Zinc in PDB 6hsg: Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149, PDB code: 6hsg 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) 43.48 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.800, 70.830, 98.350, 78.31, 75.80, 85.98
R / Rfree (%) 20.7 / 25.3

Other elements in 6hsg:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149 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 H292M Mutant Complexed with Ncc-149 (pdb code 6hsg). 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 H292M Mutant Complexed with Ncc-149, PDB code: 6hsg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hsg

Go back to Zinc Binding Sites List in 6hsg
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.6
occ:1.00
 OD2 A:ASP285 2.0 20.1 1.0
OD1 A:ASP186 2.1 19.5 1.0
ND1 A:HIS188 2.2 15.2 1.0
O21 A:GM5504 2.3 37.0 1.0
O20 A:GM5504 2.5 27.8 1.0
C18 A:GM5504 2.8 44.0 1.0
N19 A:GM5504 2.9 44.8 1.0
CG A:ASP186 2.9 13.4 1.0
CG A:ASP285 3.0 15.3 1.0
OD2 A:ASP186 3.0 17.4 1.0
CE1 A:HIS188 3.1 17.0 1.0
CG A:HIS188 3.3 17.6 1.0
OD1 A:ASP285 3.4 18.1 1.0
CB A:HIS188 3.6 9.5 1.0
N A:HIS188 3.9 20.0 1.0
C13 A:GM5504 4.0 40.9 1.0
CA A:GLY339 4.1 14.9 1.0
NE2 A:HIS188 4.3 23.3 1.0
CB A:ASP186 4.3 6.8 1.0
CB A:ASP285 4.4 20.7 1.0
N A:LEU187 4.4 17.0 1.0
CD2 A:HIS188 4.4 21.0 1.0
CA A:HIS188 4.4 16.3 1.0
OH A:TYR341 4.4 26.2 1.0
N A:GLY339 4.5 22.3 1.0
C14 A:GM5504 4.5 38.5 1.0
NE2 A:HIS141 4.6 24.5 1.0
CB A:LEU187 4.6 16.8 1.0
CE2 A:TYR341 4.7 33.3 1.0
C A:LEU187 4.7 19.7 1.0
CA A:LEU187 4.8 18.7 1.0

Zinc binding site 2 out of 4 in 6hsg

Go back to Zinc Binding Sites List in 6hsg
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.2
occ:1.00
 OD2 B:ASP285 1.9 11.5 1.0
OD1 B:ASP186 2.0 13.7 1.0
ND1 B:HIS188 2.2 15.6 1.0
O21 B:GM5504 2.3 37.6 1.0
O20 B:GM5504 2.6 26.3 1.0
C18 B:GM5504 2.7 44.9 1.0
N19 B:GM5504 2.8 46.2 1.0
CG B:ASP186 2.9 17.5 1.0
CG B:ASP285 2.9 23.8 1.0
CE1 B:HIS188 3.0 22.3 1.0
OD2 B:ASP186 3.1 19.3 1.0
CG B:HIS188 3.3 16.2 1.0
OD1 B:ASP285 3.3 24.8 1.0
CB B:HIS188 3.7 14.4 1.0
N B:HIS188 3.8 18.7 1.0
C13 B:GM5504 3.9 43.6 1.0
NE2 B:HIS188 4.1 20.2 1.0
CA B:GLY339 4.2 25.9 1.0
N B:LEU187 4.2 15.5 1.0
CB B:ASP285 4.3 8.2 1.0
CB B:ASP186 4.3 15.3 1.0
CD2 B:HIS188 4.3 18.7 1.0
CB B:LEU187 4.3 15.2 1.0
C14 B:GM5504 4.4 45.1 1.0
CA B:HIS188 4.4 11.8 1.0
OH B:TYR341 4.5 20.9 1.0
NE2 B:HIS141 4.6 16.9 1.0
CE2 B:TYR341 4.6 26.7 1.0
CA B:LEU187 4.6 16.7 1.0
N B:GLY339 4.6 27.4 1.0
C B:LEU187 4.6 15.8 1.0
CE1 B:HIS141 4.8 19.0 1.0
C12 B:GM5504 4.9 32.9 1.0
C B:ASP186 4.9 15.4 1.0

