Atomistry » Zinc » PDB 6hqy-6hyh » 6hqy
Atomistry »
  Zinc »
    PDB 6hqy-6hyh »
      6hqy »

Zinc in PDB 6hqy: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051, PDB code: 6hqy 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) 42.76 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.877, 71.053, 98.198, 78.06, 75.61, 85.45
R / Rfree (%) 18 / 25.4

Other elements in 6hqy:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051 also contains other interesting chemical elements:

Potassium (K) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051 (pdb code 6hqy). 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 Pci- 34051, PDB code: 6hqy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hqy

Go back to Zinc Binding Sites List in 6hqy
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.3
occ:1.00
OD2 A:ASP285 2.1 16.9 1.0
ND1 A:HIS188 2.1 17.2 1.0
OD1 A:ASP186 2.1 22.5 1.0
O18 A:GKW504 2.3 51.3 1.0
O16 A:GKW504 2.4 72.8 1.0
N17 A:GKW504 2.7 60.6 1.0
C15 A:GKW504 2.7 68.7 1.0
CE1 A:HIS188 2.9 14.9 1.0
CG A:ASP186 2.9 15.0 1.0
OD2 A:ASP186 3.0 12.6 1.0
CG A:ASP285 3.1 16.8 1.0
CG A:HIS188 3.2 19.8 1.0
OD1 A:ASP285 3.6 15.4 1.0
CB A:HIS188 3.7 14.8 1.0
N A:HIS188 3.9 24.0 1.0
NE2 A:HIS188 4.0 19.9 1.0
CA A:GLY339 4.0 28.1 1.0
C14 A:GKW504 4.1 71.5 1.0
CD2 A:HIS188 4.2 19.5 1.0
CB A:ASP186 4.3 9.9 1.0
N A:LEU187 4.4 18.6 1.0
CB A:ASP285 4.4 17.0 1.0
N A:GLY339 4.4 27.5 1.0
CA A:HIS188 4.4 19.0 1.0
NE2 A:HIS141 4.5 28.4 1.0
CB A:LEU187 4.6 14.2 1.0
OH A:TYR341 4.6 38.5 1.0
C A:LEU187 4.8 17.0 1.0
C13 A:GKW504 4.8 69.8 1.0
CE2 A:TYR341 4.8 31.1 1.0
CA A:LEU187 4.8 11.6 1.0
NE2 A:HIS142 4.9 28.2 1.0
C19 A:GKW504 4.9 77.1 1.0
CE1 A:HIS141 4.9 28.4 1.0

Zinc binding site 2 out of 4 in 6hqy

Go back to Zinc Binding Sites List in 6hqy
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.5
occ:1.00
OD2 B:ASP285 1.9 23.9 1.0
OD1 B:ASP186 2.2 6.1 1.0
O18 B:GKW504 2.3 30.5 1.0
ND1 B:HIS188 2.3 10.9 1.0
N17 B:GKW504 2.6 48.0 1.0
O16 B:GKW504 2.8 43.6 1.0
CG B:ASP285 2.9 27.0 1.0
C15 B:GKW504 2.9 50.4 1.0
CG B:ASP186 3.0 29.7 1.0
CE1 B:HIS188 3.1 19.3 1.0
OD2 B:ASP186 3.1 17.9 1.0
OD1 B:ASP285 3.3 28.3 1.0
CG B:HIS188 3.4 19.0 1.0
N B:HIS188 3.8 11.3 1.0
CB B:HIS188 3.8 17.6 1.0
CA B:GLY339 4.0 27.1 1.0
N B:LEU187 4.1 14.6 1.0
CB B:ASP285 4.2 17.8 1.0
C14 B:GKW504 4.2 48.0 1.0
NE2 B:HIS188 4.2 26.8 1.0
CB B:LEU187 4.4 22.0 1.0
CB B:ASP186 4.4 5.8 1.0
CD2 B:HIS188 4.4 24.6 1.0
CA B:HIS188 4.5 13.7 1.0
N B:GLY339 4.5 26.9 1.0
NE2 B:HIS141 4.5 23.0 1.0
CA B:LEU187 4.6 7.7 1.0
C B:LEU187 4.6 8.9 1.0
CE1 B:HIS141 4.7 17.4 1.0
CE2 B:TYR341 4.8 28.1 1.0
C13 B:GKW504 4.8 46.6 1.0
NE2 B:HIS142 4.8 34.0 1.0
C B:ASP186 4.9 18.5 1.0

