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Chlorine in PDB 6gxu: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3, PDB code: 6gxu 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) 46.55 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.420, 70.460, 97.910, 77.96, 75.94, 85.97
R / Rfree (%) 20.1 / 24.8

Other elements in 6gxu:

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

Chlorine binding site 1 out of 4 in 6gxu

Go back to Chlorine Binding Sites List in 6gxu
Chlorine binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3


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

b:48.5
occ:1.00
 CL A:FG8504 0.0 48.5 1.0
C12 A:FG8504 1.7 40.6 1.0
C11 A:FG8504 2.7 33.5 1.0
C13 A:FG8504 2.7 38.5 1.0
O A:PRO291 3.8 27.9 1.0
C A:PRO291 3.8 30.9 1.0
N A:HIS292 3.9 27.7 1.0
CB A:PRO291 3.9 29.1 1.0
C10 A:FG8504 4.0 38.1 1.0
C14 A:FG8504 4.0 39.6 1.0
NE2 A:HIS292 4.0 25.5 1.0
CD2 A:HIS292 4.0 26.0 1.0
CE1 A:HIS292 4.0 26.1 1.0
ND1 A:HIS292 4.0 27.8 1.0
CG A:HIS292 4.1 22.9 1.0
CA A:HIS292 4.1 24.9 1.0
CG A:PRO291 4.3 30.8 1.0
C9 A:FG8504 4.5 40.1 1.0
CA A:PRO291 4.5 26.6 1.0
CB A:HIS292 4.7 21.5 1.0

Chlorine binding site 2 out of 4 in 6gxu

Go back to Chlorine Binding Sites List in 6gxu
Chlorine binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3


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

b:49.0
occ:1.00
 CL B:FG8505 0.0 49.0 1.0
C12 B:FG8505 1.7 43.0 1.0
C13 B:FG8505 2.7 40.2 1.0
C11 B:FG8505 2.7 38.6 1.0
N B:HIS292 3.8 21.4 1.0
C B:PRO291 3.8 23.4 1.0
O B:PRO291 3.9 28.8 1.0
ND1 B:HIS292 3.9 25.7 1.0
C14 B:FG8505 4.0 38.0 1.0
C10 B:FG8505 4.0 34.2 1.0
OD2 A:ASP50 4.0 56.3 1.0
CG B:HIS292 4.0 24.5 1.0
CE1 B:HIS292 4.0 31.7 1.0
CA B:HIS292 4.0 21.3 1.0
CB B:PRO291 4.0 31.5 1.0
CG A:ASP50 4.0 53.0 1.0
NE2 B:HIS292 4.1 30.9 1.0
CD2 B:HIS292 4.1 29.5 1.0
CB A:ASP50 4.2 35.7 1.0
CG B:PRO291 4.2 20.6 1.0
O A:HOH683 4.2 34.7 1.0
C9 B:FG8505 4.5 37.7 1.0
OD1 A:ASP50 4.5 58.8 1.0
CA B:PRO291 4.6 26.5 1.0
CB B:HIS292 4.6 24.9 1.0

Chlorine binding site 3 out of 4 in 6gxu

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


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

b:38.6
occ:1.00
 CL C:FG8504 0.0 38.6 1.0
C12 C:FG8504 1.7 38.9 1.0
C11 C:FG8504 2.7 39.0 1.0
C13 C:FG8504 2.7 37.4 1.0
OD2 D:ASP50 3.7 59.3 1.0
O D:HOH696 3.8 39.6 1.0
N C:HIS292 3.9 27.6 1.0
C C:PRO291 3.9 23.5 1.0
O C:PRO291 3.9 28.9 1.0
ND1 C:HIS292 3.9 25.2 1.0
C10 C:FG8504 4.0 32.5 1.0
C14 C:FG8504 4.0 35.4 1.0
CG D:ASP50 4.0 57.4 1.0
CE1 C:HIS292 4.0 23.5 1.0
CB C:PRO291 4.1 26.6 1.0
CG C:HIS292 4.1 20.1 1.0
CB D:ASP50 4.1 45.1 1.0
CA C:HIS292 4.1 20.9 1.0
NE2 C:HIS292 4.2 22.3 1.0
CD2 C:HIS292 4.3 21.2 1.0
CG C:PRO291 4.4 23.1 1.0
C9 C:FG8504 4.5 29.7 1.0
O C:HOH754 4.5 42.9 1.0
CA C:PRO291 4.6 26.0 1.0
CB C:HIS292 4.7 20.8 1.0
OD1 D:ASP50 4.7 64.5 1.0

Chlorine binding site 4 out of 4 in 6gxu

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


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

b:51.9
occ:1.00
 CL D:FG8504 0.0 51.9 1.0
C12 D:FG8504 1.7 47.0 1.0
C13 D:FG8504 2.7 43.4 1.0
C11 D:FG8504 2.7 38.2 1.0
O D:PRO291 3.8 37.4 1.0
C D:PRO291 3.8 30.8 1.0
N D:HIS292 3.9 26.6 1.0
ND1 D:HIS292 3.9 29.6 1.0
C14 D:FG8504 4.0 47.4 1.0
C10 D:FG8504 4.0 32.8 1.0
CB D:PRO291 4.0 31.7 1.0
CE1 D:HIS292 4.0 28.4 1.0
CG D:HIS292 4.1 30.6 1.0
CA D:HIS292 4.1 25.4 1.0
NE2 D:HIS292 4.2 28.3 1.0
CD2 D:HIS292 4.2 30.5 1.0
O D:HOH721 4.5 52.2 1.0
C9 D:FG8504 4.5 43.1 1.0
CG D:PRO291 4.5 27.5 1.0
CA D:PRO291 4.6 24.1 1.0
CB D:HIS292 4.7 22.2 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 00:20:42 2024

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