Fluorine in PDB 3w74: Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
Enzymatic activity of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
All present enzymatic activity of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139:
1.3.98.1;
Protein crystallography data
The structure of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139, PDB code: 3w74
was solved by
D.K.Inaoka,
M.Iida,
T.Tabuchi,
N.Lee,
S.Hashimoto,
S.Matsuoka,
T.Kuranaga,
T.Shiba,
K.Sakamoto,
S.Suzuki,
E.O.Balogun,
T.Nara,
T.Aoki,
M.Inoue,
T.Honma,
A.Tanaka,
S.Harada,
K.Kita,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.27 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.907,
71.451,
130.293,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
22.8
|
Other elements in 3w74:
The structure of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
(pdb code 3w74). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139, PDB code: 3w74:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 1 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:36.6
occ:1.00
|
FAW
|
A:W74401
|
0.0
|
36.6
|
1.0
|
CAU
|
A:W74401
|
1.3
|
37.0
|
1.0
|
FAV
|
A:W74401
|
2.1
|
39.7
|
1.0
|
OAT
|
A:W74401
|
2.2
|
36.9
|
1.0
|
FAX
|
A:W74401
|
2.2
|
32.5
|
1.0
|
CAQ
|
A:W74401
|
2.9
|
38.1
|
1.0
|
CAR
|
A:W74401
|
3.0
|
34.5
|
1.0
|
ND2
|
A:ASN53
|
3.2
|
24.3
|
1.0
|
CA
|
A:GLY70
|
3.3
|
17.8
|
1.0
|
O
|
A:HOH501
|
3.4
|
44.3
|
1.0
|
N
|
A:GLY70
|
3.8
|
17.8
|
1.0
|
CAP
|
A:W74401
|
4.1
|
37.3
|
1.0
|
CG
|
A:ASN53
|
4.2
|
25.3
|
1.0
|
CAS
|
A:W74401
|
4.3
|
30.3
|
1.0
|
OD1
|
A:ASN53
|
4.4
|
26.9
|
1.0
|
C
|
A:GLY70
|
4.5
|
19.5
|
1.0
|
OAK
|
A:W74401
|
4.7
|
20.2
|
1.0
|
C
|
A:MET69
|
4.8
|
20.1
|
1.0
|
CD
|
A:LYS214
|
4.9
|
27.2
|
1.0
|
O
|
A:HOH526
|
4.9
|
28.2
|
1.0
|
O
|
A:SER68
|
4.9
|
19.0
|
1.0
|
C
|
A:SER68
|
5.0
|
18.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 2 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:32.5
occ:1.00
|
FAX
|
A:W74401
|
0.0
|
32.5
|
1.0
|
CAU
|
A:W74401
|
1.4
|
37.0
|
1.0
|
FAW
|
A:W74401
|
2.2
|
36.6
|
1.0
|
FAV
|
A:W74401
|
2.2
|
39.7
|
1.0
|
OAT
|
A:W74401
|
2.3
|
36.9
|
1.0
|
CAQ
|
A:W74401
|
2.7
|
38.1
|
1.0
|
O
|
A:HOH526
|
2.8
|
28.2
|
1.0
|
CAP
|
A:W74401
|
3.2
|
37.3
|
1.0
|
O
|
A:HOH573
|
3.3
|
26.8
|
1.0
|
