Bromine in PDB 7uw0: Crystal Structure of Human Clpp Protease in Complex with Tr-133
Enzymatic activity of Crystal Structure of Human Clpp Protease in Complex with Tr-133
All present enzymatic activity of Crystal Structure of Human Clpp Protease in Complex with Tr-133:
3.4.21.92;
Protein crystallography data
The structure of Crystal Structure of Human Clpp Protease in Complex with Tr-133, PDB code: 7uw0
was solved by
M.F.Mabanglo,
W.A.Houry,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.69 /
2.80
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.66,
153.798,
133.208,
90,
107.03,
90
|
R / Rfree (%)
|
26 /
30.9
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
(pdb code 7uw0). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the
Crystal Structure of Human Clpp Protease in Complex with Tr-133, PDB code: 7uw0:
Jump to Bromine binding site number:
1;
2;
3;
4;
5;
6;
7;
Bromine binding site 1 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 1 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:49.0
occ:1.00
|
BR21
|
A:P4I301
|
0.0
|
49.0
|
1.0
|
C20
|
A:P4I301
|
1.9
|
29.4
|
1.0
|
C22
|
A:P4I301
|
2.9
|
22.7
|
1.0
|
C19
|
A:P4I301
|
2.9
|
27.7
|
1.0
|
CD2
|
A:LEU79
|
3.6
|
25.1
|
1.0
|
CG
|
A:ARG78
|
3.7
|
26.8
|
1.0
|
CB
|
G:PHE105
|
3.7
|
16.0
|
1.0
|
CA
|
G:PHE105
|
4.0
|
15.8
|
1.0
|
C23
|
A:P4I301
|
4.2
|
17.7
|
1.0
|
C18
|
A:P4I301
|
4.2
|
34.9
|
1.0
|
CG
|
A:LEU79
|
4.3
|
21.9
|
1.0
|
O
|
G:ALA101
|
4.3
|
20.1
|
1.0
|
N
|
G:PHE105
|
4.3
|
18.6
|
1.0
|
CD1
|
G:PHE105
|
4.4
|
22.8
|
1.0
|
N
|
A:LEU79
|
4.4
|
25.3
|
1.0
|
CB
|
A:ARG78
|
4.4
|
30.4
|
1.0
|
O
|
A:ILE75
|
4.5
|
24.5
|
1.0
|
CG
|
G:PHE105
|
4.5
|
21.8
|
1.0
|
CG1
|
A:ILE75
|
4.5
|
15.8
|
1.0
|
CA
|
A:LEU79
|
4.5
|
20.4
|
1.0
|
C
|
A:ARG78
|
4.6
|
25.4
|
1.0
|
C17
|
A:P4I301
|
4.7
|
25.3
|
1.0
|
O
|
A:ARG78
|
4.8
|
20.3
|
1.0
|
CD
|
A:ARG78
|
4.8
|
16.9
|
1.0
|
CB
|
A:LEU79
|
4.9
|
21.3
|
1.0
|
NE
|
A:ARG78
|
5.0
|
33.6
|
1.0
|
CD1
|
A:ILE75
|
5.0
|
16.9
|
1.0
|
|
Bromine binding site 2 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 2 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br301
b:53.6
occ:1.00
|
BR21
|
B:P4I301
|
0.0
|
53.6
|
1.0
|
C20
|
B:P4I301
|
1.9
|
28.5
|
1.0
|
C22
|
B:P4I301
|
2.9
|
28.3
|
1.0
|
C19
|
B:P4I301
|
2.9
|
25.8
|
1.0
|
CD1
|
B:LEU79
|
3.6
|
29.8
|
1.0
|
CB
|
A:PHE105
|
3.6
|
21.1
|
1.0
|
CG
|
B:ARG78
|
3.9
|
29.1
|
1.0
|
CA
|
A:PHE105
|
4.0
|
