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Fluorine in PDB 3dn3: Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant

Enzymatic activity of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant

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

Protein crystallography data

The structure of Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn3 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) 27.28 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.950, 59.950, 96.168, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21

Other elements in 3dn3:

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

Iodine (I) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (pdb code 3dn3). 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, PDB code: 3dn3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 3dn3

Go back to Fluorine Binding Sites List in 3dn3
Fluorine binding site 1 out of 5 in the Iodopentafluorobenzene 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 Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:21.8
occ:1.00
 F6 A:IBF900 0.0 21.8 1.0
C6 A:IBF900 1.3 21.7 1.0
C1 A:IBF900 2.3 21.8 1.0
C5 A:IBF900 2.4 21.4 1.0
F5 A:IBF900 2.7 21.9 1.0
I1 A:IBF900 3.2 22.0 1.0
CD1 A:LEU121 3.3 9.9 1.0
CZ A:PHE153 3.4 8.8 1.0
C2 A:IBF900 3.6 21.6 1.0
CB A:ALA99 3.6 6.9 1.0
C4 A:IBF900 3.6 21.8 1.0
CD2 A:LEU118 3.7 13.9 1.0
CE1 A:PHE153 3.7 8.8 1.0
CD1 A:LEU91 4.1 8.8 1.0
C3 A:IBF900 4.2 21.9 1.0
CA A:ALA99 4.2 6.8 1.0
CE2 A:PHE153 4.5 9.5 1.0
CG1 A:VAL87 4.5 12.4 1.0
F2 A:IBF900 4.7 21.5 1.0
CG A:LEU121 4.7 9.3 1.0
F4 A:IBF900 4.7 22.6 1.0
CD1 A:PHE153 4.8 9.0 1.0
N A:ALA99 4.9 6.8 1.0
CB A:LEU121 4.9 9.7 1.0

Fluorine binding site 2 out of 5 in 3dn3

Go back to Fluorine Binding Sites List in 3dn3
Fluorine binding site 2 out of 5 in the Iodopentafluorobenzene 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 Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:21.9
occ:1.00
 F5 A:IBF900 0.0 21.9 1.0
C5 A:IBF900 1.3 21.4 1.0
C4 A:IBF900 2.3 21.8 1.0
C6 A:IBF900 2.4 21.7 1.0
F6 A:IBF900 2.7 21.8 1.0
F4 A:IBF900 2.7 22.6 1.0
CG1 A:VAL87 3.2 12.4 1.0
N A:TYR88 3.2 11.8 1.0
CB A:VAL87 3.5 12.8 1.0
C A:VAL87 3.5 12.2 1.0
CA A:TYR88 3.5 11.7 1.0
CD1 A:LEU91 3.6 8.8 1.0
C1 A:IBF900 3.6 21.8 1.0
C3 A:IBF900 3.7 21.9 1.0
O A:VAL87 3.9 11.2 1.0
CB A:TYR88 4.0 11.7 1.0
CB A:ALA99 4.0 6.9 1.0
CA A:VAL87 4.1 12.5 1.0
CD2 A:LEU118 4.1 13.9 1.0
C2 A:IBF900 4.2 21.6 1.0
O A:LEU84 4.3 18.2 1.0
CG A:LEU91 4.5 8.8 1.0
CD1 A:TYR88 4.7 11.9 1.0
CG2 A:VAL87 4.8 13.2 1.0
F3 A:IBF900 4.8 22.5 1.0
CG A:TYR88 4.9 11.9 1.0
C A:TYR88 4.9 11.5 1.0

