Atomistry » Zinc » PDB 6fju-6ful » 6fu1
Atomistry »
  Zinc »
    PDB 6fju-6ful »
      6fu1 »

Zinc 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
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate, PDB code: 6fu1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fu1

Go back to Zinc Binding Sites List in 6fu1
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501

b:25.4
occ:1.00
OD1 A:ASP186 1.9 22.1 1.0
OD2 A:ASP285 2.0 20.8 1.0
ND1 A:HIS188 2.1 20.9 1.0
O09 A:E7Q504 2.2 68.6 1.0
O07 A:E7Q504 2.2 35.3 1.0
CG A:ASP186 2.8 20.6 1.0
N08 A:E7Q504 2.8 70.5 1.0
C06 A:E7Q504 2.9 56.7 1.0
CE1 A:HIS188 3.0 26.4 1.0
OD2 A:ASP186 3.0 19.5 1.0
CG A:ASP285 3.0 23.5 1.0
CG A:HIS188 3.2 19.0 1.0
OD1 A:ASP285 3.4 21.4 1.0
CB A:HIS188 3.6 16.4 1.0
C10 A:E7Q504 3.7 78.8 1.0
N A:HIS188 3.9 17.8 1.0
CA A:GLY339 4.1 20.1 1.0
NE2 A:HIS188 4.1 22.1 1.0
CB A:ASP186 4.2 20.6 1.0
CD2 A:HIS188 4.3 21.3 1.0
C05 A:E7Q504 4.3 62.7 1.0
N A:LEU187 4.3 17.1 1.0
CB A:ASP285 4.3 20.3 1.0
C11 A:E7Q504 4.4 78.4 1.0
C02 A:E7Q504 4.4 78.7 1.0
CA A:HIS188 4.4 15.8 1.0
NE2 A:HIS141 4.4 21.1 1.0
N A:GLY339 4.4 19.5 1.0
C03 A:E7Q504 4.5 76.0 1.0
OH A:TYR341 4.6 30.7 1.0
CB A:LEU187 4.6 17.1 1.0
C A:LEU187 4.7 18.5 1.0
CE2 A:TYR341 4.7 25.9 1.0
CA A:LEU187 4.8 14.6 1.0
CE1 A:HIS141 4.8 20.2 1.0
NE2 A:HIS142 4.9 19.5 1.0
C A:ASP186 5.0 17.1 1.0
C04 A:E7Q504 5.0 67.6 1.0
CA A:ASP186 5.0 18.5 1.0

Zinc binding site 2 out of 4 in 6fu1

Go back to Zinc Binding Sites List in 6fu1
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn501

b:25.4
occ:1.00
OD1 B:ASP186 1.9 19.1 1.0
OD2 B:ASP285 2.0 18.8 1.0
N08 B:E7Q504 2.1 35.0 1.0
ND1 B:HIS188 2.1 17.2 1.0
O07 B:E7Q504 2.1 36.6 1.0
C06 B:E7Q504 2.4 38.0 1.0
O09 B:E7Q504 2.8 48.4 1.0
CG B:ASP186 2.8 19.2 1.0
CE1 B:HIS188 2.9 22.4 1.0
CG B:ASP285 3.0 21.7 1.0
OD2 B:ASP186 3.1 18.4 1.0
CG B:HIS188 3.2 16.1 1.0
OD1 B:ASP285 3.4 17.9 1.0
CB B:HIS188 3.7 16.3 1.0
N B:HIS188 3.8 16.3 1.0
C05 B:E7Q504 3.9 45.2 1.0
CA B:GLY339 4.0 17.4 1.0
NE2 B:HIS188 4.1 20.6 1.0
CB B:ASP186 4.2 18.2 1.0
CD2 B:HIS188 4.3 23.2 1.0
N B:LEU187 4.3 14.9 1.0
CB B:ASP285 4.3 16.3 1.0
OH B:TYR341 4.4 38.8 1.0
CA B:HIS188 4.4 17.6 1.0
NE2 B:HIS141 4.5 17.4 1.0
N B:GLY339 4.5 20.7 1.0
CB B:LEU187 4.5 16.8 1.0
CE1 B:TYR341 4.7 28.2 1.0
C B:LEU187 4.7 15.2 1.0
C04 B:E7Q504 4.7 59.8 1.0
CA B:LEU187 4.7 15.2 1.0
CE1 B:HIS141 4.8 18.6 1.0
NE2 B:HIS142 4.9 22.1 1.0
C B:ASP186 5.0 16.9 1.0
CA B:ASP186 5.0 16.9 1.0

