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Fluorine in PDB 3dn6: 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant

Enzymatic activity of 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant

All present enzymatic activity of 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant:
3.2.1.17;

Protein crystallography data

The structure of 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn6 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) 45.69 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 60.031, 60.031, 95.956, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 22.1

Other elements in 3dn6:

The structure of 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (pdb code 3dn6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3dn6

Go back to Fluorine Binding Sites List in 3dn6
Fluorine binding site 1 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:63.2
occ:0.55
 F1 A:F3B900 0.0 63.2 0.6
CL2 A:F3B900 1.1 15.3 0.2
C2 A:F3B900 1.3 15.1 0.2
C1 A:F3B900 1.3 63.2 0.6
C3 A:F3B900 1.7 15.0 0.2
F3 A:F3B900 1.9 14.8 0.2
C6 A:F3B900 2.4 63.2 0.6
C2 A:F3B900 2.4 63.2 0.6
C1 A:F3B900 2.6 15.1 0.2
CL6 A:F3B900 3.0 63.2 0.6
CL2 A:F3B900 3.0 63.2 0.6
C4 A:F3B900 3.1 15.0 0.2
CD2 A:LEU84 3.3 17.9 1.0
F1 A:F3B900 3.3 15.1 0.2
CG2 A:VAL103 3.3 13.2 1.0
C3 A:F3B900 3.6 63.1 0.6
C5 A:F3B900 3.6 63.1 0.6
C6 A:F3B900 3.6 15.0 0.2
CD1 A:LEU84 3.7 17.9 1.0
C5 A:F3B900 3.8 14.9 0.2
CG A:LEU84 4.0 17.1 1.0
C4 A:F3B900 4.1 63.2 0.6
CG2 A:VAL111 4.2 28.9 1.0
CG1 A:VAL111 4.2 28.7 1.0
O A:ALA99 4.3 10.2 1.0
CL4 A:F3B900 4.4 15.3 0.2
CB A:LEU84 4.5 16.8 1.0
CG1 A:ILE78 4.7 15.6 1.0
CB A:VAL111 4.7 28.2 1.0
F5 A:F3B900 4.7 63.1 0.6
F3 A:F3B900 4.7 63.2 0.6
CB A:VAL103 4.8 12.6 1.0
CD2 A:LEU118 4.8 17.8 1.0
CD1 A:ILE78 4.8 15.4 1.0
CB A:ALA99 4.9 10.5 1.0
C A:ALA99 5.0 10.2 1.0

Fluorine binding site 2 out of 6 in 3dn6

Go back to Fluorine Binding Sites List in 3dn6
Fluorine binding site 2 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:15.1
occ:0.25
 F1 A:F3B900 0.0 15.1 0.2
CL6 A:F3B900 0.4 63.2 0.6
C1 A:F3B900 1.3 15.1 0.2
C6 A:F3B900 2.0 63.2 0.6
C6 A:F3B900 2.4 15.0 0.2
C2 A:F3B900 2.4 15.1 0.2
C5 A:F3B900 2.8 63.1 0.6
F5 A:F3B900 2.8 63.1 0.6
CL6 A:F3B900 2.9 15.4 0.2
CL2 A:F3B900 2.9 15.3 0.2
CG2 A:VAL111 3.0 28.9 1.0
C1 A:F3B900 3.0 63.2 0.6
SD A:MET102 3.2 13.8 1.0
F1 A:F3B900 3.3 63.2 0.6
CE A:MET102 3.4 13.8 1.0
C5 A:F3B900 3.6 14.9 0.2
C3 A:F3B900 3.6 15.0 0.2
CB A:MET102 3.9 11.7 1.0
C4 A:F3B900 4.1 15.0 0.2
C4 A:F3B900 4.1 63.2 0.6
CG A:MET102 4.2 12.3 1.0
CB A:VAL111 4.2 28.2 1.0
C2 A:F3B900 4.3 63.2 0.6
CD2 A:LEU118 4.4 17.8 1.0
CB A:PHE114 4.7 20.2 1.0
C3 A:F3B900 4.7 63.1 0.6
F5 A:F3B900 4.7 14.6 0.2
F3 A:F3B900 4.7 14.8 0.2
CG A:PHE114 4.8 19.8 1.0
CG1 A:VAL111 4.8 28.7 1.0

