Zinc in PDB 7p3s: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12
Protein crystallography data
The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12, PDB code: 7p3s
was solved by
T.B.Shaik,
C.Romier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.52 /
1.55
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.39,
70.39,
97.94,
78.05,
75.57,
85.69
|
R / Rfree (%)
|
16.9 /
19.3
|
Other elements in 7p3s:
The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 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 A Benzohydroxamate Inhibitor 12
(pdb code 7p3s). 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 A Benzohydroxamate Inhibitor 12, PDB code: 7p3s:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7p3s
Go back to
Zinc Binding Sites List in 7p3s
Zinc binding site 1 out
of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12
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 A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:17.1
occ:1.00
|
OD2
|
A:ASP285
|
2.0
|
16.7
|
1.0
|
OD1
|
A:ASP186
|
2.0
|
14.5
|
1.0
|
ND1
|
A:HIS188
|
2.0
|
14.0
|
1.0
|
O1
|
A:5IB507
|
2.3
|
42.2
|
1.0
|
O2
|
A:5IB507
|
2.5
|
36.7
|
1.0
|
C5
|
A:5IB507
|
2.7
|
56.7
|
1.0
|
N
|
A:5IB507
|
2.9
|
45.9
|
1.0
|
CG
|
A:ASP186
|
2.9
|
15.4
|
1.0
|
CE1
|
A:HIS188
|
2.9
|
18.2
|
1.0
|
CG
|
A:ASP285
|
3.0
|
17.1
|
1.0
|
OD2
|
A:ASP186
|
3.1
|
15.8
|
1.0
|
CG
|
A:HIS188
|
3.1
|
15.2
|
1.0
|
OD1
|
A:ASP285
|
3.3
|
16.7
|
1.0
|
CB
|
A:HIS188
|
3.6
|
14.1
|
1.0
|
N
|
A:HIS188
|
3.7
|
14.6
|
1.0
|
C4
|
A:5IB507
|
3.9
|
67.0
|
1.0
|
NE2
|
A:HIS188
|
4.1
|
18.7
|
1.0
|
CA
|
A:GLY339
|
4.1
|
16.0
|
1.0
|
N
|
A:LEU187
|
4.2
|
14.5
|
1.0
|
CD2
|
A:HIS188
|
4.2
|
20.0
|
1.0
|
CB
|
A:ASP186
|
4.3
|
12.6
|
1.0
|
CA
|
A:HIS188
|
4.3
|
14.5
|
1.0
|
CB
|
A:ASP285
|
4.3
|
13.1
|
1.0
|
CB
|
A:LEU187
|
4.4
|
13.4
|
1.0
|
C6
|
A:5IB507
|
4.5
|
72.6
|
1.0
|
OH
|
A:TYR341
|
4.5
|
20.0
|
1.0
|
N
|
A:GLY339
|
4.5
|
13.8
|
1.0
|
NE2
|
A:HIS141
|
4.5
|
16.1
|
1.0
|
C
|
A:LEU187
|
4.6
|
15.9
|
1.0
|
CE2
|
A:TYR341
|
4.6
|
18.7
|
1.0
|
CA
|
A:LEU187
|
4.6
|
14.0
|
1.0
|
C3
|
A:5IB507
|
4.8
|
65.9
|
1.0
|
C
|
A:ASP186
|
4.9
|
16.9
|
1.0
|
NE2
|
A:HIS142
|
4.9
|
17.9
|
1.0
|
CE1
|
A:HIS141
|
4.9
|
14.7
|
1.0
|
CA
|
A:ASP186
|
5.0
|
12.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7p3s
Go back to
Zinc Binding Sites List in 7p3s
Zinc binding site 2 out
