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Chlorine 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:

Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dn6

Go back to Chlorine Binding Sites List in 3dn6
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:63.2
occ:0.55
 CL6 A:F3B900 0.0 63.2 0.6
F1 A:F3B900 0.4 15.1 0.2
C1 A:F3B900 1.2 15.1 0.2
C6 A:F3B900 1.8 63.2 0.6
C2 A:F3B900 2.1 15.1 0.2
C6 A:F3B900 2.4 15.0 0.2
CL2 A:F3B900 2.6 15.3 0.2
C1 A:F3B900 2.7 63.2 0.6
C5 A:F3B900 2.8 63.1 0.6
F1 A:F3B900 3.0 63.2 0.6
F5 A:F3B900 3.0 63.1 0.6
CG2 A:VAL111 3.0 28.9 1.0
CL6 A:F3B900 3.1 15.4 0.2
SD A:MET102 3.3 13.8 1.0
C3 A:F3B900 3.4 15.0 0.2
C5 A:F3B900 3.6 14.9 0.2
CE A:MET102 3.6 13.8 1.0
CB A:MET102 3.8 11.7 1.0
C4 A:F3B900 3.9 15.0 0.2
C2 A:F3B900 4.0 63.2 0.6
C4 A:F3B900 4.0 63.2 0.6
CB A:VAL111 4.2 28.2 1.0
CG A:MET102 4.2 12.3 1.0
F3 A:F3B900 4.4 14.8 0.2
CD2 A:LEU118 4.5 17.8 1.0
C3 A:F3B900 4.6 63.1 0.6
CG1 A:VAL111 4.7 28.7 1.0
F5 A:F3B900 4.7 14.6 0.2
O A:ALA99 4.9 10.2 1.0
CB A:PHE114 4.9 20.2 1.0

Chlorine binding site 2 out of 6 in 3dn6

Go back to Chlorine Binding Sites List in 3dn6
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:15.4
occ:0.25
 CL6 A:F3B900 0.0 15.4 0.2
F5 A:F3B900 0.8 63.1 0.6
C6 A:F3B900 1.8 15.0 0.2
C5 A:F3B900 2.1 63.1 0.6
C1 A:F3B900 2.7 15.1 0.2
C5 A:F3B900 2.8 14.9 0.2
F1 A:F3B900 2.9 15.1 0.2
C6 A:F3B900 2.9 63.2 0.6
F5 A:F3B900 3.1 14.6 0.2
CL6 A:F3B900 3.1 63.2 0.6
C4 A:F3B900 3.1 63.2 0.6
CD1 A:LEU121 3.2 15.8 1.0
SD A:MET102 3.5 13.8 1.0
CL4 A:F3B900 3.6 63.2 0.6
CZ A:PHE153 3.6 11.8 1.0
CE2 A:PHE153 3.8 11.8 1.0
CD2 A:LEU133 3.8 12.8 1.0
C2 A:F3B900 4.0 15.1 0.2
CD2 A:LEU118 4.0 17.8 1.0
C4 A:F3B900 4.1 15.0 0.2
C1 A:F3B900 4.3 63.2 0.6
CE A:MET102 4.3 13.8 1.0
C3 A:F3B900 4.4 63.1 0.6
CE1 A:PHE153 4.4 12.2 1.0
C3 A:F3B900 4.6 15.0 0.2
CD2 A:PHE153 4.6 11.7 1.0
CG A:LEU121 4.7 13.7 1.0
CD1 A:LEU133 4.8 11.7 1.0
C2 A:F3B900 4.8 63.2 0.6
CG A:LEU133 4.9 11.8 1.0
CG A:LEU118 5.0 15.7 1.0

