Fluorine in PDB 3dn0: Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
Enzymatic activity of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
All present enzymatic activity of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant:
3.2.1.17;
Protein crystallography data
The structure of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn0
was solved by
L.Liu,
B.W.Matthews,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.41 /
1.80
|
|
Space group
|
P 32 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.756,
59.756,
94.856,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
19.3 /
22.2
|
Other elements in 3dn0:
The structure of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
(pdb code 3dn0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the
Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 1 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:27.4
occ:0.43
|
F6
|
A:F5B900
|
0.0
|
27.4
|
0.4
|
|
C6
|
A:F5B900
|
1.3
|
27.4
|
0.4
|
|
C5
|
A:F5B900
|
1.5
|
25.6
|
0.4
|
|
C6
|
A:F5B900
|
2.3
|
25.4
|
0.4
|
|
C5
|
A:F5B900
|
2.4
|
27.6
|
0.4
|
|
C1
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
F6
|
A:F5B900
|
2.5
|
25.7
|
0.4
|
|
C4
|
A:F5B900
|
2.7
|
25.4
|
0.4
|
|
F1
|
A:F5B900
|
2.8
|
27.4
|
0.4
|
|
SD
|
A:MET102
|
3.1
|
16.8
|
1.0
|
|
F4
|
A:F5B900
|
3.1
|
25.4
|
0.4
|
|
CZ
|
A:PHE153
|
3.4
|
14.9
|
1.0
|
|
C1
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
C4
|
A:F5B900
|
3.6
|
27.6
|
0.4
|
|
C2
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
CE2
|
A:PHE153
|
3.8
|
14.5
|
1.0
|
|
C3
|
A:F5B900
|
3.9
|
25.6
|
0.4
|
|
CD1
|
A:LEU121
|
4.0
|
17.1
|
1.0
|
|
C3
|
A:F5B900
|
4.1
|
27.4
|
0.4
|
|
CE
|
A:MET102
|
4.2
|
17.2
|
1.0
|
|
CD2
|
A:LEU118
|
4.2
|
19.3
|
1.0
|
|
C2
|
A:F5B900
|
4.2
|
25.4
|
0.4
|
|
CE1
|
A:PHE153
|
4.3
|
14.5
|
1.0
|
|
CG
|
A:MET102
|
4.4
|
14.9
|
1.0
|
|
CA
|
A:ALA99
|
4.4
|
12.8
|
1.0
|
|
CB
|
A:MET102
|
4.6
|
14.3
|
1.0
|
|
CB
|
A:ALA99
|
4.6
|
12.7
|
1.0
|
|
F1
|
A:F5B900
|
4.6
|
24.8
|
0.4
|
|
F2
|
A:F5B900
|
4.7
|
26.9
|
0.4
|
|
F4
|
A:F5B900
|
4.7
|
27.6
|
0.4
|
|
CD2
|
A:LEU133
|
4.9
|
13.9
|
1.0
|
|
CD2
|
A:PHE153
|
4.9
|
15.1
|
1.0
|
|
Fluorine binding site 2 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 2 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:25.7
occ:0.40
|
F6
|
A:F5B900
|
0.0
|
25.7
|
0.4
|
|
F1
|
