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Zinc in PDB 6gxw: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4, PDB code: 6gxw 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) 48.13 / 2.07
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.800, 70.990, 98.200, 75.58, 77.93, 85.56
R / Rfree (%) 18.9 / 24.7

Other elements in 6gxw:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 4 also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 8 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6gxw

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


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:26.7
occ:1.00
 OD2 A:ASP285 2.0 20.6 1.0
OD1 A:ASP186 2.0 16.5 1.0
ND1 A:HIS188 2.1 23.2 1.0
O2 A:FGN504 2.4 38.1 1.0
O A:FGN504 2.5 66.1 1.0
CG A:ASP186 2.8 19.2 1.0
CE1 A:HIS188 2.9 34.2 1.0
C A:FGN504 3.0 66.7 1.0
OD2 A:ASP186 3.0 19.5 1.0
N A:FGN504 3.0 57.6 1.0
CG A:ASP285 3.0 25.2 1.0
CG A:HIS188 3.2 26.9 1.0
OD1 A:ASP285 3.4 25.2 1.0
CB A:HIS188 3.7 27.7 1.0
N A:HIS188 3.9 21.0 1.0
NE2 A:HIS188 4.1 33.2 1.0
CA A:GLY339 4.2 19.2 1.0
CB A:ASP186 4.2 12.9 1.0
C1 A:FGN504 4.3 73.5 1.0
CD2 A:HIS188 4.3 26.1 1.0
CB A:ASP285 4.3 19.5 1.0
N A:LEU187 4.4 20.0 1.0
CA A:HIS188 4.4 24.1 1.0
N A:GLY339 4.6 18.5 1.0
CB A:LEU187 4.6 15.3 1.0
NE2 A:HIS141 4.6 25.7 1.0
OH A:TYR341 4.7 31.6 1.0
CE2 A:TYR341 4.7 25.8 1.0
C A:LEU187 4.8 25.2 1.0
CA A:LEU187 4.8 21.4 1.0
NE2 A:HIS142 4.9 22.4 1.0
C2 A:FGN504 4.9 83.5 1.0
CE1 A:HIS141 5.0 32.3 1.0
C A:ASP186 5.0 19.9 1.0

Zinc binding site 2 out of 4 in 6gxw

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


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:24.5
occ:1.00
 OD1 B:ASP186 2.1 13.1 1.0
O2 B:FGN504 2.1 21.2 1.0
OD2 B:ASP285 2.1 21.0 1.0
ND1 B:HIS188 2.1 26.0 1.0
O B:FGN504 2.5 50.6 1.0
CE1 B:HIS188 2.8 28.8 1.0
CG B:ASP186 2.8 17.7 1.0
N B:FGN504 2.9 46.2 1.0
C B:FGN504 2.9 52.9 1.0
CG B:ASP285 3.0 23.7 1.0
OD2 B:ASP186 3.0 17.7 1.0
OD1 B:ASP285 3.2 20.4 1.0
CG B:HIS188 3.2 30.9 1.0
CB B:HIS188 3.8 25.2 1.0
N B:HIS188 3.9 25.9 1.0
NE2 B:HIS188 4.0 41.2 1.0
CD2 B:HIS188 4.2 42.7 1.0
N B:LEU187 4.2 26.3 1.0
CA B:GLY339 4.2 28.9 1.0
CB B:ASP186 4.3 19.9 1.0
C1 B:FGN504 4.3 53.8 1.0
CB B:ASP285 4.3 20.7 1.0
CB B:LEU187 4.4 18.9 1.0
CA B:HIS188 4.5 26.9 1.0
NE2 B:HIS141 4.5 23.6 1.0
CE2 B:TYR341 4.6 31.5 1.0
CA B:LEU187 4.6 21.0 1.0
N B:GLY339 4.6 16.7 1.0
C B:LEU187 4.6 27.1 1.0
OH B:TYR341 4.7 34.2 1.0
O B:HOH711 4.7 39.4 1.0
CE1 B:HIS141 4.9 20.2 1.0
C B:ASP186 4.9 22.2 1.0

