Zinc in PDB 6gxu: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3, PDB code: 6gxu 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) 46.55 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.420, 70.460, 97.910, 77.96, 75.94, 85.97
R / Rfree (%) 20.1 / 24.8

Other elements in 6gxu:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3 also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6gxu

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


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

b:29.4
occ:1.00
 OD1 A:ASP186 2.0 18.4 1.0
OD2 A:ASP285 2.0 23.8 1.0
ND1 A:HIS188 2.1 19.3 1.0
O1 A:FG8504 2.4 42.6 1.0
O A:FG8504 2.5 37.1 1.0
N A:FG8504 2.5 39.3 1.0
C A:FG8504 2.8 34.8 1.0
CG A:ASP186 2.8 32.7 1.0
CE1 A:HIS188 2.9 16.5 1.0
OD2 A:ASP186 3.0 22.4 1.0
CG A:ASP285 3.0 24.1 1.0
CG A:HIS188 3.2 21.4 1.0
OD1 A:ASP285 3.3 28.3 1.0
CB A:HIS188 3.7 16.6 1.0
N A:HIS188 3.8 17.0 1.0
NE2 A:HIS188 4.0 26.0 1.0
CA A:GLY339 4.0 25.8 1.0
C1 A:FG8504 4.1 25.4 1.0
CD2 A:HIS188 4.2 31.8 1.0
CB A:ASP186 4.2 28.9 1.0
N A:LEU187 4.3 29.2 1.0
CB A:ASP285 4.3 24.1 1.0
CA A:HIS188 4.4 18.6 1.0
N A:GLY339 4.4 24.5 1.0
NE2 A:HIS141 4.5 32.2 1.0
CB A:LEU187 4.6 19.7 1.0
OH A:TYR341 4.6 30.5 1.0
C A:LEU187 4.7 22.7 1.0
CE2 A:TYR341 4.7 28.0 1.0
CA A:LEU187 4.7 23.4 1.0
NE2 A:HIS142 4.9 18.9 1.0
CE1 A:HIS141 4.9 27.4 1.0
C A:ASP186 4.9 33.0 1.0
C2 A:FG8504 5.0 30.5 1.0
CA A:ASP186 5.0 25.4 1.0

Zinc binding site 2 out of 4 in 6gxu

Go back to Zinc Binding Sites List in 6gxu
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with An Hydroxamate 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:28.3
occ:1.00
 OD1 B:ASP186 1.9 26.9 1.0
OD2 B:ASP285 2.0 30.5 1.0
ND1 B:HIS188 2.1 25.2 1.0
O1 B:FG8505 2.2 34.3 1.0
O B:FG8505 2.5 34.2 1.0
N B:FG8505 2.6 36.6 1.0
C B:FG8505 2.7 42.7 1.0
CG B:ASP186 2.8 24.6 1.0
CE1 B:HIS188 2.9 24.2 1.0
OD2 B:ASP186 3.0 23.8 1.0
CG B:ASP285 3.0 32.5 1.0
CG B:HIS188 3.2 31.0 1.0
OD1 B:ASP285 3.3 25.2 1.0
CB B:HIS188 3.6 21.2 1.0
N B:HIS188 3.9 18.3 1.0
CA B:GLY339 4.0 25.3 1.0
C1 B:FG8505 4.0 38.1 1.0
NE2 B:HIS188 4.1 25.9 1.0
CB B:ASP186 4.2 25.7 1.0
N B:LEU187 4.2 17.6 1.0
CD2 B:HIS188 4.2 28.6 1.0
CB B:ASP285 4.3 23.1 1.0
CB B:LEU187 4.4 19.0 1.0
CA B:HIS188 4.4 30.0 1.0
N B:GLY339 4.4 21.1 1.0
NE2 B:HIS141 4.5 27.0 1.0
CA B:LEU187 4.7 24.0 1.0
OH B:TYR341 4.7 36.1 1.0
C B:LEU187 4.7 24.8 1.0
CE2 B:TYR341 4.8 25.8 1.0
CE1 B:HIS141 4.8 31.4 1.0
C2 B:FG8505 4.9 27.8 1.0
C B:ASP186 4.9 19.8 1.0
CA B:ASP186 5.0 21.9 1.0
NE2 B:HIS142 5.0 24.4 1.0