A:F5B900
|
0.3
|
27.4
|
0.4
|
|
C1
|
A:F5B900
|
1.2
|
27.4
|
0.4
|
|
C6
|
A:F5B900
|
1.3
|
25.4
|
0.4
|
|
C6
|
A:F5B900
|
2.1
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
2.3
|
27.4
|
0.4
|
|
C1
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C5
|
A:F5B900
|
2.4
|
25.6
|
0.4
|
|
F6
|
A:F5B900
|
2.5
|
27.4
|
0.4
|
|
F1
|
A:F5B900
|
2.7
|
24.8
|
0.4
|
|
F2
|
A:F5B900
|
2.8
|
26.9
|
0.4
|
|
CD1
|
A:LEU121
|
3.1
|
17.1
|
1.0
|
|
C5
|
A:F5B900
|
3.4
|
27.6
|
0.4
|
|
CZ
|
A:PHE153
|
3.4
|
14.9
|
1.0
|
|
CE1
|
A:PHE153
|
3.5
|
14.5
|
1.0
|
|
C3
|
A:F5B900
|
3.5
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
C4
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
CD2
|
A:LEU118
|
3.9
|
19.3
|
1.0
|
|
C4
|
A:F5B900
|
3.9
|
27.6
|
0.4
|
|
CB
|
A:ALA99
|
4.0
|
12.7
|
1.0
|
|
CD1
|
A:LEU91
|
4.1
|
16.4
|
1.0
|
|
C3
|
A:F5B900
|
4.1
|
25.6
|
0.4
|
|
CG1
|
A:VAL87
|
4.1
|
18.2
|
1.0
|
|
CG
|
A:LEU121
|
4.4
|
15.3
|
1.0
|
|
CE2
|
A:PHE153
|
4.5
|
14.5
|
1.0
|
|
CA
|
A:ALA99
|
4.5
|
12.8
|
1.0
|
|
CD1
|
A:PHE153
|
4.6
|
14.4
|
1.0
|
|
CB
|
A:LEU121
|
4.7
|
16.2
|
1.0
|
|
F3
|
A:F5B900
|
4.7
|
27.3
|
0.4
|
|
F2
|
A:F5B900
|
4.7
|
25.7
|
0.4
|
|
F4
|
A:F5B900
|
4.7
|
25.4
|
0.4
|
|
Fluorine binding site 3 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 3 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:27.4
occ:0.43
|
F1
|
A:F5B900
|
0.0
|
27.4
|
0.4
|
|
F6
|
A:F5B900
|
0.3
|
25.7
|
0.4
|
|
C1
|
A:F5B900
|
1.3
|
27.4
|
0.4
|
|
C6
|
A:F5B900
|
1.6
|
25.4
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C6
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C1
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
F1
|
A:F5B900
|
2.6
|
24.8
|
0.4
|
|
C5
|
A:F5B900
|
2.7
|
25.6
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
26.9
|
0.4
|
|
F6
|
A:F5B900
|
2.8
|
27.4
|
0.4
|
|
CD1
|
A:LEU121
|
2.9
|
17.1
|
1.0
|
|
CE1
|
A:PHE153
|
3.6
|
14.5
|
1.0
|
|
CZ
|
A:PHE153
|
3.6
|
14.9
|
1.0
|
|
C3
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
C5
|
A:F5B900
|
3.6
|
27.6
|
0.4
|
|
C2
|
A:F5B900
|
3.7
|
25.4
|
0.4
|
|
CG1
|
A:VAL87
|
3.8
|
18.2
|
1.0
|
|
CD2
|
A:LEU118
|
3.8
|
19.3
|
1.0
|
|
C4
|
A:F5B900
|
3.9
|
25.4
|
0.4
|
|
CD1
|
A:LEU91
|
3.9
|
16.4
|
1.0
|
|
C4
|
A:F5B900
|
4.1
|
27.6
|
0.4
|
|
CB
|
A:ALA99
|
4.2
|
12.7
|
1.0
|
|
CG
|
A:LEU121
|
4.2
|
15.3
|
1.0
|
|
C3
|
A:F5B900
|
4.3
|