Zinc binding site 3 out of 4 in 6gxw

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


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:22.8
occ:1.00
 OD2 C:ASP285 1.9 16.1 1.0
OD1 C:ASP186 2.0 15.6 1.0
ND1 C:HIS188 2.1 19.5 1.0
O2 C:FGN805 2.3 41.6 1.0
O C:FGN805 2.4 48.5 1.0
CG C:ASP186 2.8 18.0 1.0
CG C:ASP285 2.9 25.9 1.0
CE1 C:HIS188 2.9 21.4 1.0
C C:FGN805 2.9 58.2 1.0
OD2 C:ASP186 3.0 24.6 1.0
N C:FGN805 3.0 55.4 1.0
CG C:HIS188 3.2 23.5 1.0
OD1 C:ASP285 3.3 20.6 1.0
CB C:HIS188 3.7 12.6 1.0
N C:HIS188 3.9 20.0 1.0
NE2 C:HIS188 4.1 32.3 1.0
CA C:GLY339 4.2 25.2 1.0
CB C:ASP285 4.2 11.7 1.0
CB C:ASP186 4.2 18.6 1.0
CD2 C:HIS188 4.2 31.0 1.0
N C:LEU187 4.3 21.3 1.0
C1 C:FGN805 4.3 66.1 1.0
CA C:HIS188 4.4 25.2 1.0
CB C:LEU187 4.5 23.0 1.0
NE2 C:HIS141 4.6 21.3 1.0
OH C:TYR341 4.6 26.8 1.0
C C:LEU187 4.7 19.8 1.0
N C:GLY339 4.7 26.6 1.0
CE2 C:TYR341 4.7 34.6 1.0
CA C:LEU187 4.7 16.4 1.0
CE1 C:HIS141 4.9 25.6 1.0
C C:ASP186 4.9 17.5 1.0
CA C:ASP186 5.0 20.5 1.0
NE2 C:HIS142 5.0 22.3 1.0

Zinc binding site 4 out of 4 in 6gxw

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


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 An Hydroxamate 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:28.2
occ:1.00
 OD2 D:ASP285 2.1 20.8 1.0
ND1 D:HIS188 2.2 22.4 1.0
OD1 D:ASP186 2.2 20.1 1.0
O D:FGN504 2.5 38.6 1.0
O2 D:FGN504 2.6 47.4 1.0
N D:FGN504 2.7 49.2 1.0
C D:FGN504 2.8 47.9 1.0
CG D:ASP186 2.9 26.6 1.0
OD2 D:ASP186 2.9 28.4 1.0
CE1 D:HIS188 3.0 18.2 1.0
CG D:ASP285 3.1 26.0 1.0
CG D:HIS188 3.3 18.1 1.0
OD1 D:ASP285 3.5 26.9 1.0
CB D:HIS188 3.7 16.4 1.0
N D:HIS188 3.9 15.1 1.0
CA D:GLY339 4.1 25.0 1.0
C1 D:FGN504 4.1 56.6 1.0
NE2 D:HIS188 4.2 24.2 1.0
CD2 D:HIS188 4.3 19.9 1.0
N D:LEU187 4.3 20.1 1.0
CB D:ASP186 4.4 21.8 1.0
CB D:ASP285 4.4 21.6 1.0
CA D:HIS188 4.5 22.1 1.0
N D:GLY339 4.5 23.5 1.0
NE2 D:HIS141 4.6 22.8 1.0
OH D:TYR341 4.6 32.9 1.0
CE2 D:TYR341 4.7 36.4 1.0
CB D:LEU187 4.7 20.4 1.0
C D:LEU187 4.8 21.3 1.0
CA D:LEU187 4.8 19.3 1.0
C2 D:FGN504 4.9 69.0 1.0
NE2 D:HIS142 4.9 22.0 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: Mon Oct 28 22:03:58 2024

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