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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: Sun Dec 13 12:22:30 2020

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