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Chlorine in PDB 6gxa: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 2

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 2

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 2, PDB code: 6gxa 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) 43.15 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.200, 70.441, 97.721, 75.55, 78.23, 85.82
R / Rfree (%) 17.5 / 22.6

Other elements in 6gxa:

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

Chlorine binding site 1 out of 4 in 6gxa

Go back to Chlorine Binding Sites List in 6gxa
Chlorine binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 2


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

b:0.7
occ:1.00
 CL1 A:TB8504 0.0 0.7 1.0
C10 A:TB8504 1.8 85.6 1.0
C05 A:TB8504 2.8 82.8 1.0
C09 A:TB8504 2.8 83.7 1.0
C04 A:TB8504 3.0 75.5 1.0
CE A:LYS20 3.4 64.1 1.0
CD A:LYS20 3.5 54.2 1.0
CB A:PHE151 3.9 35.9 1.0
OH A:TYR341 3.9 53.0 1.0
O A:GLY150 3.9 31.3 1.0
C A:GLY150 4.0 29.7 1.0
C03 A:TB8504 4.0 69.6 1.0
C06 A:TB8504 4.1 82.1 1.0
C08 A:TB8504 4.1 83.0 1.0
N A:PHE151 4.3 29.2 1.0
CA A:GLY150 4.4 27.6 1.0
CZ A:TYR341 4.6 48.8 1.0
C07 A:TB8504 4.6 82.2 1.0
CE1 A:TYR341 4.6 48.0 1.0
NZ A:LYS20 4.7 65.2 1.0
CA A:PHE151 4.7 32.5 1.0
CG A:LYS20 4.7 46.2 1.0
O A:HOH688 4.8 44.9 1.0
CG A:PHE151 4.9 43.9 1.0
O01 A:TB8504 4.9 67.7 1.0
C02 A:TB8504 4.9 66.8 1.0

Chlorine binding site 2 out of 4 in 6gxa

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


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

b:79.2
occ:1.00
 CL1 B:TB8504 0.0 79.2 1.0
C10 B:TB8504 1.8 68.0 1.0
C09 B:TB8504 2.8 70.2 1.0
C05 B:TB8504 2.8 61.0 1.0
C04 B:TB8504 3.1 51.0 1.0
OH B:TYR341 3.3 48.8 1.0
CE B:LYS20 3.8 58.7 1.0
C03 B:TB8504 3.8 42.5 1.0
CE1 B:TYR341 3.8 43.8 1.0
CZ B:TYR341 3.9 44.1 1.0
CB B:PHE151 3.9 37.9 1.0
C08 B:TB8504 4.1 67.7 1.0
C06 B:TB8504 4.1 59.9 1.0
O B:GLY150 4.1 24.2 1.0
CG B:LYS20 4.2 36.4 1.0
C B:GLY150 4.3 31.0 1.0
CD B:LYS20 4.5 48.4 1.0
N B:PHE151 4.6 31.0 1.0
C07 B:TB8504 4.6 60.6 1.0
O01 B:TB8504 4.7 54.5 1.0
C02 B:TB8504 4.8 47.7 1.0
NZ B:LYS20 4.8 64.4 1.0
CZ B:PHE21 4.8 27.0 1.0
CA B:GLY150 4.9 30.1 1.0
CA B:PHE151 4.9 33.6 1.0
CG B:PHE151 4.9 41.7 1.0
CD1 B:TYR341 4.9 38.2 1.0
CE2 B:TYR341 5.0 42.9 1.0

Chlorine binding site 3 out of 4 in 6gxa

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


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

b:0.3
occ:1.00
 CL1 C:TB8504 0.0 0.3 1.0
C10 C:TB8504 1.8 68.2 1.0
C09 C:TB8504 2.8 68.6 1.0
C05 C:TB8504 2.8 61.4 1.0
C04 C:TB8504 3.1 49.5 1.0
CE C:LYS20 3.4 61.4 1.0
OH C:TYR341 3.5 40.6 1.0
CB C:PHE151 3.7 37.3 1.0
O C:HOH755 3.9 54.2 1.0
O C:GLY150 3.9 25.0 1.0
C C:GLY150 4.0 24.7 1.0
C03 C:TB8504 4.0 41.2 1.0
C08 C:TB8504 4.1 68.7 1.0
C06 C:TB8504 4.1 61.7 1.0
CE1 C:TYR341 4.1 37.4 1.0
CZ C:TYR341 4.2 36.8 1.0
N C:PHE151 4.2 30.6 1.0
NZ C:LYS20 4.2 67.1 1.0
CG C:LYS20 4.3 42.8 1.0
CD C:LYS20 4.4 54.1 1.0
CA C:GLY150 4.5 23.2 1.0
C07 C:TB8504 4.6 63.9 1.0
CA C:PHE151 4.6 30.0 1.0
CG C:PHE151 4.8 36.2 1.0
C02 C:TB8504 5.0 45.8 1.0

Chlorine binding site 4 out of 4 in 6gxa

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


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

b:93.5
occ:1.00
 CL1 D:TB8504 0.0 93.5 1.0
C10 D:TB8504 1.8 75.1 1.0
C09 D:TB8504 2.8 76.0 1.0
C05 D:TB8504 2.8 66.1 1.0
C04 D:TB8504 3.1 55.3 1.0
OH D:TYR341 3.7 42.3 1.0
CE D:LYS20 3.9 66.5 1.0
C03 D:TB8504 4.0 52.3 1.0
CD D:LYS20 4.0 59.5 1.0
CB D:PHE151 4.1 28.4 1.0
C08 D:TB8504 4.1 72.0 1.0
C06 D:TB8504 4.1 65.5 1.0
CE1 D:TYR341 4.2 42.6 1.0
CZ D:TYR341 4.3 45.1 1.0
NZ D:LYS20 4.3 72.1 1.0
CG D:LYS20 4.3 47.2 1.0
C D:GLY150 4.3 27.4 1.0
O D:GLY150 4.3 26.8 1.0
N D:PHE151 4.6 25.2 1.0
C07 D:TB8504 4.6 66.9 1.0
CA D:GLY150 4.8 25.9 1.0
C02 D:TB8504 4.9 53.2 1.0
CA D:PHE151 5.0 29.5 1.0
CG D:PHE151 5.0 33.3 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 00:16:26 2024

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