Zinc binding site 3 out of 4 in 6hsg

Go back to Zinc Binding Sites List in 6hsg
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:22.1
occ:1.00
 OD2 C:ASP285 1.9 13.5 1.0
OD1 C:ASP186 2.0 15.4 1.0
ND1 C:HIS188 2.2 17.4 1.0
O21 C:GM5504 2.4 38.5 1.0
O20 C:GM5504 2.6 23.7 1.0
C18 C:GM5504 2.6 41.8 1.0
N19 C:GM5504 2.7 39.0 1.0
CG C:ASP186 2.9 11.5 1.0
CG C:ASP285 2.9 22.2 1.0
CE1 C:HIS188 3.1 21.3 1.0
OD2 C:ASP186 3.1 16.5 1.0
CG C:HIS188 3.3 18.2 1.0
OD1 C:ASP285 3.3 26.3 1.0
CB C:HIS188 3.7 20.1 1.0
N C:HIS188 3.8 15.8 1.0
C13 C:GM5504 3.8 38.7 1.0
CA C:GLY339 4.1 22.1 1.0
N C:LEU187 4.2 16.0 1.0
NE2 C:HIS188 4.2 20.6 1.0
CB C:ASP285 4.3 11.9 1.0
CB C:ASP186 4.3 14.4 1.0
CD2 C:HIS188 4.3 21.5 1.0
C14 C:GM5504 4.4 42.2 1.0
CB C:LEU187 4.4 12.1 1.0
CA C:HIS188 4.4 13.6 1.0
O C:HOH663 4.5 35.8 1.0
N C:GLY339 4.5 26.8 1.0
NE2 C:HIS141 4.5 18.1 1.0
OH C:TYR341 4.6 21.7 1.0
CA C:LEU187 4.6 14.7 1.0
C C:LEU187 4.6 18.2 1.0
CE2 C:TYR341 4.8 23.7 1.0
C12 C:GM5504 4.8 41.1 1.0
CE1 C:HIS141 4.9 12.9 1.0
C C:ASP186 4.9 13.1 1.0
NE2 C:HIS142 5.0 15.2 1.0

Zinc binding site 4 out of 4 in 6hsg

Go back to Zinc Binding Sites List in 6hsg
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 H292M Mutant Complexed with Ncc-149


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 H292M Mutant Complexed with Ncc-149 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:22.3
occ:1.00
 OD2 D:ASP285 1.9 20.3 1.0
OD1 D:ASP186 2.0 24.6 1.0
ND1 D:HIS188 2.2 19.4 1.0
O21 D:GM5504 2.3 36.8 1.0
O20 D:GM5504 2.4 27.7 1.0
C18 D:GM5504 2.7 47.4 1.0
N19 D:GM5504 2.8 45.2 1.0
CG D:ASP186 2.8 16.4 1.0
CG D:ASP285 2.9 19.3 1.0
OD2 D:ASP186 3.0 21.0 1.0
CE1 D:HIS188 3.2 19.8 1.0
OD1 D:ASP285 3.2 19.2 1.0
CG D:HIS188 3.2 15.6 1.0
CB D:HIS188 3.5 11.6 1.0
N D:HIS188 3.8 19.3 1.0
C13 D:GM5504 3.9 49.7 1.0
CA D:GLY339 4.2 21.8 1.0
CB D:ASP186 4.2 12.6 1.0
NE2 D:HIS188 4.3 19.1 1.0
CA D:HIS188 4.3 17.4 1.0
CB D:ASP285 4.3 13.2 1.0
N D:LEU187 4.3 13.8 1.0
CD2 D:HIS188 4.3 16.3 1.0
OH D:TYR341 4.5 24.8 1.0
C14 D:GM5504 4.5 52.9 1.0
CB D:LEU187 4.5 10.7 1.0
N D:GLY339 4.5 21.6 1.0
NE2 D:HIS141 4.6 25.6 1.0
C D:LEU187 4.7 25.7 1.0
CE2 D:TYR341 4.7 27.4 1.0
CA D:LEU187 4.7 14.5 1.0
C12 D:GM5504 4.9 46.6 1.0
C D:ASP186 5.0 18.3 1.0
NE2 D:HIS142 5.0 20.2 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: Wed Dec 16 11:58:00 2020

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