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Chlorine in PDB 6gx3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1, PDB code: 6gx3 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) 47.89 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.449, 70.670, 98.413, 75.71, 78.40, 85.55
R / Rfree (%) 18.9 / 24

Other elements in 6gx3:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1 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 1 (pdb code 6gx3). 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 1, PDB code: 6gx3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 1 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:73.8
occ:1.00
 CL1 A:FF2504 0.0 73.8 1.0
C08 A:FF2504 1.8 66.6 1.0
C10 A:FF2504 2.8 67.2 1.0
C07 A:FF2504 2.8 63.5 1.0
C06 A:FF2504 3.1 54.8 1.0
O A:HOH625 3.2 38.6 1.0
NE2 A:HIS292 3.3 39.0 1.0
CE1 A:HIS292 3.6 35.4 1.0
C13 A:FF2504 4.1 59.7 1.0
C11 A:FF2504 4.1 64.1 1.0
CE2 A:PHE151 4.3 29.6 0.5
CZ A:PHE151 4.3 30.7 0.5
CD2 A:HIS292 4.4 38.6 1.0
C05 A:FF2504 4.5 60.0 1.0
C12 A:FF2504 4.6 58.6 1.0
ND1 A:HIS292 4.8 33.0 1.0

Chlorine binding site 2 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 2 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:88.3
occ:1.00
 CL1 A:FF2505 0.0 88.3 1.0
C08 A:FF2505 1.8 58.1 1.0
C10 A:FF2505 2.7 55.3 1.0
C07 A:FF2505 2.8 62.2 1.0
C06 A:FF2505 3.2 76.8 1.0
O A:LYS330 3.6 41.9 1.0
CD A:PRO332 3.6 35.9 1.0
N A:PRO332 3.6 34.2 1.0
C A:LYS330 3.9 41.6 1.0
CB A:GLU131 3.9 39.3 1.0
C A:VAL331 4.0 36.6 1.0
CA A:PRO332 4.0 36.7 1.0
C11 A:FF2505 4.0 53.5 1.0
C13 A:FF2505 4.1 55.3 1.0
O A:GLU131 4.4 36.6 1.0
N A:VAL331 4.4 34.3 1.0
CA A:LYS330 4.4 39.0 1.0
CA A:VAL331 4.4 38.8 1.0
OE1 A:GLU131 4.5 79.8 1.0
O A:VAL331 4.5 36.9 1.0
CA A:GLU131 4.5 35.5 1.0
CG A:PRO332 4.5 38.3 1.0
CB A:PRO332 4.5 35.7 1.0
C12 A:FF2505 4.6 53.3 1.0
C05 A:FF2505 4.6 90.2 1.0
CG A:GLU131 4.6 58.2 1.0
CB A:LYS330 4.8 40.8 1.0
CD A:GLU131 4.8 74.6 1.0
C A:GLU131 4.8 36.1 1.0

Chlorine binding site 3 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 3 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:76.0
occ:1.00
 CL1 B:FF2504 0.0 76.0 1.0
C08 B:FF2504 1.8 60.0 1.0
C10 B:FF2504 2.7 58.8 1.0
C07 B:FF2504 2.8 51.4 1.0
C06 B:FF2504 3.2 52.6 1.0
NE2 B:HIS292 3.7 44.1 1.0
CE1 B:HIS292 3.8 38.8 1.0
OD2 A:ASP50 3.9 80.7 1.0
CE2 B:PHE151 3.9 32.9 0.5
OD1 A:ASP50 4.0 81.6 1.0
CG A:ASP50 4.0 75.0 1.0
C13 B:FF2504 4.0 46.0 1.0
C11 B:FF2504 4.1 49.7 1.0
CZ B:PHE151 4.1 37.3 0.5
NZ B:LYS20 4.1 76.6 1.0
C05 B:FF2504 4.5 49.3 1.0
C12 B:FF2504 4.6 46.4 1.0
CE B:LYS20 4.6 66.8 1.0
CZ B:TYR341 4.7 43.1 1.0
CE2 B:TYR341 4.8 40.6 1.0
CE1 B:TYR341 4.8 42.7 1.0
CD2 B:HIS292 4.9 36.3 1.0
ND1 B:HIS292 4.9 33.5 1.0
CB A:ASP50 4.9 58.2 1.0
OH B:TYR341 5.0 44.5 1.0

Chlorine binding site 4 out of 8 in 6gx3

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Chlorine binding site 4 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:76.9
occ:1.00
 CL1 B:FF2505 0.0 76.9 1.0
C08 B:FF2505 1.8 42.3 1.0
C10 B:FF2505 2.7 43.1 1.0
C07 B:FF2505 2.8 45.8 1.0
C06 B:FF2505 3.2 65.1 1.0
CG B:GLU131 3.4 52.6 1.0
CB B:GLU131 3.5 43.5 1.0
O B:LYS330 3.7 41.7 1.0
N B:PRO332 3.9 28.4 1.0
C B:LYS330 3.9 37.2 1.0
C11 B:FF2505 4.0 44.8 1.0
C13 B:FF2505 4.0 43.7 1.0
C B:VAL331 4.1 32.4 1.0
CA B:PRO332 4.2 31.3 1.0
CA B:GLU131 4.2 37.8 1.0
CD B:PRO332 4.2 26.7 1.0
O B:GLU131 4.2 30.1 1.0
CG B:PRO332 4.3 31.0 1.0
N B:VAL331 4.4 28.6 1.0
CA B:LYS330 4.5 35.5 1.0
O B:VAL331 4.5 29.6 1.0
CA B:VAL331 4.5 29.3 1.0
C05 B:FF2505 4.5 78.4 1.0
C12 B:FF2505 4.6 45.5 1.0
C B:GLU131 4.6 30.5 1.0
CB B:PRO332 4.7 31.9 1.0
CD B:GLU131 4.8 63.7 1.0
CB B:LYS330 5.0 41.6 1.0

