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. Author manuscript; available in PMC: 2011 Nov 2.
Published in final edited form as: Biochemistry. 2010 Nov 2;49(43):9306–9317. doi: 10.1021/bi101336u

Figure 8.

Figure 8

Surface representation of the active site clefts of nitrososynthases, acyl-CoA dehydrogenases, and flavin-containing monooxygenases are shown colored by B-factor. Active site loops are labeled L1-L11. Surfaces of each enzyme are shown colored using a rainbow color ramp in which red corresponds to the highest B-factor and blue corresponds to the low B-factor. Areas of the surface that form the base of the active site cleft are shown in grey. Substrates and co-factors are shown as sticks with atoms colored as follows: FAD: carbons, yellow, oxygen, red; nitrogen, blue; phosphate, orange; TDP-l-evernosamine, dTDP, CoenzymeA persulfide: carbons, magenta; oxygen, red; nitrogen, blue; phosphate, orange. All panels are shown in an orientation rotated by 45° about a horizontal axis with respect to Figure 3A. (A) ORF36. Modeled FAD and TDP-l-evernosamine are displayed as sticks. In this orientation, loop L9 is concealed. The B factor color ramp gradient minimum and maximum values are 70 and 180 Å2, respectively, and for this structure, the Wilson B is 111.2 Å2 with an average protein B factor of 115.3 Å2. (B) KijD3 (PDB entry 3M9V)(11) with the dTDP of dTDP-phenol displayed as sticks. As in (A), loop L9 is concealed. The B factor color ramp minimum and maximum values for this panel are 10 and 80 Å2, and the average protein B value is 27.6 Å2. The Wilson B factor was not reported. (C) Human short/branched-chain acyl-CoA dehydrogenase (PDB entry 2JIF)(35). The FAD molecule is concealed by the protein surface in this orientation, and coenzymeA persulfide is shown in stick representation. Loops L9 and 10 are concealed in this orientation. The B factor color ramp gradient has minimum and maximum values of 14 and 60 Å2, the Wilson B is 25.84 Å2 and the average protein B factor is 22.76 Å2. (D) A. baumannii 4-hydroxyphenylacetate monooxygenase (PDB entry 2JBR)(24). FMN, 4-hydroxyphenylacetate, and loops L3, L9 and L10 are concealed in this orientation. The B factor color ramp gradient minimum and maximum values are 40 and 90 Å2, and the average protein B value is 56.77 Å2. The Wilson B factor was not reported.