OAK
|
A:W74401
|
3.5
|
20.2
|
1.0
|
CAR
|
A:W74401
|
3.5
|
34.5
|
1.0
|
CA
|
A:SER68
|
3.6
|
20.1
|
1.0
|
N
|
A:GLY70
|
3.7
|
17.8
|
1.0
|
CB
|
A:SER68
|
3.7
|
23.4
|
1.0
|
C
|
A:SER68
|
3.8
|
18.4
|
1.0
|
ND2
|
A:ASN53
|
4.0
|
24.3
|
1.0
|
CA
|
A:GLY70
|
4.0
|
17.8
|
1.0
|
N
|
A:MET69
|
4.1
|
18.1
|
1.0
|
OG
|
A:SER68
|
4.2
|
35.3
|
1.0
|
O
|
A:SER68
|
4.2
|
19.0
|
1.0
|
CAO
|
A:W74401
|
4.3
|
29.3
|
1.0
|
CAS
|
A:W74401
|
4.5
|
30.3
|
1.0
|
CAI
|
A:W74401
|
4.6
|
23.2
|
1.0
|
C
|
A:MET69
|
4.6
|
20.1
|
1.0
|
CD
|
A:LYS214
|
4.7
|
27.2
|
1.0
|
CAN
|
A:W74401
|
4.8
|
27.2
|
1.0
|
CA
|
A:MET69
|
5.0
|
18.8
|
1.0
|
N
|
A:SER68
|
5.0
|
16.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 3 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:39.7
occ:1.00
|
FAV
|
A:W74401
|
0.0
|
39.7
|
1.0
|
CAU
|
A:W74401
|
1.3
|
37.0
|
1.0
|
FAW
|
A:W74401
|
2.1
|
36.6
|
1.0
|
OAT
|
A:W74401
|
2.2
|
36.9
|
1.0
|
FAX
|
A:W74401
|
2.2
|
32.5
|
1.0
|
CD
|
A:LYS214
|
2.9
|
27.2
|
1.0
|
CAQ
|
A:W74401
|
3.5
|
38.1
|
1.0
|
ND2
|
A:ASN53
|
3.7
|
24.3
|
1.0
|
NZ
|
A:LYS214
|
3.9
|
29.4
|
1.0
|
CG
|
A:LYS214
|
3.9
|
25.3
|
1.0
|
O
|
A:HOH573
|
3.9
|
26.8
|
1.0
|
CE
|
A:LYS214
|
4.0
|
28.4
|
1.0
|
CB
|
A:SER68
|
4.1
|
23.4
|
1.0
|
O
|
A:HOH646
|
4.2
|
38.2
|
1.0
|
CAP
|
A:W74401
|
4.3
|
37.3
|
1.0
|
CAR
|
A:W74401
|
4.4
|
34.5
|
1.0
|
OG
|
A:SER68
|
4.4
|
35.3
|
1.0
|
O
|
A:HOH526
|
4.7
|
28.2
|
1.0
|
CA
|
A:SER68
|
4.8
|
20.1
|
1.0
|
CG
|
A:ASN53
|
4.9
|
25.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 4 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:50.8
occ:1.00
|
FAW
|
B:W74401
|
0.0
|
50.8
|
1.0
|
CAU
|
B:W74401
|
1.5
|
58.0
|
1.0
|
FAV
|
B:W74401
|
2.2
|
64.4
|
1.0
|
FAX
|
B:W74401
|
2.5
|
55.4
|
1.0
|
OAT
|
B:W74401
|
2.5
|
52.0
|
1.0
|
ND2
|
B:ASN53
|
3.2
|
25.6
|
1.0
|
CAQ
|
B:W74401
|
3.3
|
50.3
|
1.0
|
CAR
|
B:W74401
|
3.4
|
38.6
|
1.0
|
CA
|
B:GLY70
|
3.8
|
19.3
|
1.0
|
CG
|
B:ASN53
|
4.1
|
28.4
|
1.0
|
OG
|
B:SER68
|
4.1
|
33.3
|
1.0
|
OD1
|
B:ASN53
|
4.1
|
26.4
|
1.0
|
N
|
B:GLY70
|
4.3
|
17.7
|
1.0
|
CD
|
B:LYS214
|
4.5
|
28.7
|
1.0
|
CAP
|
B:W74401
|
4.7
|
46.4
|
1.0
|
CB
|
B:PRO131
|
4.7
|
88.0
|
1.0
|
CAS
|
B:W74401
|
4.8
|
36.5
|
1.0
|
C
|
B:GLY70
|
4.9
|
20.6
|
1.0
|
CG
|
B:PRO131
|
4.9
|
