Fluorine in PDB 5fiu: Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Enzymatic activity of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
All present enzymatic activity of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme:
2.5.1.63;
Protein crystallography data
The structure of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme, PDB code: 5fiu
was solved by
S.Thompson,
S.A.Mcmahon,
J.H.Naismith,
D.O'hagan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.67 /
1.84
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.260,
129.160,
182.330,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.808 /
19.983
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
(pdb code 5fiu). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme, PDB code: 5fiu:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 1 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1299
b:21.0
occ:1.00
|
FAB
|
A:Y3J1299
|
0.0
|
21.0
|
1.0
|
CAH
|
A:Y3J1299
|
1.3
|
20.4
|
1.0
|
FAG
|
A:Y3J1299
|
2.1
|
21.0
|
1.0
|
CAI
|
A:Y3J1299
|
2.3
|
18.5
|
1.0
|
N
|
A:TYR157
|
2.8
|
16.4
|
1.0
|
OAJ
|
A:Y3J1299
|
2.9
|
17.9
|
1.0
|
OG1
|
A:THR80
|
3.0
|
17.0
|
1.0
|
O
|
A:THR155
|
3.1
|
20.8
|
1.0
|
CA
|
A:PHE156
|
3.1
|
17.9
|
1.0
|
CB
|
A:THR80
|
3.2
|
18.5
|
1.0
|
C
|
A:PHE156
|
3.2
|
17.8
|
1.0
|
C
|
A:THR155
|
3.4
|
19.6
|
1.0
|
N
|
A:PHE156
|
3.4
|
18.8
|
1.0
|
N
|
A:SER158
|
3.5
|
16.6
|
1.0
|
CG2
|
A:THR80
|
3.5
|
17.6
|
1.0
|
CAQ
|
A:Y3J1299
|
3.7
|
17.9
|
1.0
|
CA
|
A:TYR157
|
3.8
|
17.2
|
1.0
|
O2
|
C:TLA1300
|
3.9
|
26.9
|
1.0
|
C
|
A:TYR157
|
4.1
|
17.2
|
1.0
|
CAK
|
A:Y3J1299
|
4.2
|
18.0
|
1.0
|
CB
|
A:TYR157
|
4.2
|
17.4
|
1.0
|
O
|
A:TYR77
|
4.2
|
16.6
|
1.0
|
CB
|
A:TYR77
|
4.2
|
17.4
|
1.0
|
OAS
|
A:Y3J1299
|
4.2
|
17.8
|
1.0
|
O
|
A:PHE156
|
4.2
|
17.5
|
1.0
|
OG
|
A:SER158
|
4.3
|
15.7
|
1.0
|
CD1
|
A:PHE156
|
4.3
|
17.3
|
1.0
|
CAR
|
A:Y3J1299
|
4.4
|
18.6
|
1.0
|
CB
|
A:PHE156
|
4.5
|
18.6
|
1.0
|
CA
|
A:THR155
|
4.5
|
19.5
|
1.0
|
CB
|
A:SER158
|
4.5
|
16.8
|
1.0
|
CA
|
A:SER158
|
4.6
|
16.5
|
1.0
|
CA
|
A:THR80
|
4.6
|
19.2
|
1.0
|
CG
|
A:PHE156
|
4.9
|
17.3
|
1.0
|
CG
|
A:TYR77
|
4.9
|
17.8
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 2 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1299
b:21.0
occ:1.00
|
FAG
|
A:Y3J1299
|
0.0
|
21.0
|
1.0
|
CAH
|
A:Y3J1299
|
1.2
|
20.4
|
1.0
|
FAB
|
A:Y3J1299
