Figure 2.

The catalytic site of CtFDO:free (chain A). The cofactor, modelled in reduced form (magenta C atoms), is surrounded by the His564–Ser607 pair and additionally by Asn562, Ala563 and Tyr476 on its re face and by Ala133 on its si face. The orientation of the His564 imidazole ring is stabilized by a hydrogen bond to Gln351 (His564 N^δ1–Gln351 O^ɛ1, blue dotted line). Asn562 and Ser607 have two alternative conformations. The ‘in’ (nearest standard rotamer χ₁ = −65°) and ‘out’ (χ₁ = 64°) conformations of Ser607 are labelled. The active-site water molecules (W_AS and W_DAS) binding in the catalytic site (black dashed and dotted lines, respectively) are labelled. W_AS binds between His564 N^ɛ2, Ser607 O^γ, Asn562 N^δ2, FAD O⁴ and FAD N³ in the putative binding site of the catalytically modified group of the substrate. (a) A simulated-annealing 2mF _o − DF _c composite OMIT map (calculated in Phenix; Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008 ▸) shown for the cofactor contoured at the 1σ level. (b) Labelled distances (differing values for chain B are given in parentheses) for W_AS, which is at a distance of 3.7 Å (3.9 Å in chain B) from FAD N⁵ and makes an angle of 97.5° (98.6° in chain B) with the FAD N¹⁰–FAD N⁵ atoms, i.e. it occupies the site of oxidative attack in CtFDO. (c) The isoalloxazine bend of 20.0° (21.4° in chain B) around the FAD N⁵ and FAD N¹⁰ axis (dashed line). The angle between the C⁴, N⁵ and C⁶ atoms is labelled (the value for chain B is given in parentheses). The molecular graphics were created with PyMOL (Schrödinger).