Iodine in PDB 7l3f: T4 Lysozyme L99A - 4-Iodotoluene - Rt

All present enzymatic activity of T4 Lysozyme L99A - 4-Iodotoluene - Rt:
3.2.1.17;

The structure of T4 Lysozyme L99A - 4-Iodotoluene - Rt, PDB code: 7l3f was solved by M.Fischer, S.Y.C.Bradford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.93 / 1.49
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.129, 61.129, 97.868, 90, 90, 120
R / Rfree (%)	14.8 / 17

The structure of T4 Lysozyme L99A - 4-Iodotoluene - Rt also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the T4 Lysozyme L99A - 4-Iodotoluene - Rt (pdb code 7l3f). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the T4 Lysozyme L99A - 4-Iodotoluene - Rt, PDB code: 7l3f:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the T4 Lysozyme L99A - 4-Iodotoluene - Rt


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of T4 Lysozyme L99A - 4-Iodotoluene - Rt within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:22.9 occ:0.26 I06 A:XQM203 0.0 22.9 0.3 I06 A:XQM203 1.4 28.4 0.1 C05 A:XQM203 2.1 22.9 0.3 C05 A:XQM203 2.3 26.2 0.1 C07 A:XQM203 2.6 25.8 0.1 C04 A:XQM203 3.0 23.8 0.3 C07 A:XQM203 3.0 23.3 0.3 O A:LEU84 3.5 19.3 1.0 C04 A:XQM203 3.6 25.8 0.1 N A:TYR88 3.7 15.8 1.0 CB A:TYR88 3.8 15.5 1.0 CA A:TYR88 3.9 14.9 1.0 CB A:ALA99 3.9 15.6 1.0 C08 A:XQM203 4.0 25.6 0.1 CB A:VAL87 4.1 20.4 1.0 CG1 A:VAL87 4.2 24.2 1.0 CB A:LEU84 4.2 20.0 1.0 C A:LEU84 4.3 17.6 1.0 C03 A:XQM203 4.3 24.0 0.3 C08 A:XQM203 4.3 22.9 0.3 CA A:LEU84 4.3 20.3 1.0 C A:VAL87 4.4 16.3 1.0 CD2 A:LEU84 4.4 25.1 1.0 CD1 A:TYR88 4.5 17.0 1.0 CG2 A:ILE78 4.5 18.0 1.0 CD2 A:LEU118 4.6 31.7 1.0 CG A:TYR88 4.7 16.1 1.0 C03 A:XQM203 4.7 25.6 0.1 C02 A:XQM203 4.8 25.0 0.1 C02 A:XQM203 4.8 23.4 0.3 CA A:VAL87 4.8 18.1 1.0 CG A:LEU84 4.9 22.6 1.0 CD1 A:LEU91 5.0 19.0 1.0

Iodine binding site 2 out of 2 in the T4 Lysozyme L99A - 4-Iodotoluene - Rt


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of T4 Lysozyme L99A - 4-Iodotoluene - Rt within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:28.4 occ:0.15 I06 A:XQM203 0.0 28.4 0.1 I06 A:XQM203 1.4 22.9 0.3 C05 A:XQM203 2.1 26.2 0.1 C05 A:XQM203 2.3 22.9 0.3 C04 A:XQM203 2.5 23.8 0.3 C07 A:XQM203 3.0 25.8 0.1 C04 A:XQM203 3.0 25.8 0.1 C07 A:XQM203 3.5 23.3 0.3 CB A:LEU84 3.8 20.0 1.0 CB A:ALA99 3.8 15.6 1.0 C03 A:XQM203 3.9 24.0 0.3 CG1 A:ILE78 3.9 16.6 1.0 CG2 A:ILE78 3.9 18.0 1.0 CD1 A:ILE78 4.0 21.7 1.0 CD2 A:LEU84 4.0 25.1 1.0 O A:LEU84 4.1 19.3 1.0 CG A:LEU84 4.3 22.6 1.0 C08 A:XQM203 4.3 25.6 0.1 CB A:TYR88 4.3 15.5 1.0 C03 A:XQM203 4.4 25.6 0.1 CD1 A:LEU84 4.4 22.9 1.0 CA A:LEU84 4.4 20.3 1.0 CB A:ILE78 4.5 16.6 1.0 CD1 A:TYR88 4.5 17.0 1.0 C A:LEU84 4.6 17.6 1.0 C08 A:XQM203 4.6 22.9 0.3 CG2 A:VAL103 4.6 18.3 1.0 C02 A:XQM203 4.7 23.4 0.3 CA A:ALA99 4.8 14.0 1.0 N A:TYR88 4.8 15.8 1.0 O A:ALA99 4.9 16.0 1.0 C02 A:XQM203 4.9 25.0 0.1 CA A:TYR88 4.9 14.9 1.0 CG1 A:VAL111 4.9 20.6 0.5 CG A:TYR88 4.9 16.1 1.0 C A:ALA99 5.0 14.4 1.0

S.Y.C.Bradford, L.El Khoury, Y.Ge, M.Osato, D.L.Mobley, M.Fischer. Temperature Artifacts in Protein Structures Bias Ligand-Binding Predictions. Chem Sci V. 12 11275 2021.
ISSN: ISSN 2041-6520
PubMed: 34667539
DOI: 10.1039/D1SC02751D