Fluorine binding site 3 out of 5 in 3dn3

Go back to Fluorine Binding Sites List in 3dn3
Fluorine binding site 3 out of 5 in the Iodopentafluorobenzene 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 Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:22.6
occ:1.00
 F4 A:IBF900 0.0 22.6 1.0
C4 A:IBF900 1.3 21.8 1.0
C5 A:IBF900 2.4 21.4 1.0
C3 A:IBF900 2.4 21.9 1.0
F5 A:IBF900 2.7 21.9 1.0
O A:LEU84 2.8 18.2 1.0
F3 A:IBF900 2.9 22.5 1.0
CG2 A:ILE78 3.3 13.9 1.0
CB A:TYR88 3.4 11.7 1.0
C A:LEU84 3.4 18.7 1.0
CB A:LEU84 3.4 19.9 1.0
CA A:LEU84 3.6 19.8 1.0
N A:TYR88 3.6 11.8 1.0
C6 A:IBF900 3.7 21.7 1.0
C2 A:IBF900 3.8 21.6 1.0
CA A:TYR88 3.9 11.7 1.0
C1 A:IBF900 4.2 21.8 1.0
CG A:TYR88 4.3 11.9 1.0
CD1 A:TYR88 4.4 11.9 1.0
CG A:LEU84 4.4 20.1 1.0
CD2 A:LEU84 4.4 20.1 1.0
CB A:VAL87 4.5 12.8 1.0
N A:LYS85 4.5 17.5 1.0
CG1 A:ILE78 4.5 13.6 1.0
CB A:ILE78 4.5 13.9 1.0
C A:VAL87 4.6 12.2 1.0
CD1 A:ILE78 4.6 12.6 1.0
F6 A:IBF900 4.7 21.8 1.0
CB A:ALA99 4.9 6.9 1.0
CD1 A:LEU84 4.9 20.4 1.0
F2 A:IBF900 4.9 21.5 1.0
CD2 A:LEU118 4.9 13.9 1.0
CA A:VAL87 5.0 12.5 1.0

Fluorine binding site 4 out of 5 in 3dn3

Go back to Fluorine Binding Sites List in 3dn3
Fluorine binding site 4 out of 5 in the Iodopentafluorobenzene 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 Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:22.5
occ:1.00
 F3 A:IBF900 0.0 22.5 1.0
C3 A:IBF900 1.3 21.9 1.0
C2 A:IBF900 2.5 21.6 1.0
C4 A:IBF900 2.5 21.8 1.0
F4 A:IBF900 2.9 22.6 1.0
F2 A:IBF900 2.9 21.5 1.0
CD1 A:LEU84 3.1 20.4 1.0
CB A:LEU84 3.4 19.9 1.0
CG A:LEU84 3.4 20.1 1.0
CD2 A:LEU84 3.5 20.1 1.0
CG1 A:ILE78 3.5 13.6 1.0
CG2 A:VAL103 3.5 10.4 1.0
C1 A:IBF900 3.7 21.8 1.0
C5 A:IBF900 3.7 21.4 1.0
CD1 A:ILE78 4.0 12.6 1.0
CG2 A:ILE78 4.0 13.9 1.0
CG1 A:VAL111 4.1 23.3 1.0
C6 A:IBF900 4.2 21.7 1.0
CB A:ILE78 4.2 13.9 1.0
CA A:LEU84 4.5 19.8 1.0
CA A:ILE78 4.7 14.1 1.0
F5 A:IBF900 4.8 21.9 1.0
CG2 A:VAL111 4.9 23.1 1.0

Fluorine binding site 5 out of 5 in 3dn3

Go back to Fluorine Binding Sites List in 3dn3
Fluorine binding site 5 out of 5 in the Iodopentafluorobenzene 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 Iodopentafluorobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:21.5
occ:1.00
 F2 A:IBF900 0.0 21.5 1.0
C2 A:IBF900 1.3 21.6 1.0
C1 A:IBF900 2.3 21.8 1.0
C3 A:IBF900 2.5 21.9 1.0
F3 A:IBF900 2.9 22.5 1.0
I1 A:IBF900 3.1 22.0 1.0
CG2 A:VAL111 3.1 23.1 1.0
CG2 A:VAL103 3.3 10.4 1.0
CG1 A:VAL111 3.3 23.3 1.0
C6 A:IBF900 3.6 21.7 1.0
C4 A:IBF900 3.8 21.8 1.0
CB A:VAL111 3.8 23.1 1.0
O A:ALA99 3.8 7.2 1.0
C5 A:IBF900 4.2 21.4 1.0
CB A:MET102 4.4 9.0 1.0
N A:VAL103 4.4 9.1 1.0
CB A:VAL103 4.6 9.2 1.0
F6 A:IBF900 4.7 21.8 1.0
C A:ALA99 4.7 6.9 1.0
CA A:VAL103 4.7 9.5 1.0
CD2 A:LEU118 4.8 13.9 1.0
CA A:ALA99 4.8 6.8 1.0
F4 A:IBF900 4.9 22.6 1.0
CB A:ALA99 5.0 6.9 1.0
C A:MET102 5.0 8.9 1.0
CD2 A:LEU84 5.0 20.1 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 18:02:00 2024

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