19.8
|
1.0
|
CD1
|
B:ILE75
|
4.2
|
23.9
|
1.0
|
C23
|
B:P4I301
|
4.2
|
26.5
|
1.0
|
C18
|
B:P4I301
|
4.2
|
30.1
|
1.0
|
O
|
A:ALA101
|
4.2
|
24.2
|
1.0
|
N
|
B:LEU79
|
4.3
|
30.8
|
1.0
|
N
|
A:PHE105
|
4.4
|
21.4
|
1.0
|
CB
|
B:ARG78
|
4.4
|
34.9
|
1.0
|
CG
|
A:PHE105
|
4.4
|
30.3
|
1.0
|
CA
|
B:LEU79
|
4.4
|
22.5
|
1.0
|
CD1
|
A:PHE105
|
4.4
|
28.7
|
1.0
|
C
|
B:ARG78
|
4.4
|
30.0
|
1.0
|
O
|
B:ARG78
|
4.6
|
25.3
|
1.0
|
O
|
B:ILE75
|
4.6
|
27.0
|
1.0
|
C17
|
B:P4I301
|
4.7
|
28.3
|
1.0
|
CB
|
B:LEU79
|
4.8
|
33.0
|
1.0
|
CG
|
B:LEU79
|
4.8
|
35.3
|
1.0
|
NH1
|
B:ARG78
|
4.8
|
39.8
|
1.0
|
CG1
|
B:ILE75
|
4.9
|
23.4
|
1.0
|
|
Bromine binding site 3 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 3 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br301
b:45.0
occ:1.00
|
BR21
|
C:P4I301
|
0.0
|
45.0
|
1.0
|
C20
|
C:P4I301
|
1.9
|
34.9
|
1.0
|
C22
|
C:P4I301
|
2.9
|
29.4
|
1.0
|
C19
|
C:P4I301
|
2.9
|
25.3
|
1.0
|
CD2
|
C:LEU79
|
3.6
|
19.3
|
1.0
|
CB
|
B:PHE105
|
3.8
|
18.7
|
1.0
|
CG
|
C:ARG78
|
3.9
|
26.6
|
1.0
|
CG
|
C:LEU79
|
3.9
|
29.4
|
1.0
|
O
|
B:ALA101
|
4.0
|
17.7
|
1.0
|
C23
|
C:P4I301
|
4.2
|
29.9
|
1.0
|
C18
|
C:P4I301
|
4.2
|
28.5
|
1.0
|
CA
|
B:PHE105
|
4.2
|
22.8
|
1.0
|
NH1
|
C:ARG78
|
4.3
|
33.0
|
1.0
|
N
|
C:LEU79
|
4.4
|
29.9
|
1.0
|
CD1
|
C:ILE75
|
4.4
|
15.4
|
1.0
|
N
|
B:PHE105
|
4.4
|
23.4
|
1.0
|
CA
|
C:LEU79
|
4.5
|
21.2
|
1.0
|
O
|
C:ILE75
|
4.5
|
27.3
|
1.0
|
CB
|
C:ARG78
|
4.5
|
23.0
|
1.0
|
CG1
|
C:ILE75
|
4.6
|
16.0
|
1.0
|
C
|
C:ARG78
|
4.6
|
27.2
|
1.0
|
CD1
|
B:PHE105
|
4.6
|
29.9
|
1.0
|
CG
|
B:PHE105
|
4.7
|
24.6
|
1.0
|
C17
|
C:P4I301
|
4.7
|
28.2
|
1.0
|
O
|
C:ARG78
|
4.7
|
29.9
|
1.0
|
CB
|
C:LEU79
|
4.8
|
23.6
|
1.0
|
C
|
B:ALA101
|
5.0
|
16.4
|
1.0
|
CZ
|
C:ARG78
|
5.0
|
42.3
|
1.0
|
|
Bromine binding site 4 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 4 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br301
b:42.5
occ:1.00
|
BR21
|
D:P4I301
|
0.0
|
42.5
|
1.0
|
C20
|
D:P4I301
|
1.9
|
31.9
|
1.0
|
C22
|
D:P4I301
|
2.9
|
28.4
|
1.0
|
C19
|
D:P4I301
|
2.9
|
23.8
|
1.0
|
CG
|
D:ARG78
|
3.7
|
25.5
|
1.0
|
CG
|
D:LEU79
|
3.7
|
29.0
|
1.0
|
CB
|
C:PHE105
|
3.9
|
18.9
|
1.0
|
N
|
D:LEU79
|
4.0
|
22.9
|
1.0
|
C23
|
D:P4I301
|
4.2
|
24.2
|
1.0
|
CA
|
D:LEU79
|
4.2
|
26.3
|
1.0
|
CA
|
C:PHE105
|
4.2
|
18.3
|
1.0
|
C18
|
D:P4I301
|
4.2
|
23.5
|
1.0
|
CG1
|
D:ILE75
|
4.3
|
15.6
|
1.0
|
CD2
|
D:LEU79
|
4.3
|
29.7
|
1.0
|
C
|
D:ARG78
|
4.3
|
20.8
|
1.0
|
CB
|
D:ARG78
|
4.3
|
23.6
|
1.0
|
CD1
|
C:PHE105
|
4.4
|
26.8
|
1.0
|
O
|
C:ALA101
|
4.4
|
12.8
|
1.0
|
CD1
|
D:LEU79
|
4.4
|
32.9
|
1.0
|
O
|
D:ILE75
|
4.4
|
22.9
|
1.0
|
CB
|
D:LEU79
|
4.5
|
22.6
|
1.0
|
N
|
C:PHE105
|
4.5
|
21.3
|
1.0
|
O
|
D:ARG78
|
4.6
|
21.2
|
1.0
|
CG
|
C:PHE105
|
4.6
|
20.4
|
1.0
|
C17
|
D:P4I301
|
4.7
|
27.6
|
1.0
|
NH1
|
D:ARG78
|
4.8
|
21.4
|
1.0
|
CD
|
D:ARG78
|
4.9
|
25.1
|
1.0
|
CD1
|
D:ILE75
|
4.9
|
15.4
|
1.0
|
|
Bromine binding site 5 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 5 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 5 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Br301
b:39.1
occ:1.00
|
BR21
|
E:P4I301
|
0.0
|
39.1
|
1.0
|
C20
|
E:P4I301
|
1.9
|
32.6
|
1.0
|
C22
|
E:P4I301
|
2.9
|
29.9
|
1.0
|
C19
|
E:P4I301
|
2.9
|
26.3
|
1.0
|
CD
|
E:ARG78
|
3.6
|
32.0
|
1.0
|
CD2
|
E:LEU79
|
3.6
|
21.1
|
1.0
|
CB
|
D:PHE105
|
3.6
|
16.4
|
1.0
|
CA
|
D:PHE105
|
4.0
|
17.3
|
1.0
|
O
|
D:ALA101
|
4.0
|
14.0
|
1.0
|
C23
|
E:P4I301
|
4.2
|
24.4
|
1.0
|
C18
|
E:P4I301
|
4.2
|
36.1
|
1.0
|
N
|
D:PHE105
|
4.2
|
16.0
|
1.0
|
CG
|
E:LEU79
|
4.3
|
20.8
|
1.0
|
N
|
E:LEU79
|
4.4
|
19.6
|
1.0
|
NE
|
E:ARG78
|
4.4
|
33.8
|
1.0
|
O
|
E:ILE75
|
4.4
|
23.5
|
1.0
|
CG
|
D:PHE105
|
4.5
|
19.0
|
1.0
|
CD1
|
D:PHE105
|
4.5
|
22.9
|
1.0
|
CG1
|
E:ILE75
|
4.5
|
18.3
|
1.0
|
CA
|
E:LEU79
|
4.6
|
15.9
|
1.0
|
C
|
E:ARG78
|
4.6
|
21.0
|
1.0
|
CB
|
E:ARG78
|
4.6
|
22.7
|
1.0
|
O
|
E:ARG78
|
4.7
|
16.5
|
1.0
|
CG
|
E:ARG78
|
4.7
|
21.6
|
1.0
|
C17
|
E:P4I301
|
4.7
|
30.4
|
1.0
|
CG
|
E:GLU82
|
4.8
|
23.8
|
1.0
|
CD1
|
E:ILE75
|
4.9
|
27.8
|
1.0
|
CB
|
E:LEU79
|
4.9
|
24.2
|
1.0
|
C
|
D:LEU104
|
4.9
|
21.3
|
1.0
|
C
|
D:ALA101
|
4.9
|
15.9
|
1.0
|
|
Bromine binding site 6 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 6 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 6 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Br301
b:53.0
occ:1.00
|
BR21
|
F:P4I301
|
0.0
|
53.0
|
1.0
|
C20
|
F:P4I301
|
1.9
|
26.1
|
1.0
|
C22
|
F:P4I301
|
2.9
|
27.1
|
1.0
|
C19
|
F:P4I301
|
2.9
|
21.9
|
1.0
|
CD2
|
F:LEU79
|
3.5
|
14.2
|
1.0
|
CG
|
F:ARG78
|
3.5
|
24.1
|
1.0
|
CB
|
E:PHE105
|
3.7
|
13.5
|
1.0
|
CA
|
E:PHE105
|
4.1
|
14.8
|
1.0
|
CD1
|
E:PHE105
|
4.2
|
23.8
|
1.0
|
C23
|
F:P4I301
|
4.2
|
30.6
|
1.0
|
C18
|
F:P4I301
|
4.2
|
24.7
|
1.0
|
CB
|
F:ARG78
|
4.2
|
19.0
|
1.0
|
O
|
E:ALA101
|
4.3
|
16.2
|
1.0
|
N