Fluorine binding site 3 out of 6 in 3dn6

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Fluorine binding site 3 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:63.1
occ:0.55
 F5 A:F3B900 0.0 63.1 0.6
CL6 A:F3B900 0.8 15.4 0.2
C6 A:F3B900 1.1 15.0 0.2
C5 A:F3B900 1.3 63.1 0.6
C5 A:F3B900 2.0 14.9 0.2
C1 A:F3B900 2.3 15.1 0.2
C6 A:F3B900 2.4 63.2 0.6
C4 A:F3B900 2.4 63.2 0.6
F5 A:F3B900 2.4 14.6 0.2
F1 A:F3B900 2.8 15.1 0.2
CL6 A:F3B900 3.0 63.2 0.6
CL4 A:F3B900 3.0 63.2 0.6
C4 A:F3B900 3.3 15.0 0.2
CZ A:PHE153 3.3 11.8 1.0
CD1 A:LEU121 3.4 15.8 1.0
C2 A:F3B900 3.5 15.1 0.2
C1 A:F3B900 3.6 63.2 0.6
C3 A:F3B900 3.6 63.1 0.6
SD A:MET102 3.6 13.8 1.0
CE2 A:PHE153 3.7 11.8 1.0
C3 A:F3B900 3.9 15.0 0.2
CD2 A:LEU118 3.9 17.8 1.0
CE1 A:PHE153 4.1 12.2 1.0
C2 A:F3B900 4.1 63.2 0.6
CD2 A:LEU133 4.6 12.8 1.0
CE A:MET102 4.7 13.8 1.0
F1 A:F3B900 4.7 63.2 0.6
F3 A:F3B900 4.7 63.2 0.6
CL4 A:F3B900 4.7 15.3 0.2
CD2 A:PHE153 4.7 11.7 1.0
CA A:ALA99 4.9 10.3 1.0
CG A:LEU121 4.9 13.7 1.0
CB A:ALA99 5.0 10.5 1.0

Fluorine binding site 4 out of 6 in 3dn6

Go back to Fluorine Binding Sites List in 3dn6
Fluorine binding site 4 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:14.6
occ:0.25
 F5 A:F3B900 0.0 14.6 0.2
CL4 A:F3B900 0.8 63.2 0.6
C4 A:F3B900 1.1 63.2 0.6
C5 A:F3B900 1.3 14.9 0.2
C5 A:F3B900 2.0 63.1 0.6
C3 A:F3B900 2.2 63.1 0.6
C4 A:F3B900 2.4 15.0 0.2
C6 A:F3B900 2.4 15.0 0.2
F5 A:F3B900 2.4 63.1 0.6
F3 A:F3B900 2.8 63.2 0.6
CL4 A:F3B900 2.9 15.3 0.2
CL6 A:F3B900 3.1 15.4 0.2
C6 A:F3B900 3.3 63.2 0.6
CD1 A:LEU121 3.3 15.8 1.0
C2 A:F3B900 3.4 63.2 0.6
C3 A:F3B900 3.6 15.0 0.2
C1 A:F3B900 3.6 15.1 0.2
CG1 A:VAL87 3.7 14.6 1.0
CZ A:PHE153 3.7 11.8 1.0
CE1 A:PHE153 3.8 12.2 1.0
C1 A:F3B900 3.8 63.2 0.6
CD2 A:LEU118 3.9 17.8 1.0
CD1 A:LEU91 4.0 12.2 1.0
C2 A:F3B900 4.1 15.1 0.2
CB A:ALA99 4.2 10.5 1.0
CG A:LEU121 4.5 13.7 1.0
CB A:LEU121 4.5 13.5 1.0
CB A:VAL87 4.6 14.6 1.0
F3 A:F3B900 4.7 14.8 0.2
F1 A:F3B900 4.7 15.1 0.2
CL6 A:F3B900 4.7 63.2 0.6
CE2 A:PHE153 4.8 11.8 1.0
CD1 A:PHE153 4.8 11.8 1.0
CA A:ALA99 4.8 10.3 1.0
CL2 A:F3B900 5.0 63.2 0.6