25.6
|
0.4
|
|
CB
|
A:LEU121
|
4.4
|
16.2
|
1.0
|
|
CD1
|
A:PHE153
|
4.6
|
14.4
|
1.0
|
|
CE2
|
A:PHE153
|
4.7
|
14.5
|
1.0
|
|
F3
|
A:F5B900
|
4.7
|
27.3
|
0.4
|
|
CA
|
A:ALA99
|
4.8
|
12.8
|
1.0
|
|
F2
|
A:F5B900
|
4.8
|
25.7
|
0.4
|
|
CB
|
A:VAL87
|
4.9
|
17.8
|
1.0
|
|
CG
|
A:LEU91
|
5.0
|
15.3
|
1.0
|
|
Fluorine binding site 4 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 4 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:24.8
occ:0.40
|
F1
|
A:F5B900
|
0.0
|
24.8
|
0.4
|
|
F2
|
A:F5B900
|
0.2
|
26.9
|
0.4
|
|
C2
|
A:F5B900
|
1.3
|
27.4
|
0.4
|
|
C1
|
A:F5B900
|
1.3
|
25.4
|
0.4
|
|
C1
|
A:F5B900
|
2.3
|
27.4
|
0.4
|
|
C3
|
A:F5B900
|
2.3
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C6
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
F1
|
A:F5B900
|
2.6
|
27.4
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
25.7
|
0.4
|
|
F6
|
A:F5B900
|
2.7
|
25.7
|
0.4
|
|
F3
|
A:F5B900
|
2.7
|
27.3
|
0.4
|
|
N
|
A:TYR88
|
3.3
|
17.0
|
1.0
|
|
CG1
|
A:VAL87
|
3.4
|
18.2
|
1.0
|
|
CA
|
A:TYR88
|
3.5
|
17.1
|
1.0
|
|
C6
|
A:F5B900
|
3.5
|
27.4
|
0.4
|
|
C4
|
A:F5B900
|
3.6
|
27.6
|
0.4
|
|
CB
|
A:VAL87
|
3.6
|
17.8
|
1.0
|
|
C3
|
A:F5B900
|
3.6
|
25.6
|
0.4
|
|
C5
|
A:F5B900
|
3.6
|
25.6
|
0.4
|
|
C
|
A:VAL87
|
3.7
|
17.3
|
1.0
|
|
CD1
|
A:LEU91
|
3.7
|
16.4
|
1.0
|
|
CB
|
A:ALA99
|
3.8
|
12.7
|
1.0
|
|
CB
|
A:TYR88
|
3.9
|
17.3
|
1.0
|
|
C5
|
A:F5B900
|
4.0
|
27.6
|
0.4
|
|
O
|
A:VAL87
|
4.1
|
16.6
|
1.0
|
|
C4
|
A:F5B900
|
4.1
|
25.4
|
0.4
|
|
O
|
A:LEU84
|
4.1
|
19.8
|
1.0
|
|
CA
|
A:VAL87
|
4.3
|
17.4
|
1.0
|
|
CD2
|
A:LEU118
|
4.3
|
19.3
|
1.0
|
|
CD1
|
A:TYR88
|
4.5
|
18.5
|
1.0
|
|
F6
|
A:F5B900
|
4.6
|
27.4
|
0.4
|
|
CG
|
A:LEU91
|
4.7
|
15.3
|
1.0
|
|
F4
|
A:F5B900
|
4.7
|
27.6
|
0.4
|
|
F3
|
A:F5B900
|
4.7
|
25.3
|
0.4
|
|
CG
|
A:TYR88
|
4.7
|
17.5
|
1.0
|
|
CG2
|
A:VAL87
|
4.9
|
17.9
|
1.0
|
|
C
|
A:TYR88
|
5.0
|
16.8
|
1.0
|
|
Fluorine binding site 5 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 5 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:27.6
occ:0.43
|
F4
|
A:F5B900
|
0.0
|
27.6
|
0.4
|
|
F3
|
A:F5B900
|
0.3
|
25.3
|
0.4
|
|
C3
|
A:F5B900
|
1.2
|
25.6
|
0.4
|
|
C4
|
A:F5B900
|
1.3
|
27.6
|
0.4
|
|
C4
|
A:F5B900
|
2.1
|
25.4
|
0.4
|
|
C2
|
A:F5B900
|
2.3
|
25.4
|
0.4
|
|
C5
|
A:F5B900
|
2.4
|
27.6
|
0.4
|
|
C3
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
