Iodine in PDB 7l3g: T4 Lysozyme L99A - 4-Iodotoluene - Cryo

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

The structure of T4 Lysozyme L99A - 4-Iodotoluene - Cryo, PDB code: 7l3g 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)	45.86 / 1.27
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.188, 60.188, 96.507, 90, 90, 120
R / Rfree (%)	15.6 / 17.4

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

Calcium

(Ca)

1 atom

The binding sites of Iodine atom in the T4 Lysozyme L99A - 4-Iodotoluene - Cryo (pdb code 7l3g). 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 - Cryo, PDB code: 7l3g:
Jump to Iodine binding site number: 1; 2;

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


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 - Cryo within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:17.4 occ:0.37 I06 A:XQM204 0.0 17.4 0.4 I06 A:XQM204 1.3 23.9 0.2 C05 A:XQM204 2.1 20.5 0.4 C05 A:XQM204 2.3 23.5 0.2 C07 A:XQM204 2.7 23.7 0.2 C04 A:XQM204 3.0 22.6 0.4 C07 A:XQM204 3.1 20.8 0.4 O A:LEU84 3.5 17.0 1.0 C04 A:XQM204 3.6 22.7 0.2 N A:TYR88 3.6 14.7 1.0 CB A:TYR88 3.8 15.1 1.0 CA A:TYR88 3.9 14.1 1.0 CB A:ALA99 3.9 14.1 1.0 C08 A:XQM204 4.0 23.1 0.2 CB A:VAL87 4.2 17.6 1.0 CB A:LEU84 4.2 17.1 1.0 C A:LEU84 4.2 15.6 1.0 C03 A:XQM204 4.3 22.2 0.4 CA A:LEU84 4.3 16.7 1.0 C08 A:XQM204 4.3 20.2 0.4 CG1 A:VAL87 4.4 19.5 1.0 CG2 A:ILE78 4.4 15.4 1.0 C A:VAL87 4.4 14.9 1.0 CD1 A:TYR88 4.4 15.6 1.0 CD2 A:LEU118 4.4 22.5 1.0 CD2 A:LEU84 4.5 21.8 1.0 CG A:TYR88 4.6 14.6 1.0 C03 A:XQM204 4.7 22.6 0.2 C02 A:XQM204 4.8 20.3 0.4 CA A:VAL87 4.8 15.7 1.0 C02 A:XQM204 4.9 22.6 0.2 CG A:LEU84 4.9 18.9 1.0 CD1 A:ILE78 4.9 17.6 1.0 CG1 A:ILE78 4.9 15.6 1.0

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


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 - Cryo within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:23.9 occ:0.18 I06 A:XQM204 0.0 23.9 0.2 I06 A:XQM204 1.3 17.4 0.4 C05 A:XQM204 2.1 20.5 0.4 C05 A:XQM204 2.1 23.5 0.2 C04 A:XQM204 2.5 22.6 0.4 C07 A:XQM204 3.0 23.7 0.2 C04 A:XQM204 3.0 22.7 0.2 C07 A:XQM204 3.3 20.8 0.4 C03 A:XQM204 3.8 22.2 0.4 CB A:ALA99 3.8 14.1 1.0 CB A:LEU84 3.8 17.1 1.0 CG1 A:ILE78 3.9 15.6 1.0 CG2 A:ILE78 3.9 15.4 1.0 CD1 A:ILE78 3.9 17.6 1.0 O A:LEU84 4.1 17.0 1.0 CD2 A:LEU84 4.1 21.8 1.0 CB A:TYR88 4.3 15.1 1.0 CG A:LEU84 4.3 18.9 1.0 C08 A:XQM204 4.3 23.1 0.2 C03 A:XQM204 4.3 22.6 0.2 C08 A:XQM204 4.4 20.2 0.4 CD1 A:LEU84 4.4 19.5 1.0 CA A:LEU84 4.4 16.7 1.0 CD1 A:TYR88 4.5 15.6 1.0 CB A:ILE78 4.5 14.0 1.0 C A:LEU84 4.6 15.6 1.0 C02 A:XQM204 4.6 20.3 0.4 CG2 A:VAL103 4.6 16.3 1.0 N A:TYR88 4.7 14.7 1.0 CA A:ALA99 4.8 12.3 1.0 CA A:TYR88 4.8 14.1 1.0 C02 A:XQM204 4.9 22.6 0.2 CD2 A:LEU118 4.9 22.5 1.0 CG A:TYR88 4.9 14.6 1.0 CG1 A:VAL111 4.9 21.9 0.5 O A:ALA99 4.9 12.9 1.0 C A:ALA99 5.0 11.3 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