of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12
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 A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:15.4
occ:1.00
|
OD1
|
B:ASP186
|
1.9
|
13.7
|
1.0
|
OD2
|
B:ASP285
|
1.9
|
12.8
|
1.0
|
ND1
|
B:HIS188
|
2.1
|
17.7
|
1.0
|
O1
|
B:5IB501
|
2.1
|
26.2
|
1.0
|
O2
|
B:5IB501
|
2.4
|
23.4
|
1.0
|
C5
|
B:5IB501
|
2.6
|
46.2
|
1.0
|
N
|
B:5IB501
|
2.8
|
37.2
|
1.0
|
CG
|
B:ASP186
|
2.8
|
14.5
|
1.0
|
CG
|
B:ASP285
|
2.9
|
15.1
|
1.0
|
CE1
|
B:HIS188
|
3.0
|
19.6
|
1.0
|
OD2
|
B:ASP186
|
3.1
|
12.6
|
1.0
|
CG
|
B:HIS188
|
3.2
|
13.7
|
1.0
|
OD1
|
B:ASP285
|
3.3
|
13.5
|
1.0
|
CB
|
B:HIS188
|
3.6
|
11.7
|
1.0
|
C4
|
B:5IB501
|
3.8
|
52.4
|
1.0
|
N
|
B:HIS188
|
3.8
|
11.6
|
1.0
|
CA
|
B:GLY339
|
4.1
|
12.6
|
1.0
|
NE2
|
B:HIS188
|
4.1
|
16.8
|
1.0
|
N
|
B:LEU187
|
4.2
|
11.6
|
1.0
|
CB
|
B:ASP186
|
4.2
|
11.8
|
1.0
|
CD2
|
B:HIS188
|
4.2
|
14.1
|
1.0
|
C6
|
B:5IB501
|
4.3
|
58.1
|
1.0
|
CB
|
B:ASP285
|
4.3
|
13.1
|
1.0
|
CA
|
B:HIS188
|
4.3
|
13.0
|
1.0
|
CB
|
B:LEU187
|
4.4
|
11.4
|
1.0
|
NE2
|
B:HIS141
|
4.5
|
12.8
|
1.0
|
OH
|
B:TYR341
|
4.5
|
19.8
|
1.0
|
N
|
B:GLY339
|
4.5
|
14.1
|
1.0
|
CE2
|
B:TYR341
|
4.6
|
13.0
|
1.0
|
C
|
B:LEU187
|
4.6
|
13.6
|
1.0
|
CA
|
B:LEU187
|
4.7
|
9.7
|
1.0
|
CE1
|
B:HIS141
|
4.8
|
11.9
|
1.0
|
C3
|
B:5IB501
|
4.8
|
47.1
|
1.0
|
C
|
B:ASP186
|
4.9
|
11.6
|
1.0
|
NE2
|
B:HIS142
|
4.9
|
17.6
|
1.0
|
CA
|
B:ASP186
|
5.0
|
11.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7p3s
Go back to
Zinc Binding Sites List in 7p3s
Zinc binding site 3 out
of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12
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 A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:15.2
occ:1.00
|
OD1
|
C:ASP186
|
1.9
|
12.5
|
1.0
|
OD2
|
C:ASP285
|
2.0
|
13.8
|
1.0
|
ND1
|
C:HIS188
|
2.1
|
16.2
|
1.0
|
O1
|
C:5IB501
|
2.2
|
44.2
|
1.0
|
O2
|
C:5IB501
|
2.3
|
35.9
|
1.0
|
C5
|
C:5IB501
|
2.5
|
52.6
|
1.0
|
N
|
C:5IB501
|
2.6
|
34.9
|
1.0
|
CG
|
C:ASP186
|
2.8
|
13.4
|
1.0
|
CG
|
C:ASP285
|
3.0
|
15.3
|
1.0
|
CE1
|
C:HIS188
|
3.0
|
17.1
|
1.0
|
OD2
|
C:ASP186
|
3.0
|
12.1
|
1.0
|
CG
|
C:HIS188
|
3.2
|
12.3
|
1.0
|
OD1
|
C:ASP285
|
3.3
|
12.6
|
1.0
|
CB
|
C:HIS188
|
3.6
|
11.0
|
1.0
|
C4
|
C:5IB501
|
3.8
|
60.7
|
1.0
|
N
|
C:HIS188
|
3.8
|
10.4
|
1.0
|
CA
|
C:GLY339
|
4.1
|
12.4
|
1.0
|
NE2
|
C:HIS188