F4
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
F3
|
A:F5B900
|
2.7
|
27.3
|
0.4
|
|
F2
|
A:F5B900
|
2.9
|
25.7
|
0.4
|
|
CG2
|
A:VAL103
|
3.0
|
15.1
|
1.0
|
|
C5
|
A:F5B900
|
3.4
|
25.6
|
0.4
|
|
CD2
|
A:LEU84
|
3.5
|
21.4
|
1.0
|
|
C1
|
A:F5B900
|
3.5
|
25.4
|
0.4
|
|
CD1
|
A:LEU84
|
3.6
|
21.6
|
1.0
|
|
C6
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
CG1
|
A:ILE78
|
3.8
|
19.6
|
1.0
|
|
CG
|
A:LEU84
|
3.9
|
21.2
|
1.0
|
|
C6
|
A:F5B900
|
3.9
|
25.4
|
0.4
|
|
C1
|
A:F5B900
|
4.1
|
27.4
|
0.4
|
|
CG2
|
A:VAL111
|
4.1
|
34.9
|
1.0
|
|
O
|
A:ALA99
|
4.1
|
12.8
|
1.0
|
|
CB
|
A:LEU84
|
4.2
|
21.5
|
1.0
|
|
CD1
|
A:ILE78
|
4.2
|
19.7
|
1.0
|
|
CG1
|
A:VAL111
|
4.4
|
34.8
|
1.0
|
|
CB
|
A:VAL103
|
4.4
|
14.6
|
1.0
|
|
CB
|
A:VAL111
|
4.5
|
34.5
|
1.0
|
|
F1
|
A:F5B900
|
4.7
|
24.8
|
0.4
|
|
F6
|
A:F5B900
|
4.7
|
27.4
|
0.4
|
|
F2
|
A:F5B900
|
4.7
|
26.9
|
0.4
|
|
CB
|
A:ALA99
|
4.7
|
12.7
|
1.0
|
|
C
|
A:ALA99
|
4.8
|
12.9
|
1.0
|
|
CB
|
A:ILE78
|
4.9
|
19.5
|
1.0
|
|
CG2
|
A:ILE78
|
4.9
|
19.2
|
1.0
|
|
Fluorine binding site 6 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 6 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:25.4
occ:0.40
|
F4
|
A:F5B900
|
0.0
|
25.4
|
0.4
|
|
C4
|
A:F5B900
|
1.3
|
25.4
|
0.4
|
|
C5
|
A:F5B900
|
1.5
|
27.6
|
0.4
|
|
C4
|
A:F5B900
|
2.2
|
27.6
|
0.4
|
|
C3
|
A:F5B900
|
2.4
|
25.6
|
0.4
|
|
C5
|
A:F5B900
|
2.4
|
25.6
|
0.4
|
|
F4
|
A:F5B900
|
2.4
|
27.6
|
0.4
|
|
C6
|
A:F5B900
|
2.7
|
27.4
|
0.4
|
|
F3
|
A:F5B900
|
2.7
|
25.3
|
0.4
|
|
CG1
|
A:VAL111
|
3.1
|
34.8
|
1.0
|
|
F6
|
A:F5B900
|
3.1
|
27.4
|
0.4
|
|
CB
|
A:VAL111
|
3.5
|
34.5
|
1.0
|
|
C3
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
C6
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
CB
|
A:MET102
|
3.6
|
14.3
|
1.0
|
|
CG2
|
A:VAL103
|
3.7
|
15.1
|
1.0
|
|
O
|
A:ALA99
|
3.8
|
12.8
|
1.0
|
|
C1
|
A:F5B900
|
3.9
|
27.4
|
0.4
|
|
CG2
|
A:VAL111
|
4.0
|
34.9
|
1.0
|
|
SD
|
A:MET102
|
4.1
|
16.8
|
1.0
|
|
C1
|
A:F5B900
|
4.1
|
25.4
|
0.4
|
|
C2
|
A:F5B900
|
4.2
|
27.4
|
0.4
|
|
N
|
A:VAL103
|
4.4
|
14.4
|
1.0
|
|
CG
|
A:MET102
|
4.5
|
14.9
|
1.0
|
|
CE
|
A:MET102
|
4.5
|
17.2
|
1.0
|
|
F3
|
A:F5B900
|
4.6
|
27.3
|
0.4
|
|
C
|
A:ALA99
|
4.7
|
12.9
|
1.0
|
|
CA
|
A:ALA99
|
4.7
|
12.8
|
1.0
|
|
CD2
|
A:LEU84
|
4.7
|
21.4
|
1.0
|
|
F2
|
A:F5B900
|
4.7
|
25.7
|
0.4
|
|
F6
|
A:F5B900
