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. 2011 Sep 22;286(47):41105–41114. doi: 10.1074/jbc.M111.282467

FIGURE 6.

FIGURE 6.

O2-flavin distance classes after substrate diffusion by PELE corresponding to different O2 (red sticks) distributions inside the active site. A, native AAO; B, F501A variant; C, F501Y variant; D, F501W variant. The O2 substrate molecule was placed near flavin C4a, and PELE (37) was instructed to diffuse it freely inside the active-site cavity (by using low temperatures and small perturbations). The distances between flavin C4a and the O2 atoms were estimated in ∼1000 positions, and the values obtained were distributed in 10 frequency classes. O2 distribution is shown in the different images, where nearly 200 selected O2 positions are shown, together with the cofactor flavin ring and Tyr-92 (top), His-546 (right), His-502 (middle), and Phe/Ala/Tyr/Trp-501 (left) (as CPK-colored sticks).