84.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 5 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:55.4
occ:1.00
|
FAX
|
B:W74401
|
0.0
|
55.4
|
1.0
|
CAU
|
B:W74401
|
1.5
|
58.0
|
1.0
|
FAV
|
B:W74401
|
2.2
|
64.4
|
1.0
|
OAT
|
B:W74401
|
2.4
|
52.0
|
1.0
|
FAW
|
B:W74401
|
2.5
|
50.8
|
1.0
|
CAQ
|
B:W74401
|
2.8
|
50.3
|
1.0
|
O
|
B:HOH573
|
3.1
|
33.8
|
1.0
|
OG
|
B:SER68
|
3.2
|
33.3
|
1.0
|
CAR
|
B:W74401
|
3.2
|
38.6
|
1.0
|
N
|
B:GLY70
|
3.5
|
17.7
|
1.0
|
OAK
|
B:W74401
|
3.5
|
22.4
|
1.0
|
CAP
|
B:W74401
|
3.6
|
46.4
|
1.0
|
O
|
B:HOH575
|
3.6
|
27.7
|
1.0
|
CA
|
B:SER68
|
3.7
|
20.6
|
1.0
|
ND2
|
B:ASN53
|
3.7
|
25.6
|
1.0
|
C
|
B:SER68
|
3.7
|
20.5
|
1.0
|
CA
|
B:GLY70
|
3.9
|
19.3
|
1.0
|
CB
|
B:SER68
|
4.0
|
26.6
|
1.0
|
N
|
B:MET69
|
4.0
|
18.9
|
1.0
|
O
|
B:SER68
|
4.1
|
19.8
|
1.0
|
CAS
|
B:W74401
|
4.3
|
36.5
|
1.0
|
C
|
B:MET69
|
4.5
|
16.6
|
1.0
|
CAI
|
B:W74401
|
4.5
|
24.6
|
1.0
|
CAO
|
B:W74401
|
4.6
|
41.6
|
1.0
|
CD
|
B:LYS214
|
4.7
|
28.7
|
1.0
|
CA
|
B:MET69
|
4.9
|
17.2
|
1.0
|
CAN
|
B:W74401
|
4.9
|
33.4
|
1.0
|
CG
|
B:ASN53
|
4.9
|
28.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3w74
Go back to
Fluorine Binding Sites List in 3w74
Fluorine binding site 6 out
of 6 in the Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:64.4
occ:1.00
|
FAV
|
B:W74401
|
0.0
|
64.4
|
1.0
|
CAU
|
B:W74401
|
1.2
|
58.0
|
1.0
|
OAT
|
B:W74401
|
2.1
|
52.0
|
1.0
|
FAX
|
B:W74401
|
2.2
|
55.4
|
1.0
|
FAW
|
B:W74401
|
2.2
|
50.8
|
1.0
|
CD
|
B:LYS214
|
2.8
|
28.7
|
1.0
|
OG
|
B:SER68
|
3.2
|
33.3
|
1.0
|
NZ
|
B:LYS214
|
3.3
|
31.2
|
1.0
|
CAQ
|
B:W74401
|
3.4
|
50.3
|
1.0
|
O
|
B:HOH575
|
3.5
|
27.7
|
1.0
|
CE
|
B:LYS214
|
3.7
|
30.8
|
1.0
|
CG
|
B:LYS214
|
3.9
|
24.8
|
1.0
|
O
|
B:HOH582
|
4.0
|
33.9
|
1.0
|
ND2
|
B:ASN53
|
4.1
|
25.6
|
1.0
|
CAR
|
B:W74401
|
4.2
|
38.6
|
1.0
|
CAP
|
B:W74401
|
4.2
|
46.4
|
1.0
|
CB
|
B:SER68
|
4.3
|
26.6
|
1.0
|
O
|
B:HOH573
|
4.5
|
33.8
|
1.0
|
CA
|
B:SER68
|
4.8
|
20.6
|
1.0
|
|
Reference:
D.K.Inaoka,
M.Iida,
T.Tabuchi,
N.Lee,
S.Hashimoto,
S.Matsuoka,
T.Kuranaga,
T.Shiba,
K.Sakamoto,
S.Suzuki,
E.O.Balogun,
T.Nara,
T.Aoki,
M.Inoue,
T.Honma,
A.Tanaka,
S.Harada,
K.Kita.
Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with Mii-4-139 To Be Published.
Page generated: Wed Jul 31 23:30:04 2024
|