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Fluorine in PDB 3dn8: Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)

Enzymatic activity of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)

All present enzymatic activity of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version):
3.2.1.17;

Protein crystallography data

The structure of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version), PDB code: 3dn8 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) 21.89 / 1.70
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 (%) 19.6 / 22.3

Other elements in 3dn8:

The structure of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) also contains other interesting chemical elements:

Iodine (I) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) (pdb code 3dn8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version), PDB code: 3dn8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 3dn8

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Fluorine binding site 1 out of 5 in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:19.9
occ:1.00
 F6 A:IBF900 0.0 19.9 1.0
C6 A:IBF900 1.3 19.6 1.0
C5 A:IBF900 2.4 19.4 1.0
C1 A:IBF900 2.4 19.4 1.0
F5 A:IBF900 2.7 19.8 1.0
I1 A:IBF900 3.2 19.2 1.0
CD1 A:LEU121 3.4 11.6 1.0
CZ A:PHE153 3.5 11.2 1.0
CB A:ALA99 3.6 8.7 1.0
C4 A:IBF900 3.6 19.6 1.0
C2 A:IBF900 3.6 19.3 1.0
CD2 A:LEU118 3.6 16.4 1.0
CE1 A:PHE153 3.7 10.9 1.0
CD1 A:LEU91 4.0 12.2 1.0
C3 A:IBF900 4.2 19.4 1.0
CA A:ALA99 4.2 8.5 1.0
CG1 A:VAL87 4.5 14.8 1.0
CE2 A:PHE153 4.5 11.5 1.0
CG A:LEU121 4.7 11.7 1.0
F4 A:IBF900 4.7 20.0 1.0
F2 A:IBF900 4.7 19.1 1.0
CD1 A:PHE153 4.9 10.7 1.0
N A:ALA99 4.9 8.4 1.0
CB A:LEU121 4.9 12.4 1.0

Fluorine binding site 2 out of 5 in 3dn8

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Fluorine binding site 2 out of 5 in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:19.8
occ:1.00
 F5 A:IBF900 0.0 19.8 1.0
C5 A:IBF900 1.3 19.4 1.0
C4 A:IBF900 2.4 19.6 1.0
C6 A:IBF900 2.4 19.6 1.0
F6 A:IBF900 2.7 19.9 1.0
F4 A:IBF900 2.7 20.0 1.0
N A:TYR88 3.2 14.1 1.0
CG1 A:VAL87 3.2 14.8 1.0
CA A:TYR88 3.4 13.6 1.0
C A:VAL87 3.5 14.6 1.0
CB A:VAL87 3.5 15.3 1.0
CD1 A:LEU91 3.6 12.2 1.0
C1 A:IBF900 3.6 19.4 1.0
C3 A:IBF900 3.7 19.4 1.0
O A:VAL87 3.9 14.3 1.0
CB A:TYR88 4.0 13.9 1.0
CB A:ALA99 4.1 8.7 1.0
CA A:VAL87 4.1 14.9 1.0
C2 A:IBF900 4.2 19.3 1.0
CD2 A:LEU118 4.4 16.4 1.0
O A:LEU84 4.4 19.2 1.0
CG A:LEU91 4.5 11.2 1.0
CD1 A:TYR88 4.7 14.5 1.0
CG2 A:VAL87 4.8 15.9 1.0
C A:TYR88 4.8 13.3 1.0
CG A:TYR88 4.8 14.1 1.0
F3 A:IBF900 4.8 20.0 1.0

