Fig. 6: Late Lumi-R intermediate.
From: Protein control of photochemistry and transient intermediates in phytochromes
a−d Distance distributions computed for the OD ⋯ Arg466, Tyr263 ⋯ Asp207, ND ⋯ Tyr263, and OB ⋯  Ser257 interactions, respectively. e Probabilities for the main hydrogen-bonding interactions around the D-ring f Probabilities of having 0, 1, or 2 contacts between Asp207 and Arg466. We define a contact if the Asp207 oxygens, and Arg466 nitrogens are less than 3 Å apart. We compared the Early Lumi-R (in blue) against the Late Lumi-R (in orange). The Early Lumi-R analysis was performed on 20,000 frames, while the Late Lumi-R analysis was performed on 10,000 frames. For the Early Lumi-R, the error is less than 2 ⋅ 10−4, while for Late Lumi-R it is less than 4 ⋅ 10−3. A representative structure of the late intermediate can be found in Fig 1. Source data are available in the Zenodo repository89.
