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:
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
|