|
4.7
|
25.7
|
0.4
|
|
C
|
A:MET102
|
4.8
|
14.3
|
1.0
|
|
CA
|
A:MET102
|
4.8
|
14.6
|
1.0
|
|
CB
|
A:VAL103
|
4.9
|
14.6
|
1.0
|
|
CA
|
A:VAL103
|
5.0
|
14.8
|
1.0
|
|
CA
|
A:VAL111
|
5.0
|
34.5
|
1.0
|
|
CB
|
A:ALA99
|
5.0
|
12.7
|
1.0
|
|
Fluorine binding site 7 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 7 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:27.3
occ:0.43
|
F3
|
A:F5B900
|
0.0
|
27.3
|
0.4
|
|
F2
|
A:F5B900
|
0.2
|
25.7
|
0.4
|
|
C2
|
A:F5B900
|
1.2
|
25.4
|
0.4
|
|
C3
|
A:F5B900
|
1.3
|
27.4
|
0.4
|
|
C3
|
A:F5B900
|
2.2
|
25.6
|
0.4
|
|
C1
|
A:F5B900
|
2.3
|
25.4
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C4
|
A:F5B900
|
2.4
|
27.6
|
0.4
|
|
F3
|
A:F5B900
|
2.6
|
25.3
|
0.4
|
|
F1
|
A:F5B900
|
2.7
|
24.8
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
26.9
|
0.4
|
|
F4
|
A:F5B900
|
2.7
|
27.6
|
0.4
|
|
CB
|
A:LEU84
|
3.3
|
21.5
|
1.0
|
|
CG2
|
A:ILE78
|
3.4
|
19.2
|
1.0
|
|
O
|
A:LEU84
|
3.4
|
19.8
|
1.0
|
|
C4
|
A:F5B900
|
3.5
|
25.4
|
0.4
|
|
C6
|
A:F5B900
|
3.5
|
25.4
|
0.4
|
|
C1
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
C5
|
A:F5B900
|
3.6
|
27.6
|
0.4
|
|
CB
|
A:TYR88
|
3.8
|
17.3
|
1.0
|
|
CA
|
A:LEU84
|
3.8
|
21.3
|
1.0
|
|
C
|
A:LEU84
|
3.8
|
20.4
|
1.0
|
|
CG1
|
A:ILE78
|
3.9
|
19.6
|
1.0
|
|
CD2
|
A:LEU84
|
3.9
|
21.4
|
1.0
|
|
C5
|
A:F5B900
|
4.0
|
25.6
|
0.4
|
|
CG
|
A:LEU84
|
4.1
|
21.2
|
1.0
|
|
C6
|
A:F5B900
|
4.1
|
27.4
|
0.4
|
|
CD1
|
A:ILE78
|
4.2
|
19.7
|
1.0
|
|
CB
|
A:ILE78
|
4.2
|
19.5
|
1.0
|
|
CD1
|
A:TYR88
|
4.3
|
18.5
|
1.0
|
|
CB
|
A:ALA99
|
4.3
|
12.7
|
1.0
|
|
N
|
A:TYR88
|
4.3
|
17.0
|
1.0
|
|
CA
|
A:TYR88
|
4.4
|
17.1
|
1.0
|
|
CG
|
A:TYR88
|
4.5
|
17.5
|
1.0
|
|
CD1
|
A:LEU84
|
4.5
|
21.6
|
1.0
|
|
F4
|
A:F5B900
|
4.6
|
25.4
|
0.4
|
|
F6
|
A:F5B900
|
4.7
|
25.7
|
0.4
|
|
F1
|
A:F5B900
|
4.7
|
27.4
|
0.4
|
|
CD2
|
A:LEU118
|
4.9
|
19.3
|
1.0
|
|
N
|
A:LYS85
|
4.9
|
19.5
|
1.0
|
|
Fluorine binding site 8 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 8 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:25.3
occ:0.40
|
F3
|
A:F5B900
|
0.0
|
25.3
|
0.4
|
|
F4
|
A:F5B900
|
0.3
|
27.6
|
0.4
|
|
C3
|
A:F5B900
|
1.3
|
25.6
|
0.4
|
|
C4
|
A:F5B900
|
1.5
|
27.6
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C4
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C3
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