|
4.1
|
17.4
|
1.0
|
N
|
C:LEU187
|
4.2
|
12.6
|
1.0
|
CB
|
C:ASP186
|
4.2
|
10.5
|
1.0
|
CD2
|
C:HIS188
|
4.2
|
17.1
|
1.0
|
C6
|
C:5IB501
|
4.3
|
66.7
|
1.0
|
CB
|
C:ASP285
|
4.3
|
11.0
|
1.0
|
CA
|
C:HIS188
|
4.3
|
12.1
|
1.0
|
CB
|
C:LEU187
|
4.4
|
10.9
|
1.0
|
NE2
|
C:HIS141
|
4.5
|
14.6
|
1.0
|
OH
|
C:TYR341
|
4.5
|
18.6
|
1.0
|
N
|
C:GLY339
|
4.5
|
12.5
|
1.0
|
CE2
|
C:TYR341
|
4.6
|
16.4
|
1.0
|
C
|
C:LEU187
|
4.6
|
13.0
|
1.0
|
CA
|
C:LEU187
|
4.6
|
10.8
|
1.0
|
CE1
|
C:HIS141
|
4.8
|
12.8
|
1.0
|
C3
|
C:5IB501
|
4.8
|
58.7
|
1.0
|
C
|
C:ASP186
|
4.9
|
13.5
|
1.0
|
CA
|
C:ASP186
|
4.9
|
10.6
|
1.0
|
NE2
|
C:HIS142
|
4.9
|
16.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7p3s
Go back to
Zinc Binding Sites List in 7p3s
Zinc binding site 4 out
of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12
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 A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:17.5
occ:1.00
|
OD2
|
D:ASP285
|
1.9
|
16.3
|
1.0
|
OD1
|
D:ASP186
|
1.9
|
15.2
|
1.0
|
ND1
|
D:HIS188
|
2.1
|
16.6
|
1.0
|
O1
|
D:5IB501
|
2.3
|
39.7
|
1.0
|
O2
|
D:5IB501
|
2.4
|
36.6
|
1.0
|
C5
|
D:5IB501
|
2.7
|
57.9
|
1.0
|
N
|
D:5IB501
|
2.7
|
51.9
|
1.0
|
CG
|
D:ASP186
|
2.8
|
14.7
|
1.0
|
CG
|
D:ASP285
|
3.0
|
16.9
|
1.0
|
CE1
|
D:HIS188
|
3.0
|
19.2
|
1.0
|
OD2
|
D:ASP186
|
3.1
|
14.9
|
1.0
|
CG
|
D:HIS188
|
3.2
|
14.2
|
1.0
|
OD1
|
D:ASP285
|
3.4
|
16.3
|
1.0
|
CB
|
D:HIS188
|
3.6
|
14.9
|
1.0
|
N
|
D:HIS188
|
3.8
|
14.4
|
1.0
|
C4
|
D:5IB501
|
3.9
|
57.9
|
1.0
|
CA
|
D:GLY339
|
4.1
|
13.7
|
1.0
|
NE2
|
D:HIS188
|
4.2
|
18.0
|
1.0
|
N
|
D:LEU187
|
4.2
|
13.8
|
1.0
|
CB
|
D:ASP186
|
4.2
|
13.0
|
1.0
|
CD2
|
D:HIS188
|
4.3
|
16.9
|
1.0
|
CB
|
D:ASP285
|
4.3
|
14.5
|
1.0
|
CA
|
D:HIS188
|
4.3
|
15.0
|
1.0
|
OH
|
D:TYR341
|
4.4
|
20.8
|
1.0
|
CB
|
D:LEU187
|
4.4
|
15.3
|
1.0
|
N
|
D:GLY339
|
4.5
|
16.7
|
1.0
|
C6
|
D:5IB501
|
4.5
|
60.6
|
1.0
|
NE2
|
D:HIS141
|
4.5
|
16.9
|
1.0
|
CE2
|
D:TYR341
|
4.6
|
23.3
|
1.0
|
C
|
D:LEU187
|
4.6
|
15.6
|
1.0
|
CA
|
D:LEU187
|
4.7
|
16.0
|
1.0
|
C3
|
D:5IB501
|
4.8
|
54.3
|
1.0
|
CE1
|
D:HIS141
|
4.9
|
14.8
|
1.0
|
C
|
D:ASP186
|
4.9
|
16.3
|
1.0
|
NE2
|
D:HIS142
|
4.9
|
18.0
|
1.0
|
CA
|
D:ASP186
|
5.0
|
14.5
|
1.0
|
|
Reference:
T.B.Shaik,
C.Romier.
Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 To Be Published.
Page generated: Wed Oct 30 08:59:54 2024
|