Chlorine binding site 5 out of 8 in 6gx3

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Chlorine binding site 5 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:0.3
occ:1.00
 CL1 C:FF2504 0.0 0.3 1.0
C08 C:FF2504 1.8 57.9 1.0
C10 C:FF2504 2.8 60.9 1.0
C07 C:FF2504 2.8 48.4 1.0
C06 C:FF2504 3.1 45.6 1.0
NE2 C:HIS292 3.5 38.5 1.0
CE1 C:HIS292 3.6 38.3 1.0
O C:HOH646 3.7 40.0 1.0
OD1 D:ASP50 3.9 56.1 1.0
O D:HOH692 4.0 50.5 1.0
CZ C:PHE151 4.0 33.8 0.4
CE2 C:PHE151 4.0 36.8 0.4
C13 C:FF2504 4.1 44.7 1.0
C11 C:FF2504 4.1 56.5 1.0
CG D:ASP50 4.3 64.6 1.0
NZ C:LYS20 4.3 75.0 1.0
OD2 D:ASP50 4.4 63.0 1.0
C05 C:FF2504 4.5 47.8 1.0
C12 C:FF2504 4.6 47.2 1.0
CD2 C:HIS292 4.7 29.3 1.0
ND1 C:HIS292 4.8 36.9 1.0
CZ C:TYR341 4.9 35.1 1.0
CE2 C:TYR341 4.9 34.9 1.0

Chlorine binding site 6 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 6 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl505

b:70.4
occ:1.00
 CL1 C:FF2505 0.0 70.4 1.0
C08 C:FF2505 1.8 53.3 1.0
C10 C:FF2505 2.7 50.1 1.0
C07 C:FF2505 2.8 55.8 1.0
C06 C:FF2505 3.2 71.0 1.0
CB C:GLU131 3.5 37.3 1.0
O C:LYS330 3.6 39.6 1.0
N C:PRO332 3.8 27.1 1.0
C C:LYS330 3.9 35.9 1.0
CG C:GLU131 4.0 57.0 1.0
C C:VAL331 4.0 29.1 1.0
CD C:PRO332 4.0 29.0 1.0
C11 C:FF2505 4.0 48.1 1.0
C13 C:FF2505 4.1 50.9 1.0
CA C:PRO332 4.1 32.7 1.0
O C:GLU131 4.1 29.6 1.0
CA C:GLU131 4.2 30.6 1.0
CG C:PRO332 4.2 33.5 1.0
N C:VAL331 4.3 29.0 1.0
O C:VAL331 4.4 24.2 1.0
OE1 C:GLU131 4.4 77.1 1.0
CA C:VAL331 4.5 25.3 1.0
CA C:LYS330 4.5 31.9 1.0
C12 C:FF2505 4.5 51.1 1.0
C05 C:FF2505 4.6 82.4 1.0
C C:GLU131 4.6 24.3 1.0
CB C:PRO332 4.7 40.1 1.0
CD C:GLU131 4.7 73.5 1.0
CB C:LYS330 4.9 35.0 1.0

Chlorine binding site 7 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 7 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:66.0
occ:1.00
 CL1 D:FF2504 0.0 66.0 1.0
C08 D:FF2504 1.8 62.0 1.0
C10 D:FF2504 2.7 61.0 1.0
C07 D:FF2504 2.8 57.7 1.0
C06 D:FF2504 3.2 52.5 1.0
NE2 D:HIS292 3.6 45.8 1.0
O D:HOH660 3.9 40.1 1.0
CE1 D:HIS292 4.0 43.0 1.0
CE2 D:PHE151 4.0 57.8 1.0
C13 D:FF2504 4.0 52.2 1.0
C11 D:FF2504 4.0 54.6 1.0
CZ D:PHE151 4.1 57.7 1.0
C12 D:FF2504 4.5 51.2 1.0
C05 D:FF2504 4.6 49.8 1.0
CD2 D:HIS292 4.8 47.6 1.0

Chlorine binding site 8 out of 8 in 6gx3

Go back to Chlorine Binding Sites List in 6gx3
Chlorine binding site 8 out of 8 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:68.6
occ:1.00
 CL1 D:FF2505 0.0 68.6 1.0
C08 D:FF2505 1.8 65.9 1.0
C10 D:FF2505 2.7 57.1 1.0
C07 D:FF2505 2.8 76.6 1.0
C06 D:FF2505 3.1 86.5 1.0
O D:LYS330 3.3 34.5 1.0
N D:PRO332 3.3 35.2 1.0
C D:VAL331 3.5 34.2 1.0
CD D:PRO332 3.5 36.0 1.0
C D:LYS330 3.6 36.7 1.0
CG D:PRO332 3.7 37.7 1.0
CA D:PRO332 3.8 32.0 1.0
CA D:VAL331 3.9 36.9 1.0
N D:VAL331 3.9 36.3 1.0
O D:VAL331 3.9 34.6 1.0
C11 D:FF2505 4.0 64.0 1.0
C13 D:FF2505 4.1 75.2 1.0
CB D:GLU131 4.2 41.0 1.0
O D:GLU131 4.3 34.9 1.0
CA D:LYS330 4.4 37.0 1.0
CB D:PRO332 4.4 31.7 1.0
C05 D:FF2505 4.5 96.7 1.0
CG D:GLU131 4.5 60.3 1.0
C12 D:FF2505 4.6 72.0 1.0
CA D:GLU131 4.6 33.6 1.0
C D:GLU131 4.9 36.3 1.0
CB D:LYS330 4.9 40.2 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 00:16:25 2024

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