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Zinc in PDB 6gx3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1, PDB code: 6gx3 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) 47.89 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.449, 70.670, 98.413, 75.71, 78.40, 85.55
R / Rfree (%) 18.9 / 24

Other elements in 6gx3:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1 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 1 (pdb code 6gx3). 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 1, PDB code: 6gx3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6gx3

Go back to Zinc Binding Sites List in 6gx3
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:37.4
occ:1.00
 OD1 A:ASP186 1.9 34.5 1.0
OD2 A:ASP285 2.0 32.5 1.0
O04 A:FF2504 2.2 47.4 1.0
ND1 A:HIS188 2.3 42.1 1.0
O01 A:FF2504 2.5 64.1 1.0
N03 A:FF2504 2.5 58.5 1.0
C02 A:FF2504 2.7 63.8 1.0
CG A:ASP186 2.7 26.0 1.0
OD2 A:ASP186 2.8 24.8 1.0
CG A:ASP285 3.0 32.2 1.0
CE1 A:HIS188 3.2 40.5 1.0
CG A:HIS188 3.3 34.4 1.0
OD1 A:ASP285 3.4 32.8 1.0
CB A:HIS188 3.6 25.4 1.0
N A:HIS188 3.8 30.1 1.0
C05 A:FF2504 4.0 60.0 1.0
CA A:GLY339 4.1 27.2 1.0
CB A:ASP186 4.2 22.5 1.0
N A:LEU187 4.2 28.5 1.0
NE2 A:HIS188 4.3 39.1 1.0
CA A:HIS188 4.3 27.8 1.0
CB A:ASP285 4.4 24.9 1.0
CD2 A:HIS188 4.4 30.9 1.0
N A:GLY339 4.5 34.1 1.0
NE2 A:HIS141 4.5 27.6 1.0
CB A:LEU187 4.5 33.6 1.0
C A:LEU187 4.7 31.8 1.0
CA A:LEU187 4.7 35.7 1.0
OH A:TYR341 4.7 48.3 1.0
C06 A:FF2504 4.8 54.8 1.0
NE2 A:HIS142 4.8 33.6 1.0
C A:ASP186 4.9 28.2 1.0
CE2 A:TYR341 4.9 40.6 1.0
CE1 A:HIS141 4.9 22.3 1.0
CA A:ASP186 4.9 24.5 1.0

Zinc binding site 2 out of 4 in 6gx3

Go back to Zinc Binding Sites List in 6gx3
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:36.5
occ:1.00
 OD2 B:ASP285 2.0 28.9 1.0
OD1 B:ASP186 2.1 26.5 1.0
ND1 B:HIS188 2.3 27.1 1.0
O04 B:FF2504 2.5 39.3 1.0
O01 B:FF2504 2.5 53.6 1.0
N03 B:FF2504 2.8 42.7 1.0
CG B:ASP186 2.8 26.2 1.0
C02 B:FF2504 2.8 51.4 1.0
OD2 B:ASP186 3.0 31.2 1.0
CG B:ASP285 3.0 30.3 1.0
CE1 B:HIS188 3.2 30.1 1.0
OD1 B:ASP285 3.2 28.5 1.0
CG B:HIS188 3.3 21.4 1.0
CB B:HIS188 3.6 19.8 1.0
N B:HIS188 3.9 25.5 1.0
CA B:GLY339 4.0 30.2 1.0
C05 B:FF2504 4.1 49.3 1.0
CB B:ASP186 4.3 25.0 1.0
CB B:ASP285 4.3 17.4 1.0
N B:LEU187 4.3 26.3 1.0
NE2 B:HIS188 4.3 34.5 1.0
CA B:HIS188 4.4 18.2 1.0
CD2 B:HIS188 4.4 28.7 1.0
NE2 B:HIS141 4.4 29.9 1.0
CB B:LEU187 4.4 26.2 1.0
N B:GLY339 4.5 28.6 1.0
C B:LEU187 4.7 28.8 1.0
CA B:LEU187 4.7 25.9 1.0
CE1 B:HIS141 4.8 24.7 1.0
CE1 B:TYR341 4.8 42.7 1.0
OH B:TYR341 4.8 44.5 1.0
C B:ASP186 4.9 21.5 1.0
C06 B:FF2504 4.9 52.6 1.0
NE2 B:HIS142 5.0 35.5 1.0