Zinc binding site 3 out of 4 in 6hqy

Go back to Zinc Binding Sites List in 6hqy
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:24.4
occ:1.00
OD2 C:ASP285 2.1 13.5 1.0
O18 C:GKW504 2.1 42.9 1.0
OD1 C:ASP186 2.2 10.5 1.0
ND1 C:HIS188 2.3 10.6 1.0
N17 C:GKW504 2.6 52.8 1.0
O16 C:GKW504 2.9 53.2 1.0
CG C:ASP186 3.0 20.4 1.0
C15 C:GKW504 3.0 55.9 1.0
CG C:ASP285 3.0 19.1 1.0
OD2 C:ASP186 3.1 11.0 1.0
CE1 C:HIS188 3.1 16.6 1.0
OD1 C:ASP285 3.3 25.9 1.0
CG C:HIS188 3.4 16.0 1.0
CB C:HIS188 3.8 9.0 1.0
N C:HIS188 3.9 14.1 1.0
CA C:GLY339 4.1 13.7 1.0
N C:LEU187 4.2 10.9 1.0
NE2 C:HIS188 4.3 23.0 1.0
CB C:LEU187 4.3 18.1 1.0
C14 C:GKW504 4.4 55.8 1.0
CB C:ASP285 4.4 8.6 1.0
CD2 C:HIS188 4.5 18.9 1.0
CB C:ASP186 4.5 3.4 1.0
NE2 C:HIS141 4.5 21.0 1.0
CA C:HIS188 4.5 9.2 1.0
N C:GLY339 4.5 23.7 1.0
CA C:LEU187 4.6 5.2 1.0
C C:LEU187 4.7 13.8 1.0
NE2 C:HIS142 4.7 41.7 1.0
CE1 C:HIS141 4.8 23.2 1.0
CE1 C:TYR341 4.9 32.6 1.0
C C:ASP186 5.0 13.3 1.0
C13 C:GKW504 5.0 50.0 1.0

Zinc binding site 4 out of 4 in 6hqy

Go back to Zinc Binding Sites List in 6hqy
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Pci- 34051


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 Pci- 34051 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:24.1
occ:1.00
OD2 D:ASP285 2.0 20.6 1.0
OD1 D:ASP186 2.1 24.1 1.0
ND1 D:HIS188 2.1 16.0 1.0
O18 D:GKW504 2.1 38.6 1.0
O16 D:GKW504 2.5 66.5 1.0
N17 D:GKW504 2.5 54.1 1.0
C15 D:GKW504 2.7 63.8 1.0
CE1 D:HIS188 2.9 7.5 1.0
CG D:ASP186 2.9 10.8 1.0
OD2 D:ASP186 3.1 12.3 1.0
CG D:ASP285 3.1 21.4 1.0
CG D:HIS188 3.2 14.0 1.0
OD1 D:ASP285 3.6 23.6 1.0
CB D:HIS188 3.7 14.2 1.0
N D:HIS188 3.9 26.2 1.0
C14 D:GKW504 4.0 68.0 1.0
CA D:GLY339 4.1 32.9 1.0
NE2 D:HIS188 4.1 14.8 1.0
CD2 D:HIS188 4.3 11.4 1.0
CB D:ASP186 4.3 10.8 1.0
CB D:ASP285 4.4 22.6 1.0
CA D:HIS188 4.4 22.4 1.0
N D:LEU187 4.5 18.9 1.0
N D:GLY339 4.5 23.2 1.0
NE2 D:HIS141 4.5 29.4 1.0
C13 D:GKW504 4.7 66.6 1.0
CB D:LEU187 4.8 7.7 1.0
C D:LEU187 4.8 24.3 1.0
NE2 D:HIS142 4.8 34.4 1.0
CA D:LEU187 4.9 14.8 1.0
CE1 D:HIS141 4.9 25.6 1.0
OH D:TYR341 4.9 35.7 1.0
C19 D:GKW504 5.0 74.7 1.0
CE2 D:TYR341 5.0 31.1 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Mon Oct 28 23:13:25 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy