Fluorine in PDB 1o3o: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Enzymatic activity of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
All present enzymatic activity of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors:
3.4.21.4;
Protein crystallography data
The structure of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors, PDB code: 1o3o
was solved by
B.A.Katz,
K.Elrod,
E.Verner,
R.L.Mackman,
C.Luong,
W.D.Shrader,
M.Sendzik,
J.R.Spencer,
P.A.Sprengeler,
A.Kolesnikov,
V.W.Tai,
H.C.Hui,
J.G.Breitenbucher,
D.Allen,
J.W.Janc,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
7.00 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.280,
61.800,
69.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
20.9
|
Other elements in 1o3o:
The structure of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
(pdb code 1o3o). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors, PDB code: 1o3o:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 1 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:36.2
occ:0.17
|
FV'
|
A:785246
|
0.0
|
36.2
|
0.2
|
C3X
|
A:785246
|
1.4
|
34.2
|
0.2
|
HC5'
|
A:785246
|
1.7
|
32.8
|
0.3
|
FX'
|
A:785246
|
2.2
|
34.9
|
0.2
|
FW'
|
A:785246
|
2.2
|
33.1
|
0.2
|
O3'
|
A:785246
|
2.3
|
34.5
|
0.5
|
C5'
|
A:785246
|
2.7
|
33.1
|
0.3
|
HC4'
|
A:785246
|
3.1
|
33.4
|
0.3
|
C4'
|
A:785246
|
3.3
|
33.3
|
0.3
|
C3'
|
A:785246
|
3.4
|
32.0
|
0.5
|
C6'
|
A:785246
|
3.8
|
30.4
|
0.3
|
O6'
|
A:785246
|
4.0
|
29.3
|
0.3
|
HC2'
|
A:785246
|
4.0
|
30.0
|
0.5
|
HE21
|
A:GLN192
|
4.1
|
29.5
|
0.4
|
C2'
|
A:785246
|
4.2
|
29.9
|
0.5
|
HC4'
|
A:785246
|
4.3
|
31.5
|
0.5
|
C4'
|
A:785246
|
4.3
|
31.1
|
0.5
|
HE22
|
A:GLN192
|
4.6
|
29.2
|
0.4
|
NE2
|
A:GLN192
|
4.6
|
28.8
|
0.4
|
C3'
|
A:785246
|
4.7
|
33.8
|
0.3
|
|
Fluorine binding site 2 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 2 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:36.8
occ:0.12
|
FV'
|
A:785246
|
0.0
|
36.8
|
0.1
|
C3X
|
A:785246
|
1.4
|
36.6
|
0.1
|
HC5'
|
A:785246
|
1.9
|
29.9
|
0.5
|
FX'
|
A:785246
|
2.2
|
37.4
|
0.1
|
FW'
|
A:785246
|
2.3
|
37.3
|
0.1
|
O3'
|
A:785246
|
2.3
|
36.7
|
0.3
|
C5'
|
A:785246
|
2.8
|
30.6
|
0.5
|
HC4'
|
A:785246
|
3.1
|
31.5
|
0.5
|
C4'
|
A:785246
|
3.3
|
31.1
|
0.5
|
C3'
|
A:785246
|
3.5
|
33.8
|
0.3
|
HD2
|
A:HIS57
|
3.7
|
19.9
|
1.0
|
C6'
|
A:785246
|
3.9
|
27.4
|
0.5
|
H1
|
A:HOH371
|
3.9
|
54.1
|
1.0
|
H1
|
A:HOH383