|
F:LEU79
|
4.3
|
18.8
|
1.0
|
C
|
F:ARG78
|
4.4
|
17.2
|
1.0
|
CG
|
F:LEU79
|
4.4
|
18.6
|
1.0
|
N
|
E:PHE105
|
4.4
|
17.5
|
1.0
|
CA
|
F:LEU79
|
4.4
|
14.3
|
1.0
|
CG
|
E:PHE105
|
4.4
|
16.8
|
1.0
|
O
|
F:ARG78
|
4.5
|
16.3
|
1.0
|
O
|
F:ILE75
|
4.5
|
15.8
|
1.0
|
CD1
|
F:ILE75
|
4.6
|
15.2
|
1.0
|
CG1
|
F:ILE75
|
4.6
|
8.7
|
1.0
|
CD
|
F:ARG78
|
4.7
|
23.1
|
1.0
|
C17
|
F:P4I301
|
4.7
|
24.4
|
1.0
|
NH1
|
F:ARG78
|
4.9
|
23.7
|
1.0
|
CA
|
F:ARG78
|
5.0
|
22.9
|
1.0
|
NE
|
F:ARG78
|
5.0
|
39.1
|
1.0
|
CB
|
F:LEU79
|
5.0
|
15.6
|
1.0
|
|
Bromine binding site 7 out
of 7 in 7uw0
Go back to
Bromine Binding Sites List in 7uw0
Bromine binding site 7 out
of 7 in the Crystal Structure of Human Clpp Protease in Complex with Tr-133
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 7 of Crystal Structure of Human Clpp Protease in Complex with Tr-133 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Br301
b:39.4
occ:1.00
|
BR21
|
G:P4I301
|
0.0
|
39.4
|
1.0
|
C20
|
G:P4I301
|
1.9
|
26.9
|
1.0
|
C22
|
G:P4I301
|
2.9
|
25.0
|
1.0
|
C19
|
G:P4I301
|
2.9
|
30.3
|
1.0
|
CB
|
F:PHE105
|
3.5
|
23.4
|
1.0
|
CD2
|
G:LEU79
|
3.7
|
21.4
|
1.0
|
CG
|
G:ARG78
|
3.9
|
20.7
|
1.0
|
CA
|
F:PHE105
|
3.9
|
23.1
|
1.0
|
C23
|
G:P4I301
|
4.2
|
25.6
|
1.0
|
CD1
|
F:PHE105
|
4.2
|
23.0
|
1.0
|
N
|
F:PHE105
|
4.2
|
24.0
|
1.0
|
C18
|
G:P4I301
|
4.2
|
34.0
|
1.0
|
O
|
F:ALA101
|
4.3
|
18.6
|
1.0
|
CG
|
G:LEU79
|
4.3
|
26.1
|
1.0
|
CG
|
F:PHE105
|
4.3
|
25.6
|
1.0
|
N
|
G:LEU79
|
4.5
|
24.6
|
1.0
|
O
|
G:ARG78
|
4.5
|
20.6
|
1.0
|
C
|
G:ARG78
|
4.5
|
23.4
|
1.0
|
NH1
|
G:ARG78
|
4.5
|
30.6
|
1.0
|
CB
|
G:ARG78
|
4.5
|
20.4
|
1.0
|
CA
|
G:LEU79
|
4.6
|
20.1
|
1.0
|
O
|
G:ILE75
|
4.6
|
20.7
|
1.0
|
CG1
|
G:ILE75
|
4.6
|
20.3
|
1.0
|
C17
|
G:P4I301
|
4.7
|
26.6
|
1.0
|
CG
|
G:GLU82
|
4.8
|
26.9
|
1.0
|
CD1
|
G:ILE75
|
4.9
|
20.2
|
1.0
|
C
|
F:LEU104
|
5.0
|
23.4
|
1.0
|
CZ
|
G:ARG78
|
5.0
|
31.0
|
1.0
|
CB
|
G:LEU79
|
5.0
|
27.0
|
1.0
|
|
Reference:
M.F.Mabanglo,
K.S.Wong,
M.M.Barghash,
E.Leung,
S.H.W.Chuang,
A.Ardalan,
E.M.Majaesic,
C.J.Wong,
S.Zhang,
H.Lang,
D.S.Karanewsky,
A.A.Iwanowicz,
L.M.Graves,
E.J.Iwanowicz,
A.C.Gingras,
W.A.Houry.
Potent Clpp Agonists with Anticancer Properties Bind with Improved Structural Complementarity and Alter the Mitochondrial N-Terminome. Structure 2022.
ISSN: ISSN 0969-2126
PubMed: 36586405
DOI: 10.1016/J.STR.2022.12.002
Page generated: Thu Jul 11 04:38:34 2024
|