Iodine in PDB 3dn4: Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant

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

The structure of Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn4 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 (°)	59.982, 59.982, 95.991, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 22.3

The binding sites of Iodine atom in the Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant (pdb code 3dn4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant, PDB code: 3dn4:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:I900 b:20.3 occ:0.50 I6 A:PIH900 0.0 20.3 0.5 C3 A:PIH900 0.5 24.3 0.5 C2 A:PIH900 1.1 24.6 0.5 C4 A:PIH900 1.9 24.4 0.5 C6 A:PIH900 2.1 20.1 0.5 C1 A:PIH900 2.3 24.3 0.5 C5 A:PIH900 2.8 24.4 0.5 C6 A:PIH900 2.9 24.2 0.5 C1 A:PIH900 3.0 20.2 0.5 C5 A:PIH900 3.0 20.0 0.5 SD A:MET102 3.3 18.3 1.0 CZ A:PHE153 3.9 16.7 1.0 CB A:MET102 4.0 16.6 1.0 CD1 A:LEU118 4.1 22.5 1.0 CA A:ALA99 4.1 15.4 1.0 CG A:MET102 4.1 17.1 1.0 CE A:MET102 4.2 20.0 1.0 CE2 A:PHE153 4.2 17.6 1.0 C4 A:PIH900 4.4 19.5 0.5 C2 A:PIH900 4.4 20.1 0.5 O A:ALA99 4.4 15.8 1.0 CG1 A:VAL111 4.5 30.4 1.0 CB A:ALA99 4.5 15.6 1.0 CD1 A:LEU121 4.8 18.2 1.0 C A:ALA99 4.8 15.4 1.0 C3 A:PIH900 4.9 20.1 0.5 CG2 A:VAL111 5.0 29.7 1.0

Iodine binding site 2 out of 2 in the Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Iodobenzene Binding in the Hydrophobic Cavity of T4 Lysozyme L99A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:I900 b:24.8 occ:0.49 I6 A:PIH900 0.0 24.8 0.5 C3 A:PIH900 0.4 20.1 0.5 C4 A:PIH900 1.2 19.5 0.5 C2 A:PIH900 1.8 20.1 0.5 C6 A:PIH900 2.1 24.2 0.5 C5 A:PIH900 2.4 20.0 0.5 C1 A:PIH900 2.7 20.2 0.5 C6 A:PIH900 2.9 20.1 0.5 C5 A:PIH900 3.0 24.4 0.5 C1 A:PIH900 3.0 24.3 0.5 O A:LEU84 3.4 21.1 1.0 N A:TYR88 3.7 18.4 1.0 CB A:TYR88 3.9 18.8 1.0 CA A:TYR88 4.0 18.8 1.0 CB A:VAL87 4.1 18.6 1.0 CB A:ALA99 4.2 15.6 1.0 CB A:LEU84 4.2 22.6 1.0 C A:LEU84 4.2 21.7 1.0 CG1 A:VAL87 4.3 18.0 1.0 CA A:LEU84 4.3 22.4 1.0 C A:VAL87 4.3 18.3 1.0 C4 A:PIH900 4.3 24.4 0.5 CG2 A:ILE78 4.4 20.5 1.0 C2 A:PIH900 4.4 24.6 0.5 CD1 A:TYR88 4.5 19.9 1.0 CD2 A:LEU84 4.7 22.5 1.0 CG A:TYR88 4.7 19.0 1.0 CA A:VAL87 4.8 18.1 1.0 C3 A:PIH900 4.9 24.3 0.5 CG A:LEU84 5.0 22.1 1.0 CD1 A:LEU91 5.0 16.2 1.0

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