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:
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: Mon Oct 28 22:03:58 2024
|