F3
|
A:F5B900
|
2.6
|
27.3
|
0.4
|
|
C5
|
A:F5B900
|
2.7
|
27.6
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
25.7
|
0.4
|
|
F4
|
A:F5B900
|
2.7
|
25.4
|
0.4
|
|
CG2
|
A:VAL103
|
3.0
|
15.1
|
1.0
|
|
CD1
|
A:LEU84
|
3.3
|
21.6
|
1.0
|
|
CD2
|
A:LEU84
|
3.4
|
21.4
|
1.0
|
|
CG1
|
A:ILE78
|
3.5
|
19.6
|
1.0
|
|
C1
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
C5
|
A:F5B900
|
3.6
|
25.6
|
0.4
|
|
CG
|
A:LEU84
|
3.7
|
21.2
|
1.0
|
|
C2
|
A:F5B900
|
3.7
|
27.4
|
0.4
|
|
CB
|
A:LEU84
|
3.9
|
21.5
|
1.0
|
|
C6
|
A:F5B900
|
3.9
|
27.4
|
0.4
|
|
CD1
|
A:ILE78
|
4.0
|
19.7
|
1.0
|
|
C6
|
A:F5B900
|
4.1
|
25.4
|
0.4
|
|
CG2
|
A:VAL111
|
4.2
|
34.9
|
1.0
|
|
O
|
A:ALA99
|
4.3
|
12.8
|
1.0
|
|
C1
|
A:F5B900
|
4.3
|
27.4
|
0.4
|
|
CB
|
A:VAL103
|
4.5
|
14.6
|
1.0
|
|
CB
|
A:ILE78
|
4.6
|
19.5
|
1.0
|
|
CG2
|
A:ILE78
|
4.6
|
19.2
|
1.0
|
|
CG1
|
A:VAL111
|
4.7
|
34.8
|
1.0
|
|
F1
|
A:F5B900
|
4.7
|
24.8
|
0.4
|
|
CB
|
A:VAL111
|
4.7
|
34.5
|
1.0
|
|
F2
|
A:F5B900
|
4.8
|
26.9
|
0.4
|
|
CB
|
A:ALA99
|
4.8
|
12.7
|
1.0
|
|
C
|
A:ALA99
|
5.0
|
12.9
|
1.0
|
|
Fluorine binding site 9 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 9 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:26.9
occ:0.43
|
F2
|
A:F5B900
|
0.0
|
26.9
|
0.4
|
|
F1
|
A:F5B900
|
0.2
|
24.8
|
0.4
|
|
C2
|
A:F5B900
|
1.3
|
27.4
|
0.4
|
|
C1
|
A:F5B900
|
1.4
|
25.4
|
0.4
|
|
C1
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C3
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C6
|
A:F5B900
|
2.5
|
25.4
|
0.4
|
|
F1
|
A:F5B900
|
2.7
|
27.4
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
25.7
|
0.4
|
|
F3
|
A:F5B900
|
2.7
|
27.3
|
0.4
|
|
F6
|
A:F5B900
|
2.8
|
25.7
|
0.4
|
|
N
|
A:TYR88
|
3.2
|
17.0
|
1.0
|
|
CG1
|
A:VAL87
|
3.2
|
18.2
|
1.0
|
|
CB
|
A:VAL87
|
3.4
|
17.8
|
1.0
|
|
CA
|
A:TYR88
|
3.5
|
17.1
|
1.0
|
|
C
|
A:VAL87
|
3.5
|
17.3
|
1.0
|
|
C6
|
A:F5B900
|
3.6
|
27.4
|
0.4
|
|
C4
|
A:F5B900
|
3.6
|
27.6
|
0.4
|
|
C3
|
A:F5B900
|
3.7
|
25.6
|
0.4
|
|
C5
|
A:F5B900
|
3.7
|
25.6
|
0.4
|
|
CD1
|
A:LEU91
|
3.8
|
16.4
|
1.0
|
|
CB
|
A:TYR88
|
3.9
|
17.3
|
1.0
|
|
CB
|
A:ALA99
|
4.0
|
12.7
|
1.0
|
|
O
|
A:LEU84
|
4.0
|
19.8
|
1.0
|
|
O
|
A:VAL87
|
4.0
|
16.6
|
1.0
|
|
CA
|
A:VAL87
|
4.1
|
17.4
|
1.0
|
|
C5
|
A:F5B900
|
4.1
|
27.6
|
0.4
|
|
C4
|
A:F5B900
|
4.2
|
25.4
|
0.4
|
|
CD2
|
A:LEU118
|
4.2
|
19.3
|
1.0