Zinc binding site 3 out of 4 in 6gxu

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


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

b:30.7
occ:1.00
 OD2 C:ASP285 2.0 24.2 1.0
OD1 C:ASP186 2.0 21.6 1.0
ND1 C:HIS188 2.1 24.8 1.0
O1 C:FG8504 2.3 30.0 1.0
O C:FG8504 2.5 32.4 1.0
N C:FG8504 2.6 34.4 1.0
C C:FG8504 2.7 33.6 1.0
CE1 C:HIS188 2.9 26.8 1.0
CG C:ASP186 2.9 26.1 1.0
CG C:ASP285 2.9 24.8 1.0
OD2 C:ASP186 3.2 21.1 1.0
OD1 C:ASP285 3.2 24.1 1.0
CG C:HIS188 3.2 18.7 1.0
CB C:HIS188 3.7 24.0 1.0
N C:HIS188 3.9 24.5 1.0
NE2 C:HIS188 4.1 27.5 1.0
C1 C:FG8504 4.1 33.6 1.0
CA C:GLY339 4.2 22.1 1.0
CD2 C:HIS188 4.3 29.4 1.0
CB C:ASP285 4.3 21.6 1.0
CB C:ASP186 4.3 17.9 1.0
N C:LEU187 4.3 21.0 1.0
NE2 C:HIS141 4.4 25.3 1.0
CA C:HIS188 4.4 22.3 1.0
N C:GLY339 4.5 22.2 1.0
OH C:TYR341 4.5 34.8 1.0
CB C:LEU187 4.6 19.9 1.0
CE1 C:HIS141 4.7 29.0 1.0
C C:LEU187 4.7 26.2 1.0
CE2 C:TYR341 4.8 28.1 1.0
CA C:LEU187 4.8 20.6 1.0
NE2 C:HIS142 4.9 23.9 1.0
C2 C:FG8504 4.9 27.7 1.0
C C:ASP186 5.0 18.9 1.0

Zinc binding site 4 out of 4 in 6gxu

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


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

b:32.6
occ:1.00
 OD2 D:ASP285 2.0 30.9 1.0
OD1 D:ASP186 2.0 26.0 1.0
ND1 D:HIS188 2.0 20.0 1.0
O1 D:FG8504 2.4 34.3 1.0
O D:FG8504 2.5 50.8 1.0
N D:FG8504 2.5 42.1 1.0
C D:FG8504 2.7 48.1 1.0
CG D:ASP186 2.9 29.0 1.0
CE1 D:HIS188 2.9 28.8 1.0
OD2 D:ASP186 3.0 30.2 1.0
CG D:ASP285 3.0 33.3 1.0
CG D:HIS188 3.1 26.3 1.0
OD1 D:ASP285 3.3 28.9 1.0
CB D:HIS188 3.6 26.0 1.0
N D:HIS188 3.8 26.2 1.0
C1 D:FG8504 4.0 49.3 1.0
NE2 D:HIS188 4.1 31.3 1.0
CA D:GLY339 4.1 22.2 1.0
CD2 D:HIS188 4.2 32.1 1.0
CB D:ASP186 4.3 30.2 1.0
CB D:ASP285 4.3 22.7 1.0
CA D:HIS188 4.4 25.5 1.0
N D:LEU187 4.4 15.8 1.0
N D:GLY339 4.5 23.5 1.0
CB D:LEU187 4.5 24.6 1.0
NE2 D:HIS141 4.6 29.8 1.0
C D:LEU187 4.7 24.1 1.0
OH D:TYR341 4.7 29.8 1.0
CA D:LEU187 4.8 21.8 1.0
CE2 D:TYR341 4.8 29.8 1.0
C2 D:FG8504 4.8 39.4 1.0
NE2 D:HIS142 4.9 23.9 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: Wed Dec 16 11:53:34 2020

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