Figure illustrates an important result of this work revealed in classical molecular dynamics simulations. According to these simulations either without or with the uracil molecule in the active site, the oxygen molecule can be trapped in several binding pockets in the protein; five of them are schematically shown in Fig. . The retention time of oxygen in these pockets varies from hundreds of picoseconds to tens of nanoseconds. It is important to note that the overall protein structure is stable along trajectories, as shown in Fig. for the protein backbone. The RMSD fluctuations through the graph are mainly due to the region of amino acids #290-310, which is not properly resolved in the crystal structures. The FMN coordination and position is very stable for more than 400 ns trajectory (Fig. ), while uracil position fluctuates during the trajectory (Fig. ). The hump in the uracil RMSD chart (Fig. ) during the ~200-250 ns window is associated with oxygen entering the pocket-5 (Fig. ) and consequently pushing off the uracil molecule. We remind that the starting coordinates for trajectory runs were selected from the crystal structures PDB ID 6SGG and PDB ID 6TEG. The identified pocket-1 roughly corresponds to the structural motifs in the crystal structures. In this site, the oxygen molecule fluctuates in the region between the flavin moiety near atom N5 of flavin (see Fig. ), polar residues Asn134, Thr105 and a hydrophobic cluster of Leu65, Met67 and Phe25 sidechains (see Fig. ). Here, the oxygen and uracil molecule are located at different sides of the plane of the isoalloxazine ring (see Fig. ). In pocket-5, the O2 molecule is surrounded by water molecules and resides closer to the C4a atom of the flavin molecule. Here, the oxygen and uracil molecule are located at the same side of the plane of the isoalloxazine ring. In other pockets, the oxygen molecule stays farther from the FMN ligand. Pocket-2 is mostly hydrophobic; it is formed by the sidechains of Asn134, Phe224, Ala206, Leu65 and flavin. Pocket-3 consists of the sidechains Phe222, Phe224, Tyr257, Ile204, Phe63; it is close to the protein surface, showing one of the obvious ways connecting the pocket-1 to the bulk. Pocket-4 is formed by the FMN phosphate group, the Tyr160, Cys205 sidechains and nearby main chain of beta-strands. Pockets 1 and 5 are the most perspective sites for the uracil oxygenation reaction in RutA. Therefore, selected frames along classical MD trajectories in the areas corresponding to pocket-1 and pocket-5 were taken to initiate trajectories with the QM/MM potentials.