Chlorine binding site 3 out of 6 in 3dn6

Go back to Chlorine Binding Sites List in 3dn6
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:63.2
occ:0.55
 CL4 A:F3B900 0.0 63.2 0.6
F5 A:F3B900 0.8 14.6 0.2
C4 A:F3B900 1.8 63.2 0.6
C5 A:F3B900 2.1 14.9 0.2
C3 A:F3B900 2.7 63.1 0.6
C5 A:F3B900 2.8 63.1 0.6
F3 A:F3B900 2.9 63.2 0.6
C4 A:F3B900 3.0 15.0 0.2
F5 A:F3B900 3.0 63.1 0.6
C6 A:F3B900 3.1 15.0 0.2
CD1 A:LEU121 3.2 15.8 1.0
CL4 A:F3B900 3.2 15.3 0.2
CD1 A:LEU91 3.4 12.2 1.0
CE1 A:PHE153 3.4 12.2 1.0
CG1 A:VAL87 3.5 14.6 1.0
CL6 A:F3B900 3.6 15.4 0.2
CZ A:PHE153 3.7 11.8 1.0
CB A:LEU121 4.0 13.5 1.0
C2 A:F3B900 4.0 63.2 0.6
C6 A:F3B900 4.1 63.2 0.6
CG A:LEU121 4.1 13.7 1.0
CG A:LEU91 4.3 11.4 1.0
C3 A:F3B900 4.3 15.0 0.2
CB A:ALA99 4.4 10.5 1.0
CD1 A:PHE153 4.4 11.8 1.0
CD2 A:LEU91 4.4 11.6 1.0
C1 A:F3B900 4.4 15.1 0.2
CD2 A:LEU118 4.5 17.8 1.0
C1 A:F3B900 4.6 63.2 0.6
CB A:VAL87 4.6 14.6 1.0
CD2 A:LEU121 4.7 14.9 1.0
CE2 A:PHE153 4.8 11.8 1.0
C2 A:F3B900 4.9 15.1 0.2

Chlorine binding site 4 out of 6 in 3dn6

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:15.3
occ:0.25
 CL4 A:F3B900 0.0 15.3 0.2
F3 A:F3B900 0.4 63.2 0.6
C3 A:F3B900 1.2 63.1 0.6
C4 A:F3B900 1.8 15.0 0.2
C2 A:F3B900 2.1 63.2 0.6
C4 A:F3B900 2.4 63.2 0.6
CL2 A:F3B900 2.6 63.2 0.6
C5 A:F3B900 2.7 14.9 0.2
C3 A:F3B900 2.7 15.0 0.2
F5 A:F3B900 2.9 14.6 0.2
F3 A:F3B900 3.0 14.8 0.2
CL4 A:F3B900 3.2 63.2 0.6
N A:TYR88 3.3 13.6 1.0
C1 A:F3B900 3.4 63.2 0.6
CA A:TYR88 3.4 13.6 1.0
CB A:ALA99 3.5 10.5 1.0
C5 A:F3B900 3.6 63.1 0.6
CB A:TYR88 3.6 13.9 1.0
C A:VAL87 3.8 14.0 1.0
CG1 A:VAL87 3.9 14.6 1.0
C6 A:F3B900 3.9 63.2 0.6
O A:LEU84 3.9 15.3 1.0
CD1 A:LEU91 3.9 12.2 1.0
CB A:VAL87 4.0 14.6 1.0
C2 A:F3B900 4.0 15.1 0.2
C6 A:F3B900 4.0 15.0 0.2
CD1 A:TYR88 4.2 15.2 1.0
O A:VAL87 4.4 13.5 1.0
CG A:TYR88 4.4 14.0 1.0
F1 A:F3B900 4.4 63.2 0.6
CA A:VAL87 4.5 14.3 1.0
C1 A:F3B900 4.5 15.1 0.2
F5 A:F3B900 4.7 63.1 0.6
CD2 A:LEU118 4.8 17.8 1.0
CA A:ALA99 4.8 10.3 1.0
C A:TYR88 4.9 13.5 1.0
C A:LEU84 5.0 16.0 1.0

