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. Author manuscript; available in PMC: 2017 May 12.
Published in final edited form as: Nat Struct Mol Biol. 2016 Aug 29;23(10):941–948. doi: 10.1038/nsmb.3282

Figure 6.

Figure 6

The active sites and the ligand binding stoichiometries of the wild-type and Y115A structures of TrmD. (a) The mean value of solvent accessible surface area (SASA) of active site A (light grey) and active site B (dark grey). In active site A, the knot is from chain A and the CTD is from chain B, whereas in active site B, the knot is from chain B and the CTD is from chain A. (b) The mean RMSD of AdoMet A (light grey) and AdoMet B (dark grey). Error bars are s.d. (n = 3 independent simulations). (c, d) Binding stoichiometry of tRNA to TrmD dimers. Determination of binding stoichiometry by monitoring the quenching of TrmD intrinsic tryptophan fluorescence with increasing amounts of tRNA to the wild-type dimer (c) and the Y115A dimer (d). (e, f) Biding stoichiometry of AdoMet to TrmD dimers. Determination of binding stoichiometry by monitoring the quenching of TrmD intrinsic tryptophan fluorescence with increasing amounts of AdoMet to the wild-type dimer (c) and the Y115A dimer (d). Error bars are s.d. (n = 3 independent measurements).