Zinc binding site 3 out of 4 in 6fu1

Go back to Zinc Binding Sites List in 6fu1
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
C:Zn501

b:24.6
occ:1.00
OD1 C:ASP186 1.9 16.2 1.0
OD2 C:ASP285 2.0 19.1 1.0
ND1 C:HIS188 2.1 21.4 1.0
CG C:ASP186 2.8 18.1 1.0
CE1 C:HIS188 3.0 25.0 1.0
CG C:ASP285 3.0 19.7 1.0
OD2 C:ASP186 3.1 20.6 1.0
CG C:HIS188 3.2 17.2 1.0
OD1 C:ASP285 3.4 20.0 1.0
CB C:HIS188 3.7 14.3 1.0
N C:HIS188 3.8 15.6 1.0
CA C:GLY339 4.0 17.6 1.0
NE2 C:HIS188 4.1 21.2 1.0
CB C:ASP186 4.2 15.9 1.0
N C:LEU187 4.2 15.8 1.0
CD2 C:HIS188 4.3 21.2 1.0
CB C:ASP285 4.3 18.5 1.0
CA C:HIS188 4.4 16.1 1.0
CB C:LEU187 4.4 18.3 1.0
N C:GLY339 4.4 18.6 1.0
NE2 C:HIS141 4.5 18.3 1.0
OH C:TYR341 4.6 33.3 1.0
CE1 C:TYR341 4.7 24.8 1.0
C C:LEU187 4.7 17.4 1.0
CA C:LEU187 4.7 15.8 1.0
NE2 C:HIS142 4.8 21.5 1.0
CE1 C:HIS141 4.8 21.4 1.0
C C:ASP186 4.9 17.7 1.0
CA C:ASP186 5.0 15.1 1.0

Zinc binding site 4 out of 4 in 6fu1

Go back to Zinc Binding Sites List in 6fu1
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A N- Alkyl Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:25.2
occ:1.00
OD1 D:ASP186 1.9 19.4 1.0
OD2 D:ASP285 2.0 24.2 1.0
ND1 D:HIS188 2.1 23.8 1.0
CG D:ASP186 2.8 21.4 1.0
CE1 D:HIS188 3.0 24.4 1.0
OD2 D:ASP186 3.0 21.7 1.0
CG D:ASP285 3.0 22.8 1.0
CG D:HIS188 3.2 23.2 1.0
OD1 D:ASP285 3.4 22.3 1.0
CB D:HIS188 3.6 17.4 1.0
N D:HIS188 3.8 18.3 1.0
CA D:GLY339 4.1 20.7 1.0
NE2 D:HIS188 4.2 22.8 1.0
CB D:ASP186 4.2 18.2 1.0
N D:LEU187 4.2 17.2 1.0
CD2 D:HIS188 4.3 23.5 1.0
CB D:ASP285 4.3 20.7 1.0
CA D:HIS188 4.4 15.6 1.0
NE2 D:HIS141 4.4 22.4 1.0
N D:GLY339 4.4 24.1 1.0
CB D:LEU187 4.5 16.6 1.0
OH D:TYR341 4.6 41.8 1.0
C D:LEU187 4.7 20.4 1.0
CA D:LEU187 4.7 17.1 1.0
CE1 D:TYR341 4.7 29.2 1.0
CE1 D:HIS141 4.8 20.9 1.0
NE2 D:HIS142 4.8 21.2 1.0
C D:ASP186 4.9 18.7 1.0
CA D:ASP186 5.0 19.8 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: Wed Dec 16 11:49:25 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy