Iodine in PDB 7l3b: T4 Lysozyme L99A - Iodobenzene - Rt

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

The structure of T4 Lysozyme L99A - Iodobenzene - Rt, PDB code: 7l3b 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)	35.84 / 1.27
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.75, 60.75, 97.921, 90, 90, 120
R / Rfree (%)	14.9 / 16.7

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

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the T4 Lysozyme L99A - Iodobenzene - Rt (pdb code 7l3b). 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 - Iodobenzene - Rt, PDB code: 7l3b:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the T4 Lysozyme L99A - Iodobenzene - 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 - Iodobenzene - Rt within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:20.4 occ:0.32 I6 A:PIH205 0.0 20.4 0.3 C3 A:PIH205 0.3 12.2 0.2 C2 A:PIH205 1.3 12.3 0.2 C4 A:PIH205 1.6 11.2 0.2 C6 A:PIH205 2.1 20.2 0.3 C1 A:PIH205 2.3 12.9 0.2 C5 A:PIH205 2.5 11.1 0.2 C6 A:PIH205 2.8 13.0 0.2 C1 A:PIH205 3.0 19.2 0.3 C5 A:PIH205 3.0 20.3 0.3 O A:LEU84 3.4 16.3 1.0 N A:TYR88 3.7 13.1 1.0 CB A:TYR88 3.9 13.4 1.0 CB A:VAL87 4.0 17.4 1.0 CA A:TYR88 4.0 12.8 1.0 CB A:LEU84 4.1 16.8 1.0 C A:LEU84 4.2 15.3 1.0 CB A:ALA99 4.2 12.7 1.0 CG1 A:VAL87 4.2 19.5 1.0 CA A:LEU84 4.2 16.1 1.0 CD2 A:LEU84 4.3 20.9 1.0 C2 A:PIH205 4.3 20.0 0.3 C4 A:PIH205 4.3 20.1 0.3 CD2 A:LEU118 4.4 25.9 1.0 C A:VAL87 4.4 13.6 1.0 CG2 A:ILE78 4.6 15.6 1.0 CD1 A:TYR88 4.6 14.5 1.0 CG A:LEU84 4.7 18.7 1.0 CA A:VAL87 4.8 15.1 1.0 CG A:TYR88 4.8 13.7 1.0 C3 A:PIH205 4.9 20.4 0.3 I6 A:PIH205 4.9 14.8 0.2

Iodine binding site 2 out of 2 in the T4 Lysozyme L99A - Iodobenzene - 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 - Iodobenzene - Rt within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:14.8 occ:0.19 I6 A:PIH205 0.0 14.8 0.2 C3 A:PIH205 0.2 20.4 0.3 C4 A:PIH205 1.2 20.1 0.3 C2 A:PIH205 1.6 20.0 0.3 C6 A:PIH205 2.1 13.0 0.2 C5 A:PIH205 2.3 20.3 0.3 C1 A:PIH205 2.5 19.2 0.3 C6 A:PIH205 2.8 20.2 0.3 C1 A:PIH205 3.0 12.9 0.2 C5 A:PIH205 3.1 11.1 0.2 SD A:MET102 3.3 16.8 1.0 CG1 A:VAL111 3.5 23.4 0.4 CZ A:PHE153 4.0 16.7 1.0 CB A:MET102 4.0 12.3 1.0 CG A:MET102 4.1 13.9 1.0 CA A:ALA99 4.2 11.1 1.0 CE A:MET102 4.2 18.7 1.0 CD2 A:LEU118 4.3 25.9 1.0 CE2 A:PHE153 4.3 17.4 1.0 C2 A:PIH205 4.3 12.3 0.2 C4 A:PIH205 4.4 11.2 0.2 CB A:ALA99 4.4 12.7 1.0 O A:ALA99 4.5 11.6 1.0 CG2 A:VAL111 4.7 22.3 0.4 CB A:VAL111 4.7 22.2 0.4 C A:ALA99 4.9 10.8 1.0 C3 A:PIH205 4.9 12.2 0.2 CD1 A:LEU121 4.9 17.6 1.0 I6 A:PIH205 4.9 20.4 0.3 CG1 A:VAL111 4.9 22.2 0.6

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