Zinc binding site 3 out of 4 in 6gx3

Go back to Zinc Binding Sites List in 6gx3
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:35.4
occ:1.00
 OD1 C:ASP186 1.9 22.5 1.0
OD2 C:ASP285 2.1 27.2 1.0
ND1 C:HIS188 2.2 27.9 1.0
O01 C:FF2504 2.5 42.8 1.0
O04 C:FF2504 2.5 41.3 1.0
C02 C:FF2504 2.7 46.5 1.0
N03 C:FF2504 2.7 36.8 1.0
CG C:ASP186 2.8 19.7 1.0
CE1 C:HIS188 3.0 31.7 1.0
OD2 C:ASP186 3.1 28.4 1.0
CG C:ASP285 3.1 34.7 1.0
CG C:HIS188 3.2 31.6 1.0
OD1 C:ASP285 3.3 31.8 1.0
CB C:HIS188 3.7 27.4 1.0
N C:HIS188 3.8 32.0 1.0
C05 C:FF2504 4.0 47.8 1.0
NE2 C:HIS188 4.1 31.9 1.0
CA C:GLY339 4.1 23.6 1.0
CB C:ASP186 4.2 26.3 1.0
CD2 C:HIS188 4.2 33.4 1.0
N C:LEU187 4.3 18.0 1.0
CB C:LEU187 4.4 18.6 1.0
CA C:HIS188 4.4 29.5 1.0
CB C:ASP285 4.4 20.5 1.0
NE2 C:HIS141 4.5 26.6 1.0
N C:GLY339 4.5 29.0 1.0
C C:LEU187 4.6 29.8 1.0
CA C:LEU187 4.7 19.7 1.0
OH C:TYR341 4.7 44.0 1.0
C06 C:FF2504 4.8 45.6 1.0
CE2 C:TYR341 4.8 34.9 1.0
CE1 C:HIS141 4.9 26.5 1.0
NE2 C:HIS142 4.9 31.7 1.0
C C:ASP186 4.9 26.7 1.0
CA C:ASP186 5.0 24.8 1.0

Zinc binding site 4 out of 4 in 6gx3

Go back to Zinc Binding Sites List in 6gx3
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:36.3
occ:1.00
 OD1 D:ASP186 2.0 33.2 1.0
OD2 D:ASP285 2.1 32.2 1.0
O01 D:FF2504 2.3 50.2 1.0
ND1 D:HIS188 2.3 36.9 1.0
O04 D:FF2504 2.4 38.3 1.0
C02 D:FF2504 2.6 50.4 1.0
N03 D:FF2504 2.6 45.5 1.0
CG D:ASP186 2.8 26.1 1.0
OD2 D:ASP186 3.0 31.1 1.0
CG D:ASP285 3.0 33.4 1.0
CE1 D:HIS188 3.2 39.4 1.0
OD1 D:ASP285 3.3 27.8 1.0
CG D:HIS188 3.3 30.0 1.0
CB D:HIS188 3.7 20.7 1.0
N D:HIS188 3.9 18.9 1.0
C05 D:FF2504 3.9 49.8 1.0
CA D:GLY339 4.1 26.7 1.0
CB D:ASP186 4.2 28.2 1.0
NE2 D:HIS188 4.3 41.2 1.0
CB D:ASP285 4.4 24.8 1.0
CD2 D:HIS188 4.4 29.8 1.0
N D:LEU187 4.4 25.3 1.0
CA D:HIS188 4.4 22.9 1.0
NE2 D:HIS141 4.4 32.7 1.0
N D:GLY339 4.5 31.3 1.0
CB D:LEU187 4.6 21.8 1.0
OH D:TYR341 4.7 39.2 1.0
C D:LEU187 4.8 28.3 1.0
C06 D:FF2504 4.8 52.5 1.0
CA D:LEU187 4.8 26.5 1.0
CE1 D:HIS141 4.8 33.4 1.0
CE2 D:TYR341 4.8 33.9 1.0
NE2 D:HIS142 4.9 31.0 1.0
C D:ASP186 5.0 30.0 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 22:02:08 2024

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