|
|
CD1
|
A:TYR88
|
4.6
|
18.5
|
1.0
|
|
CG
|
A:LEU91
|
4.7
|
15.3
|
1.0
|
|
CG2
|
A:VAL87
|
4.7
|
17.9
|
1.0
|
|
F6
|
A:F5B900
|
4.7
|
27.4
|
0.4
|
|
F4
|
A:F5B900
|
4.7
|
27.6
|
0.4
|
|
CG
|
A:TYR88
|
4.7
|
17.5
|
1.0
|
|
F3
|
A:F5B900
|
4.8
|
25.3
|
0.4
|
|
C
|
A:TYR88
|
4.9
|
16.8
|
1.0
|
|
Fluorine binding site 10 out
of 10 in 3dn0
Go back to
Fluorine Binding Sites List in 3dn0
Fluorine binding site 10 out
of 10 in the Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Pentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F900
b:25.7
occ:0.40
|
F2
|
A:F5B900
|
0.0
|
25.7
|
0.4
|
|
F3
|
A:F5B900
|
0.2
|
27.3
|
0.4
|
|
C2
|
A:F5B900
|
1.3
|
25.4
|
0.4
|
|
C3
|
A:F5B900
|
1.5
|
27.4
|
0.4
|
|
C3
|
A:F5B900
|
2.4
|
25.6
|
0.4
|
|
C1
|
A:F5B900
|
2.4
|
25.4
|
0.4
|
|
C2
|
A:F5B900
|
2.4
|
27.4
|
0.4
|
|
C4
|
A:F5B900
|
2.5
|
27.6
|
0.4
|
|
F3
|
A:F5B900
|
2.7
|
25.3
|
0.4
|
|
F1
|
A:F5B900
|
2.7
|
24.8
|
0.4
|
|
F2
|
A:F5B900
|
2.7
|
26.9
|
0.4
|
|
F4
|
A:F5B900
|
2.9
|
27.6
|
0.4
|
|
CG2
|
A:ILE78
|
3.3
|
19.2
|
1.0
|
|
O
|
A:LEU84
|
3.3
|
19.8
|
1.0
|
|
CB
|
A:LEU84
|
3.4
|
21.5
|
1.0
|
|
C6
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
CB
|
A:TYR88
|
3.6
|
17.3
|
1.0
|
|
C4
|
A:F5B900
|
3.6
|
25.4
|
0.4
|
|
C1
|
A:F5B900
|
3.7
|
27.4
|
0.4
|
|
C5
|
A:F5B900
|
3.8
|
27.6
|
0.4
|
|
C
|
A:LEU84
|
3.8
|
20.4
|
1.0
|
|
CA
|
A:LEU84
|
3.8
|
21.3
|
1.0
|
|
CG1
|
A:ILE78
|
3.8
|
19.6
|
1.0
|
|
CD2
|
A:LEU84
|
4.0
|
21.4
|
1.0
|
|
C5
|
A:F5B900
|
4.1
|
25.6
|
0.4
|
|
CD1
|
A:TYR88
|
4.2
|
18.5
|
1.0
|
|
CB
|
A:ILE78
|
4.2
|
19.5
|
1.0
|
|
CG
|
A:LEU84
|
4.2
|
21.2
|
1.0
|
|
CD1
|
A:ILE78
|
4.2
|
19.7
|
1.0
|
|
N
|
A:TYR88
|
4.2
|
17.0
|
1.0
|
|
C6
|
A:F5B900
|
4.2
|
27.4
|
0.4
|
|
CB
|
A:ALA99
|
4.3
|
12.7
|
1.0
|
|
CA
|
A:TYR88
|
4.3
|
17.1
|
1.0
|
|
CG
|
A:TYR88
|
4.3
|
17.5
|
1.0
|
|
CD1
|
A:LEU84
|
4.6
|
21.6
|
1.0
|
|
F6
|
A:F5B900
|
4.7
|
25.7
|
0.4
|
|
F4
|
A:F5B900
|
4.7
|
25.4
|
0.4
|
|
F1
|
A:F5B900
|
4.8
|
27.4
|
0.4
|
|
N
|
A:LYS85
|
4.9
|
19.5
|
1.0
|
|
CA
|
A:ILE78
|
5.0
|
19.8
|
1.0
|
|
Reference:
L.Liu,
W.A.Baase,
B.W.Matthews.
Halogenated Benzenes Bound Within A Non-Polar Cavity in T4 Lysozyme Provide Examples of I...S and I...Se Halogen-Bonding. J.Mol.Biol. V. 385 595 2009.
ISSN: ISSN 0022-2836
PubMed: 19014950
DOI: 10.1016/J.JMB.2008.10.086
Page generated: Wed Jul 31 18:00:59 2024
|
