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Chlorine in PDB 6fu1: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate, PDB code: 6fu1 was solved by M.Marek, T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.710, 70.690, 99.190, 75.33, 77.78, 84.80
R / Rfree (%) 19.9 / 22.3

Other elements in 6fu1:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate 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 A N- Alkyl Hydroxamate (pdb code 6fu1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate, PDB code: 6fu1:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6fu1

Go back to Chlorine Binding Sites List in 6fu1
Chlorine binding site 1 out of 3 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 A N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:94.6
occ:1.00
CL A:E7Q504 0.0 94.6 1.0
C18 A:E7Q504 1.7 90.7 1.0
C20 A:E7Q504 2.7 87.3 1.0
C17 A:E7Q504 2.7 87.3 1.0
OD2 A:ASP100 2.9 75.7 1.0
CD1 A:PHE216 3.8 26.9 1.0
C21 A:E7Q504 4.0 83.8 1.0
C16 A:E7Q504 4.0 85.2 1.0
CG A:ASP100 4.0 73.0 1.0
O A:HOH689 4.1 34.1 1.0
CE1 A:PHE216 4.2 31.4 1.0
C15 A:E7Q504 4.5 82.5 1.0
CG A:PHE216 4.7 22.4 1.0
OD1 A:ASP100 4.7 72.4 1.0
CB A:ASP100 4.9 71.4 1.0

Chlorine binding site 2 out of 3 in 6fu1

Go back to Chlorine Binding Sites List in 6fu1
Chlorine binding site 2 out of 3 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 A N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:39.3
occ:1.00
CL A:E7Q506 0.0 39.3 1.0
C18 A:E7Q506 1.7 28.2 1.0
C20 A:E7Q506 2.7 24.9 1.0
C17 A:E7Q506 2.7 30.4 1.0
O A:HOH665 3.5 28.3 1.0
O C:HOH712 3.6 32.2 1.0
NH2 A:ARG239 3.7 43.7 1.0
O A:HOH661 4.0 27.9 1.0
C21 A:E7Q506 4.0 22.9 1.0
C16 A:E7Q506 4.0 25.8 1.0
O A:LEU421 4.1 31.5 1.0
NE A:ARG239 4.1 49.0 1.0
CZ A:ARG239 4.2 43.3 1.0
OD2 C:ASP388 4.3 26.6 1.0
O C:HOH764 4.4 34.4 1.0
C15 A:E7Q506 4.5 22.2 1.0
O C:HOH607 4.7 40.9 1.0

Chlorine binding site 3 out of 3 in 6fu1

Go back to Chlorine Binding Sites List in 6fu1
Chlorine binding site 3 out of 3 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


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 A N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:38.2
occ:1.00
CL B:E7Q505 0.0 38.2 1.0
C18 B:E7Q505 1.7 31.4 1.0
C17 B:E7Q505 2.7 33.3 1.0
C20 B:E7Q505 2.7 26.5 1.0
O D:HOH688 3.5 28.3 1.0
O B:HOH708 3.6 31.9 1.0
NH2 D:ARG239 3.7 42.6 1.0
O D:HOH625 4.0 30.1 1.0
C16 B:E7Q505 4.0 31.1 1.0
C21 B:E7Q505 4.0 22.8 1.0
O D:LEU421 4.1 31.6 1.0
NE D:ARG239 4.2 46.6 1.0
CZ D:ARG239 4.3 40.2 1.0
OD2 B:ASP388 4.3 26.8 1.0
C15 B:E7Q505 4.5 24.6 1.0
O B:HOH604 4.6 33.5 1.0
O B:HOH756 5.0 52.6 1.0

Reference:

C.V.Simoben, D.Robaa, A.Chakrabarti, K.Schmidtkunz, M.Marek, J.Lancelot, S.Kannan, J.Melesina, T.B.Shaik, R.J.Pierce, C.Romier, M.Jung, W.Sippl. A Novel Class of Schistosoma Mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified By Structure-Based Virtual Screening and in Vitro Testing. Molecules V. 23 2018.
ISSN: ESSN 1420-3049
PubMed: 29498707
DOI: 10.3390/MOLECULES23030566
Page generated: Sat Dec 12 12:59:54 2020

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