2018.
ISSN: ESSN 1860-7187
PubMed: 29806110
DOI: 10.1002/CMDC.201800238
Page generated: Sun Jul 28 00:20:42 2024

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