Chlorine binding site 5 out of 6 in 3dn6

Go back to Chlorine Binding Sites List in 3dn6
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:63.2
occ:0.55
 CL2 A:F3B900 0.0 63.2 0.6
F3 A:F3B900 1.1 14.8 0.2
C2 A:F3B900 1.8 63.2 0.6
C3 A:F3B900 2.2 15.0 0.2
CL4 A:F3B900 2.6 15.3 0.2
C4 A:F3B900 2.7 15.0 0.2
C3 A:F3B900 2.7 63.1 0.6
C1 A:F3B900 2.8 63.2 0.6
F3 A:F3B900 3.0 63.2 0.6
F1 A:F3B900 3.0 63.2 0.6
CG2 A:ILE78 3.3 15.1 1.0
CB A:LEU84 3.4 16.8 1.0
C2 A:F3B900 3.4 15.1 0.2
O A:LEU84 3.5 15.3 1.0
CG1 A:ILE78 3.6 15.6 1.0
CD1 A:ILE78 3.9 15.4 1.0
CD2 A:LEU84 3.9 17.9 1.0
CB A:TYR88 3.9 13.9 1.0
C A:LEU84 4.0 16.0 1.0
CA A:LEU84 4.0 16.8 1.0
CG A:LEU84 4.0 17.1 1.0
CB A:ILE78 4.0 15.5 1.0
C4 A:F3B900 4.0 63.2 0.6
C6 A:F3B900 4.0 63.2 0.6
CL2 A:F3B900 4.1 15.3 0.2
C5 A:F3B900 4.1 14.9 0.2
CD1 A:LEU84 4.2 17.9 1.0
CB A:ALA99 4.3 10.5 1.0
CD1 A:TYR88 4.3 15.2 1.0
CG A:TYR88 4.5 14.0 1.0
C5 A:F3B900 4.6 63.1 0.6
C1 A:F3B900 4.6 15.1 0.2
N A:TYR88 4.6 13.6 1.0
CA A:TYR88 4.7 13.6 1.0
C6 A:F3B900 4.9 15.0 0.2
CA A:ILE78 4.9 15.6 1.0
CG2 A:VAL103 4.9 13.2 1.0
F5 A:F3B900 5.0 14.6 0.2
N A:LYS85 5.0 15.4 1.0

Chlorine binding site 6 out of 6 in 3dn6

Go back to Chlorine Binding Sites List in 3dn6
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl900

b:15.3
occ:0.25
 CL2 A:F3B900 0.0 15.3 0.2
F1 A:F3B900 1.1 63.2 0.6
C2 A:F3B900 1.8 15.1 0.2
C1 A:F3B900 2.2 63.2 0.6
CL6 A:F3B900 2.6 63.2 0.6
C1 A:F3B900 2.7 15.1 0.2
C6 A:F3B900 2.8 63.2 0.6
C3 A:F3B900 2.8 15.0 0.2
F1 A:F3B900 2.9 15.1 0.2
F3 A:F3B900 3.0 14.8 0.2
CG2 A:VAL103 3.0 13.2 1.0
CG1 A:VAL111 3.3 28.7 1.0
CG2 A:VAL111 3.3 28.9 1.0
C2 A:F3B900 3.5 63.2 0.6
CD2 A:LEU84 3.6 17.9 1.0
CB A:VAL111 3.7 28.2 1.0
CD1 A:LEU84 4.0 17.9 1.0
C6 A:F3B900 4.0 15.0 0.2
C4 A:F3B900 4.0 15.0 0.2
CL2 A:F3B900 4.1 63.2 0.6
C5 A:F3B900 4.1 63.1 0.6
O A:ALA99 4.4 10.2 1.0
CG A:LEU84 4.4 17.1 1.0
CB A:VAL103 4.4 12.6 1.0
C5 A:F3B900 4.5 14.9 0.2
N A:VAL103 4.6 12.1 1.0
C3 A:F3B900 4.6 63.1 0.6
CB A:MET102 4.7 11.7 1.0
CA A:VAL103 4.7 12.7 1.0
C4 A:F3B900 4.9 63.2 0.6

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: Fri Jul 11 04:33:30 2025

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