|
2.1
|
21.0
|
1.0
|
CAI
|
A:Y3J1299
|
2.3
|
18.5
|
1.0
|
CAQ
|
A:Y3J1299
|
2.8
|
17.9
|
1.0
|
OG
|
A:SER158
|
2.8
|
15.7
|
1.0
|
OAS
|
A:Y3J1299
|
2.9
|
17.8
|
1.0
|
CB
|
A:SER158
|
2.9
|
16.8
|
1.0
|
N
|
A:SER158
|
3.2
|
16.6
|
1.0
|
CD1
|
A:PHE156
|
3.4
|
17.3
|
1.0
|
OAJ
|
A:Y3J1299
|
3.5
|
17.9
|
1.0
|
CA
|
A:SER158
|
3.6
|
16.5
|
1.0
|
O2
|
C:TLA1300
|
3.6
|
26.9
|
1.0
|
CD2
|
A:LEU17
|
3.8
|
16.4
|
1.0
|
CA
|
A:PHE156
|
3.9
|
17.9
|
1.0
|
CE1
|
A:PHE156
|
3.9
|
17.3
|
1.0
|
C
|
A:PHE156
|
3.9
|
17.8
|
1.0
|
N
|
A:TYR157
|
4.0
|
16.4
|
1.0
|
CAR
|
A:Y3J1299
|
4.1
|
18.6
|
1.0
|
O
|
A:THR155
|
4.2
|
20.8
|
1.0
|
C
|
A:TYR157
|
4.3
|
17.2
|
1.0
|
CB
|
A:TYR77
|
4.4
|
17.4
|
1.0
|
O
|
A:PHE156
|
4.5
|
17.5
|
1.0
|
CG
|
A:PHE156
|
4.5
|
17.3
|
1.0
|
C2
|
C:TLA1300
|
4.5
|
25.1
|
1.0
|
CAK
|
A:Y3J1299
|
4.5
|
18.0
|
1.0
|
C
|
A:SER158
|
4.6
|
16.9
|
1.0
|
N
|
A:ARG159
|
4.6
|
17.9
|
1.0
|
CA
|
A:TYR157
|
4.7
|
17.2
|
1.0
|
CB
|
A:PHE156
|
4.8
|
18.6
|
1.0
|
N
|
A:PHE156
|
4.8
|
18.8
|
1.0
|
C
|
A:THR155
|
4.9
|
19.6
|
1.0
|
C3
|
C:TLA1300
|
4.9
|
25.9
|
1.0
|
CG
|
A:LEU17
|
5.0
|
16.5
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 3 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1299
b:21.1
occ:1.00
|
FAB
|
B:Y3J1299
|
0.0
|
21.1
|
1.0
|
CAH
|
B:Y3J1299
|
1.3
|
21.3
|
1.0
|
FAG
|
B:Y3J1299
|
2.2
|
22.4
|
1.0
|
CAI
|
B:Y3J1299
|
2.3
|
19.5
|
1.0
|
CAQ
|
B:Y3J1299
|
2.8
|
19.5
|
1.0
|
OG
|
B:SER158
|
2.9
|
19.2
|
1.0
|
OAS
|
B:Y3J1299
|
2.9
|
18.6
|
1.0
|
CB
|
B:SER158
|
3.0
|
18.1
|
1.0
|
N
|
B:SER158
|
3.2
|
18.1
|
1.0
|
CD1
|
B:PHE156
|
3.3
|
20.6
|
1.0
|
OAJ
|
B:Y3J1299
|
3.5
|
19.4
|
1.0
|
CA
|
B:SER158
|
3.7
|
18.0
|
1.0
|
O2
|
A:TLA1300
|
3.7
|
26.5
|
1.0
|
CD2
|
B:LEU17
|
3.8
|
18.2
|
1.0
|
CE1
|
B:PHE156
|
3.8
|
20.4
|
1.0
|
CA
|
B:PHE156
|
3.9
|
19.1
|
1.0
|
C
|
B:PHE156
|
4.0
|
19.0
|
1.0
|
N
|
B:TYR157
|
4.0
|
19.1
|
1.0
|
CAR
|
B:Y3J1299
|
4.1
|
20.3
|
1.0
|
O
|
B:THR155
|
4.2
|
20.8
|
1.0
|
CG
|
B:PHE156
|
4.4
|
20.2
|
1.0
|
C
|
B:TYR157
|
4.4
|
18.9
|
1.0
|
O
|
B:PHE156
|
4.5
|
18.8
|
1.0
|
C2
|
A:TLA1300
|
4.5
|
26.1
|
1.0
|
CB
|
B:TYR77
|
4.5
|
17.8
|
1.0
|
CAK
|
B:Y3J1299
|
4.5
|
19.1
|
1.0
|
N
|
B:ARG159
|
4.6
|
17.6
|
1.0
|
C
|
B:SER158
|
4.7
|
17.6
|
1.0
|
CB
|
B:PHE156
|
4.7
|
19.3
|
1.0
|
CA
|
B:TYR157
|
4.8
|
19.8
|
1.0
|
N
|
B:PHE156
|
4.8
|
19.0
|
1.0
|
C3
|
A:TLA1300
|