Fluorine binding site 3 out of 5 in 3dn8

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Fluorine binding site 3 out of 5 in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:20.0
occ:1.00
 F4 A:IBF900 0.0 20.0 1.0
C4 A:IBF900 1.3 19.6 1.0
C5 A:IBF900 2.4 19.4 1.0
C3 A:IBF900 2.4 19.4 1.0
F5 A:IBF900 2.7 19.8 1.0
O A:LEU84 2.8 19.2 1.0
F3 A:IBF900 2.8 20.0 1.0
CG2 A:ILE78 3.4 15.9 1.0
CB A:TYR88 3.4 13.9 1.0
C A:LEU84 3.6 19.4 1.0
N A:TYR88 3.6 14.1 1.0
C6 A:IBF900 3.7 19.6 1.0
CB A:LEU84 3.7 20.2 1.0
C2 A:IBF900 3.8 19.3 1.0
CA A:TYR88 3.9 13.6 1.0
CA A:LEU84 3.9 20.1 1.0
C1 A:IBF900 4.2 19.4 1.0
CB A:VAL87 4.3 15.3 1.0
CG A:TYR88 4.3 14.1 1.0
CD1 A:TYR88 4.4 14.5 1.0
CD2 A:LEU84 4.4 19.5 1.0
CB A:ILE78 4.5 16.3 1.0
CG1 A:ILE78 4.5 16.3 1.0
C A:VAL87 4.5 14.6 1.0
CG A:LEU84 4.6 20.0 1.0
N A:LYS85 4.6 18.6 1.0
CD1 A:ILE78 4.7 15.6 1.0
F6 A:IBF900 4.7 19.9 1.0
F2 A:IBF900 4.9 19.1 1.0
CA A:VAL87 4.9 14.9 1.0
CG1 A:VAL87 4.9 14.8 1.0
CD1 A:LEU84 4.9 19.7 1.0
CB A:ALA99 5.0 8.7 1.0

Fluorine binding site 4 out of 5 in 3dn8

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Fluorine binding site 4 out of 5 in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:20.0
occ:1.00
 F3 A:IBF900 0.0 20.0 1.0
C3 A:IBF900 1.3 19.4 1.0
C2 A:IBF900 2.4 19.3 1.0
C4 A:IBF900 2.5 19.6 1.0
F2 A:IBF900 2.8 19.1 1.0
F4 A:IBF900 2.8 20.0 1.0
CD1 A:LEU84 3.3 19.7 1.0
CG1 A:ILE78 3.6 16.3 1.0
CD2 A:LEU84 3.6 19.5 1.0
CG2 A:VAL103 3.7 11.6 1.0
C1 A:IBF900 3.7 19.4 1.0
C5 A:IBF900 3.7 19.4 1.0
CG A:LEU84 3.7 20.0 1.0
CB A:LEU84 3.8 20.2 1.0
CG2 A:ILE78 4.1 15.9 1.0
CD1 A:ILE78 4.1 15.6 1.0
C6 A:IBF900 4.2 19.6 1.0
CB A:ILE78 4.3 16.3 1.0
CA A:ILE78 4.7 16.6 1.0
F5 A:IBF900 4.8 19.8 1.0
CA A:LEU84 4.9 20.1 1.0

Fluorine binding site 5 out of 5 in 3dn8

Go back to Fluorine Binding Sites List in 3dn8
Fluorine binding site 5 out of 5 in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (Seleno Version) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:19.1
occ:1.00
 F2 A:IBF900 0.0 19.1 1.0
C2 A:IBF900 1.3 19.3 1.0
C1 A:IBF900 2.4 19.4 1.0
C3 A:IBF900 2.4 19.4 1.0
F3 A:IBF900 2.8 20.0 1.0
CG1 A:VAL111 3.0 27.9 1.0
I1 A:IBF900 3.1 19.2 1.0
CG2 A:VAL103 3.3 11.6 1.0
CG2 A:VAL111 3.3 27.1 1.0
CB A:VAL111 3.5 27.4 1.0
C6 A:IBF900 3.6 19.6 1.0
C4 A:IBF900 3.8 19.6 1.0
O A:ALA99 4.0 9.0 1.0
C5 A:IBF900 4.2 19.4 1.0
N A:VAL103 4.5 11.2 1.0
CB A:MSE102 4.5 10.8 1.0
CB A:VAL103 4.6 11.2 1.0
CD2 A:LEU118 4.7 16.4 1.0
F6 A:IBF900 4.7 19.9 1.0
CA A:VAL103 4.8 11.1 1.0
C A:ALA99 4.8 8.7 1.0
F4 A:IBF900 4.9 20.0 1.0
CA A:ALA99 5.0 8.5 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 15:56:30 2025

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