|
4.1
|
32.5
|
0.8
|
O
|
A:HOH371
|
4.1
|
53.6
|
1.0
|
HC2'
|
A:785246
|
4.1
|
31.7
|
0.3
|
O
|
A:HOH353
|
4.1
|
53.7
|
1.0
|
O6'
|
A:785246
|
4.2
|
21.5
|
0.5
|
C2'
|
A:785246
|
4.3
|
31.6
|
0.3
|
HC4'
|
A:785246
|
4.3
|
33.4
|
0.3
|
C4'
|
A:785246
|
4.3
|
33.3
|
0.3
|
H2
|
A:HOH371
|
4.4
|
53.8
|
1.0
|
HE2
|
A:HIS57
|
4.5
|
22.1
|
1.0
|
H2
|
A:HOH353
|
4.6
|
53.4
|
1.0
|
H1
|
A:HOH353
|
4.6
|
53.1
|
1.0
|
HG
|
A:SER195
|
4.6
|
15.6
|
0.3
|
O
|
A:HOH383
|
4.6
|
34.0
|
0.8
|
C3'
|
A:785246
|
4.6
|
32.0
|
0.5
|
CD2
|
A:HIS57
|
4.7
|
18.9
|
1.0
|
HG
|
A:SER195
|
4.7
|
21.9
|
0.7
|
HD2
|
A:PHE41
|
4.7
|
12.6
|
1.0
|
O
|
A:PHE41
|
4.8
|
15.4
|
1.0
|
HB2
|
A:PHE41
|
4.8
|
12.7
|
1.0
|
HA
|
A:CYS58
|
4.9
|
15.7
|
1.0
|
SG
|
A:CYS42
|
5.0
|
14.0
|
1.0
|
NE2
|
A:HIS57
|
5.0
|
22.6
|
1.0
|
O
|
A:HIS57
|
5.0
|
15.2
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 3 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:33.1
occ:0.17
|
FW'
|
A:785246
|
0.0
|
33.1
|
0.2
|
C3X
|
A:785246
|
1.4
|
34.2
|
0.2
|
HC5'
|
A:785246
|
1.9
|
32.8
|
0.3
|
C5'
|
A:785246
|
2.1
|
33.1
|
0.3
|
FV'
|
A:785246
|
2.2
|
36.2
|
0.2
|
FX'
|
A:785246
|
2.3
|
34.9
|
0.2
|
O3'
|
A:785246
|
2.4
|
34.5
|
0.5
|
C4'
|
A:785246
|
2.6
|
33.3
|
0.3
|
C3'
|
A:785246
|
2.7
|
32.0
|
0.5
|
C6'
|
A:785246
|
2.8
|
30.4
|
0.3
|
HC4'
|
A:785246
|
2.9
|
33.4
|
0.3
|
C2'
|
A:785246
|
3.1
|
29.9
|
0.5
|
HC2'
|
A:785246
|
3.1
|
30.0
|
0.5
|
O6'
|
A:785246
|
3.3
|
29.3
|
0.3
|
C4'
|
A:785246
|
3.5
|
31.1
|
0.5
|
C3'
|
A:785246
|
3.6
|
33.8
|
0.3
|
C1'
|
A:785246
|
3.8
|
30.0
|
0.3
|
HC4'
|
A:785246
|
3.9
|
31.5
|
0.5
|
C2'
|
A:785246
|
4.1
|
31.6
|
0.3
|
C1'
|
A:785246
|
4.2
|
28.3
|
0.5
|
C5'
|
A:785246
|
4.5
|
30.6
|
0.5
|
O3'
|
A:785246
|
4.5
|
36.7
|
0.3
|
C6'
|
A:785246
|
4.8
|
27.4
|
0.5
|
C8
|
A:785246
|
5.0
|
27.0
|
0.3
|
HE22
|
A:GLN192
|
5.0
|
29.2
|
0.4
|
|
Fluorine binding site 4 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 4 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:37.3
occ:0.12
|
FW'
|
A:785246
|
0.0
|
37.3
|
0.1
|
C3X
|
A:785246
|
1.4
|
36.6
|
0.1
|
FV'
|
A:785246
|
2.3
|
36.8
|
0.1
|
FX'
|
A:785246
|
2.3
|
37.4
|
0.1
|
O3'
|
A:785246
|
2.4
|
36.7
|
0.3
|
HC4'
|
A:785246
|
2.4
|
31.5
|
0.5
|
C4'
|
A:785246
|
2.5
|
31.1
|
0.5
|
C5'
|
A:785246
|
2.6
|
30.6
|
0.5
|
HC5'
|
A:785246
|
2.6
|
29.9
|
0.5
|
C3'
|
A:785246
|
2.8
|
33.8
|
0.3
|
C4'
|
A:785246
|
3.3
|
33.3
|
0.3
|
HC4'
|
A:785246
|
3.3
|
33.4
|
0.3
|
C3'
|
A:785246
|
3.4
|
32.0
|
0.5
|
HE22
|
A:GLN192
|
3.4
|
29.2
|
0.4
|
C6'
|
A:785246
|
3.6
|
27.4
|
0.5
|
C2'
|
A:785246
|
3.6
|
31.6
|
0.3
|
HB2
|
A:GLN192
|
3.6
|
24.4
|
1.0
|
H1
|
A:HOH383
|
3.8
|
32.5
|
0.8
|
HC2'
|
A:785246
|
3.8
|
31.7
|
0.3
|
O3'
|
A:785246
|
4.0
|
34.5
|
0.5
|
NE2
|
A:GLN192
|
4.1
|
28.8
|
0.4
|
C2'
|
A:785246
|
4.1
|
29.9
|
0.5
|
O
|
A:HOH383
|
4.2
|
34.0
|
0.8
|
C1'
|
A:785246
|
4.2
|
28.3
|
0.5
|
HE21
|
A:GLN192
|
4.3
|
29.5
|
0.4
|
C5'
|
A:785246
|
4.3
|
33.1
|
0.3
|
O6'
|
A:785246
|
4.4
|
21.5
|
0.5
|
H
|
A:GLY193
|
4.4
|
19.1
|
1.0
|
H1
|
A:HOH322
|
4.6
|
49.2
|
1.0
|
C1'
|
A:785246
|
4.6
|
30.0
|
0.3
|
CB
|
A:GLN192
|
4.7
|
24.8
|
1.0
|
HG
|
A:SER195
|
4.8
|
15.6
|
0.3
|
C6'
|
A:785246
|
4.9
|
30.4
|
0.3
|
HB3
|
A:GLN192
|
4.9
|
24.7
|
1.0
|
N
|
A:GLY193
|
5.0
|
17.1
|
1.0
|
HC5'
|
A:785246
|
5.0
|
32.8
|
0.3
|
|
Fluorine binding site 5 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 5 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:34.9
occ:0.17
|
FX'
|
A:785246
|
0.0
|
34.9
|
0.2
|
HC5'
|
A:785246
|
1.3
|
32.8
|
0.3
|
C3X
|
A:785246
|
1.4
|
34.2
|
0.2
|
O6'
|
A:785246
|
1.8
|
29.3
|
0.3
|
C5'
|
A:785246
|
1.9
|
33.1
|
0.3
|
C6'
|
A:785246
|
2.2
|
30.4
|
0.3
|
FV'
|
A:785246
|
2.2
|
36.2
|
0.2
|
HC2'
|
A:785246
|
2.2
|
30.0
|
0.5
|
FW'
|
A:785246
|
2.3
|
33.1
|
0.2
|
O3'
|
A:785246
|
2.4
|
34.5
|
0.5
|
C2'
|
A:785246
|
2.9
|
29.9
|
0.5
|
C3'
|
A:785246
|
3.0
|
32.0
|
0.5
|
C4'
|
A:785246
|
3.3
|
33.3
|
0.3
|
C1'
|
A:785246
|
3.6
|
30.0
|
0.3
|
HC4'
|
A:785246
|
3.8
|
33.4
|
0.3
|
HE22
|
A:GLN192
|
3.9
|
29.2
|
0.4
|
HB3
|
A:GLN192
|
4.0
|
24.7
|
1.0
|
HE21
|
A:GLN192
|
4.1
|
29.5
|
0.4
|
NE2
|
A:GLN192
|
4.1
|
28.8
|
0.4
|
C1'
|
A:785246
|
4.2
|
28.3
|
0.5
|
C4'
|
A:785246
|
4.3
|
31.1
|
0.5
|
C3'
|
A:785246
|
4.3
|
33.8
|
0.3
|
C2'
|
A:785246
|
4.4
|
31.6
|
0.3
|
C8
|
A:785246
|
4.5
|
27.0
|
0.3
|
N4
|
A:785246
|
4.5
|
25.2
|
0.5
|
N4
|
A:785246
|
4.5
|
26.3
|
0.3
|
CD
|
A:GLN192
|
4.8
|
29.5
|
0.4
|
C8
|
A:785246
|
4.8
|
25.7
|
0.5
|
HC4'
|
A:785246
|
4.8
|
31.5
|
0.5
|
CB
|
A:GLN192
|
4.9
|
24.8
|
1.0
|
HB2
|
A:GLN192
|
5.0
|
24.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 1o3o
Go back to
Fluorine Binding Sites List in 1o3o
Fluorine binding site 6 out
of 6 in the Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F246
b:37.4
occ:0.12
|
FX'
|
A:785246
|
0.0
|
37.4
|
0.1
|
C3X
|
A:785246
|
1.4
|
36.6
|
0.1
|
HC5'
|
A:785246
|
1.8
|
29.9
|
0.5
|
H1
|
A:HOH383
|
1.9
|
32.5
|
0.8
|
C5'
|
A:785246
|
2.1
|
30.6
|
0.5
|
FV'
|
A:785246
|
2.2
|
36.8
|
0.1
|
FW'
|
A:785246
|
2.3
|
37.3
|
0.1
|
O3'
|
A:785246
|
2.3
|
36.7
|
0.3
|
C6'
|
A:785246
|
2.4
|
27.4
|
0.5
|
O
|
A:HOH383
|
2.4
|
34.0
|
0.8
|
HC2'
|
A:785246
|
2.4
|
31.7
|
0.3
|
O6'
|
A:785246
|
2.5
|
21.5
|
0.5
|
HG
|
A:SER195
|
2.6
|
15.6
|
0.3
|
C3'
|
A:785246
|
2.8
|
33.8
|
0.3
|
HG
|
A:SER195
|
2.9
|
21.9
|
0.7
|
C2'
|
A:785246
|
2.9
|
31.6
|
0.3
|
H2
|
A:HOH383
|
3.0
|
32.1
|
0.8
|
C4'
|
A:785246
|
3.1
|
31.1
|
0.5
|
OG
|
A:SER195
|
3.1
|
15.0
|
0.3
|
HE2
|
A:HIS57
|
3.2
|
22.1
|
1.0
|
HB2
|
A:SER195
|
3.3
|
17.9
|
0.7
|
H
|
A:GLY193
|
3.5
|
19.1
|
1.0
|
C1'
|
A:785246
|
3.5
|
28.3
|
0.5
|
HC4'
|
A:785246
|
3.6
|
31.5
|
0.5
|
HN3
|
A:785246
|
3.6
|
24.7
|
0.3
|
OG
|
A:SER195
|
3.7
|
24.1
|
0.7
|
HN3
|
A:785246
|
3.7
|
24.1
|
0.5
|
HD2
|
A:HIS57
|
3.8
|
19.9
|
1.0
|
HB2
|
A:SER195
|
3.8
|
15.0
|
0.3
|
CB
|
A:SER195
|
3.9
|
17.2
|
0.7
|
CB
|
A:SER195
|
3.9
|
14.8
|
0.3
|
NE2
|
A:HIS57
|
4.0
|
22.6
|
1.0
|
HB2
|
A:GLN192
|
4.0
|
24.4
|
1.0
|
C3'
|
A:785246
|
4.0
|
32.0
|
0.5
|
C4'
|
A:785246
|
4.0
|
33.3
|
0.3
|
C1'
|
A:785246
|
4.1
|
30.0
|
0.3
|
HB3
|
A:SER195
|
4.2
|
14.9
|
0.3
|
C2'
|
A:785246
|
4.2
|
29.9
|
0.5
|
HA
|
A:GLN192
|
4.2
|
21.8
|
1.0
|
HB3
|
A:SER195
|
4.3
|
17.8
|
0.7
|
CD2
|
A:HIS57
|
4.3
|
18.9
|
1.0
|
N
|
A:GLY193
|
4.4
|
17.1
|
1.0
|
N3
|
A:785246
|
4.4
|
24.2
|
0.5
|
O
|
A:PHE41
|
4.4
|
15.4
|
1.0
|
C8
|
A:785246
|
4.5
|
25.7
|
0.5
|
N3
|
A:785246
|
4.5
|
24.6
|
0.3
|
HC4'
|
A:785246
|
4.5
|
33.4
|
0.3
|
HE22
|
A:GLN192
|
4.6
|
29.2
|
0.4
|
H2
|
A:HOH623
|
4.6
|
47.2
|
1.0
|
SG
|
A:CYS42
|
4.6
|
14.0
|
1.0
|
C8
|
A:785246
|
4.8
|
27.0
|
0.3
|
HA2
|
A:GLY193
|
4.9
|
17.8
|
1.0
|
CB
|
A:GLN192
|
4.9
|
24.8
|
1.0
|
H
|
A:SER195
|
4.9
|
15.8
|
0.7
|
H
|
A:SER195
|
4.9
|
15.7
|
0.3
|
CA
|
A:GLN192
|
4.9
|
23.7
|
1.0
|
C5'
|
A:785246
|
5.0
|
33.1
|
0.3
|
|
Reference:
B.A.Katz,
K.Elrod,
E.Verner,
R.L.Mackman,
C.Luong,
W.D.Shrader,
M.Sendzik,
J.R.Spencer,
P.A.Sprengeler,
A.Kolesnikov,
V.W.Tai,
H.C.Hui,
J.G.Breitenbucher,
D.Allen,
J.W.Janc.
Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors. J.Mol.Biol. V. 329 93 2003.
ISSN: ISSN 0022-2836
PubMed: 12742021
DOI: 10.1016/S0022-2836(03)00399-1
Page generated: Wed Jul 31 12:13:04 2024
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