4.8
|
27.1
|
1.0
|
C
|
B:THR155
|
4.9
|
20.4
|
1.0
|
CG
|
B:LEU17
|
4.9
|
18.1
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 4 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1299
b:22.4
occ:1.00
|
FAG
|
B:Y3J1299
|
0.0
|
22.4
|
1.0
|
CAH
|
B:Y3J1299
|
1.4
|
21.3
|
1.0
|
FAB
|
B:Y3J1299
|
2.2
|
21.1
|
1.0
|
CAI
|
B:Y3J1299
|
2.3
|
19.5
|
1.0
|
N
|
B:TYR157
|
2.8
|
19.1
|
1.0
|
OAJ
|
B:Y3J1299
|
2.9
|
19.4
|
1.0
|
OG1
|
B:THR80
|
3.0
|
18.5
|
1.0
|
CA
|
B:PHE156
|
3.1
|
19.1
|
1.0
|
O
|
B:THR155
|
3.2
|
20.8
|
1.0
|
CB
|
B:THR80
|
3.2
|
19.9
|
1.0
|
C
|
B:PHE156
|
3.2
|
19.0
|
1.0
|
N
|
B:SER158
|
3.5
|
18.1
|
1.0
|
N
|
B:PHE156
|
3.5
|
19.0
|
1.0
|
C
|
B:THR155
|
3.5
|
20.4
|
1.0
|
CG2
|
B:THR80
|
3.6
|
20.3
|
1.0
|
CAQ
|
B:Y3J1299
|
3.7
|
19.5
|
1.0
|
CA
|
B:TYR157
|
3.8
|
19.8
|
1.0
|
O2
|
A:TLA1300
|
4.0
|
26.5
|
1.0
|
CB
|
B:TYR77
|
4.1
|
17.8
|
1.0
|
C
|
B:TYR157
|
4.1
|
18.9
|
1.0
|
O
|
B:TYR77
|
4.1
|
18.6
|
1.0
|
OAS
|
B:Y3J1299
|
4.1
|
18.6
|
1.0
|
CAK
|
B:Y3J1299
|
4.1
|
19.1
|
1.0
|
CB
|
B:TYR157
|
4.1
|
20.5
|
1.0
|
OG
|
B:SER158
|
4.2
|
19.2
|
1.0
|
O
|
B:PHE156
|
4.2
|
18.8
|
1.0
|
CD1
|
B:PHE156
|
4.3
|
20.6
|
1.0
|
CAR
|
B:Y3J1299
|
4.4
|
20.3
|
1.0
|
CB
|
B:SER158
|
4.5
|
18.1
|
1.0
|
CB
|
B:PHE156
|
4.5
|
19.3
|
1.0
|
CA
|
B:SER158
|
4.6
|
18.0
|
1.0
|
CA
|
B:THR155
|
4.6
|
20.9
|
1.0
|
CA
|
B:THR80
|
4.6
|
20.6
|
1.0
|
CG
|
B:TYR77
|
4.9
|
18.4
|
1.0
|
CG
|
B:PHE156
|
4.9
|
20.2
|
1.0
|
C
|
B:TYR77
|
5.0
|
18.0
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 5 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1299
b:21.2
occ:1.00
|
FAB
|
C:Y3J1299
|
0.0
|
21.2
|
1.0
|
CAH
|
C:Y3J1299
|
1.2
|
20.5
|
1.0
|
FAG
|
C:Y3J1299
|
2.1
|
21.3
|
1.0
|
CAI
|
C:Y3J1299
|
2.3
|
18.9
|
1.0
|
CAQ
|
C:Y3J1299
|
2.8
|
20.0
|
1.0
|
OAS
|
C:Y3J1299
|
2.9
|
18.9
|
1.0
|
OG
|
C:SER158
|
2.9
|
16.4
|
1.0
|
CB
|
C:SER158
|
3.0
|
16.8
|
1.0
|
N
|
C:SER158
|
3.2
|
17.6
|
1.0
|
CD1
|
C:PHE156
|
3.3
|
18.2
|
1.0
|
OAJ
|
C:Y3J1299
|
3.4
|
18.5
|
1.0
|
O2
|
B:TLA1300
|
3.7
|
28.0
|
1.0
|
CA
|
C:SER158
|
3.7
|
17.5
|
1.0
|
CA
|
C:PHE156
|
3.8
|
18.2
|
1.0
|
CE1
|
C:PHE156
|
3.8
|
18.2
|
1.0
|
CD2
|
C:LEU17
|
3.8
|
18.2
|
1.0
|
C
|
C:PHE156
|
3.9
|
18.7
|
1.0
|
N
|
C:TYR157
|
4.0
|
17.9
|
1.0
|
O
|
C:THR155
|
4.1
|
19.1
|
1.0
|
CAR
|
C:Y3J1299
|
4.1
|
20.9
|
1.0
|
C
|
C:TYR157
|
4.4
|
17.4
|
1.0
|
CG
|