Fluorine binding site 5 out of 6 in 3dn6

Go back to Fluorine Binding Sites List in 3dn6
Fluorine binding site 5 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:63.2
occ:0.55
 F3 A:F3B900 0.0 63.2 0.6
CL4 A:F3B900 0.4 15.3 0.2
C3 A:F3B900 1.3 63.1 0.6
C4 A:F3B900 2.0 15.0 0.2
C4 A:F3B900 2.4 63.2 0.6
C2 A:F3B900 2.4 63.2 0.6
C5 A:F3B900 2.8 14.9 0.2
F5 A:F3B900 2.8 14.6 0.2
CL4 A:F3B900 2.9 63.2 0.6
CL2 A:F3B900 3.0 63.2 0.6
C3 A:F3B900 3.0 15.0 0.2
N A:TYR88 3.2 13.6 1.0
CA A:TYR88 3.3 13.6 1.0
F3 A:F3B900 3.3 14.8 0.2
CB A:ALA99 3.6 10.5 1.0
C A:VAL87 3.6 14.0 1.0
C5 A:F3B900 3.6 63.1 0.6
C1 A:F3B900 3.6 63.2 0.6
CD1 A:LEU91 3.6 12.2 1.0
CB A:TYR88 3.6 13.9 1.0
CG1 A:VAL87 3.7 14.6 1.0
CB A:VAL87 3.8 14.6 1.0
O A:VAL87 4.1 13.5 1.0
O A:LEU84 4.1 15.3 1.0
C6 A:F3B900 4.1 15.0 0.2
C6 A:F3B900 4.1 63.2 0.6
CD1 A:TYR88 4.3 15.2 1.0
C2 A:F3B900 4.3 15.1 0.2
CA A:VAL87 4.3 14.3 1.0
CG A:TYR88 4.5 14.0 1.0
CG A:LEU91 4.7 11.4 1.0
C1 A:F3B900 4.7 15.1 0.2
F5 A:F3B900 4.7 63.1 0.6
F1 A:F3B900 4.7 63.2 0.6
C A:TYR88 4.8 13.5 1.0
CD2 A:LEU118 4.8 17.8 1.0
CA A:ALA99 4.9 10.3 1.0

Fluorine binding site 6 out of 6 in 3dn6

Go back to Fluorine Binding Sites List in 3dn6
Fluorine binding site 6 out of 6 in the 1,3,5-Trifluoro-2,4,6-Trichlorobenzene 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 1,3,5-Trifluoro-2,4,6-Trichlorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:14.8
occ:0.25
 F3 A:F3B900 0.0 14.8 0.2
CL2 A:F3B900 1.1 63.2 0.6
C2 A:F3B900 1.3 63.2 0.6
C3 A:F3B900 1.3 15.0 0.2
C1 A:F3B900 1.8 63.2 0.6
F1 A:F3B900 1.9 63.2 0.6
C4 A:F3B900 2.4 15.0 0.2
C2 A:F3B900 2.4 15.1 0.2
C3 A:F3B900 2.6 63.1 0.6
CL4 A:F3B900 3.0 15.3 0.2
CL2 A:F3B900 3.0 15.3 0.2
C6 A:F3B900 3.1 63.2 0.6
F3 A:F3B900 3.3 63.2 0.6
CD2 A:LEU84 3.5 17.9 1.0
C1 A:F3B900 3.6 15.1 0.2
C5 A:F3B900 3.6 14.9 0.2
C4 A:F3B900 3.7 63.2 0.6
CB A:LEU84 3.7 16.8 1.0
CG1 A:ILE78 3.8 15.6 1.0
C5 A:F3B900 3.9 63.1 0.6
CG A:LEU84 3.9 17.1 1.0
CD1 A:LEU84 3.9 17.9 1.0
CD1 A:ILE78 3.9 15.4 1.0
CG2 A:ILE78 4.1 15.1 1.0
CB A:ALA99 4.1 10.5 1.0
C6 A:F3B900 4.1 15.0 0.2
CG2 A:VAL103 4.1 13.2 1.0
O A:LEU84 4.4 15.3 1.0
CL6 A:F3B900 4.4 63.2 0.6
CA A:LEU84 4.5 16.8 1.0
CB A:ILE78 4.6 15.5 1.0
O A:ALA99 4.6 10.2 1.0
F5 A:F3B900 4.7 14.6 0.2
F1 A:F3B900 4.7 15.1 0.2
C A:LEU84 4.8 16.0 1.0
CA A:ALA99 4.8 10.3 1.0
C A:ALA99 4.9 10.2 1.0
CB A:TYR88 5.0 13.9 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: Mon Jul 14 15:56:11 2025

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