C:PHE156
|
4.4
|
18.2
|
1.0
|
O
|
C:PHE156
|
4.4
|
18.9
|
1.0
|
C2
|
B:TLA1300
|
4.4
|
26.6
|
1.0
|
CB
|
C:TYR77
|
4.5
|
17.1
|
1.0
|
CAK
|
C:Y3J1299
|
4.5
|
18.6
|
1.0
|
N
|
C:ARG159
|
4.6
|
17.3
|
1.0
|
C
|
C:SER158
|
4.7
|
17.1
|
1.0
|
CA
|
C:TYR157
|
4.7
|
18.4
|
1.0
|
CB
|
C:PHE156
|
4.7
|
19.0
|
1.0
|
N
|
C:PHE156
|
4.7
|
18.2
|
1.0
|
C
|
C:THR155
|
4.8
|
18.5
|
1.0
|
C3
|
B:TLA1300
|
4.8
|
28.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 5fiu
Go back to
Fluorine Binding Sites List in 5fiu
Fluorine binding site 6 out
of 6 in the Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Binding and Structural Studies of A 5,5-Difluoromethyl Adenosine Nucleoside with the Fluorinase Enzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1299
b:21.3
occ:1.00
|
FAG
|
C:Y3J1299
|
0.0
|
21.3
|
1.0
|
CAH
|
C:Y3J1299
|
1.3
|
20.5
|
1.0
|
FAB
|
C:Y3J1299
|
2.1
|
21.2
|
1.0
|
CAI
|
C:Y3J1299
|
2.2
|
18.9
|
1.0
|
N
|
C:TYR157
|
2.8
|
17.9
|
1.0
|
OAJ
|
C:Y3J1299
|
2.9
|
18.5
|
1.0
|
OG1
|
C:THR80
|
3.0
|
17.1
|
1.0
|
O
|
C:THR155
|
3.1
|
19.1
|
1.0
|
CA
|
C:PHE156
|
3.1
|
18.2
|
1.0
|
CB
|
C:THR80
|
3.2
|
18.4
|
1.0
|
C
|
C:PHE156
|
3.2
|
18.7
|
1.0
|
C
|
C:THR155
|
3.5
|
18.5
|
1.0
|
N
|
C:PHE156
|
3.5
|
18.2
|
1.0
|
N
|
C:SER158
|
3.5
|
17.6
|
1.0
|
CG2
|
C:THR80
|
3.6
|
18.0
|
1.0
|
CAQ
|
C:Y3J1299
|
3.6
|
20.0
|
1.0
|
CA
|
C:TYR157
|
3.8
|
18.4
|
1.0
|
O2
|
B:TLA1300
|
4.0
|
28.0
|
1.0
|
OAS
|
C:Y3J1299
|
4.1
|
18.9
|
1.0
|
C
|
C:TYR157
|
4.1
|
17.4
|
1.0
|
CB
|
C:TYR77
|
4.1
|
17.1
|
1.0
|
O
|
C:TYR77
|
4.1
|
16.7
|
1.0
|
CAK
|
C:Y3J1299
|
4.1
|
18.6
|
1.0
|
CB
|
C:TYR157
|
4.1
|
19.1
|
1.0
|
O
|
C:PHE156
|
4.2
|
18.9
|
1.0
|
OG
|
C:SER158
|
4.2
|
16.4
|
1.0
|
CD1
|
C:PHE156
|
4.3
|
18.2
|
1.0
|
CAR
|
C:Y3J1299
|
4.4
|
20.9
|
1.0
|
CB
|
C:SER158
|
4.5
|
16.8
|
1.0
|
CB
|
C:PHE156
|
4.5
|
19.0
|
1.0
|
CA
|
C:THR155
|
4.6
|
17.8
|
1.0
|
CA
|
C:SER158
|
4.6
|
17.5
|
1.0
|
CA
|
C:THR80
|
4.6
|
19.1
|
1.0
|
CG
|
C:PHE156
|
4.8
|
18.2
|
1.0
|
CG
|
C:TYR77
|
4.9
|
17.2
|
1.0
|
|
Reference:
S.Thompson,
S.A.Mcmahon,
J.H.Naismith,
D.O'hagan.
Exploration of A Potential Difluoromethyl-Nucleoside Substrate with the Fluorinase Enzyme. Bioorg.Chem. V. 64 37 2015.
ISSN: ISSN 0045-2068
PubMed: 26642178
DOI: 10.1016/J.BIOORG.2015.11.003
Page generated: Thu Aug 1 09:25:39 2024
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