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Figure 2.
Figure 2 Ball-and-stick and electron-density maps of the
engineered U·U mismatch at the top of helix 2 (H2). (a)
The U-5·A14 base pair as observed in one of two molecules
in the asymmetric unit of the 4WJ structure (PDB code 1m5k ). O
atoms are colored red and N atoms are blue. Dashed gray lines
indicate putative hydrogen bonds with corresponding distances.
(b) The minimal junctionless ribozyme 64-mer structure (PDB code
1x9k ) with an orientation equivalent to that in (a). Two
symmetry-related U-5 residues are separated by a 3 Å
translation and are not base-paired. (c) The original syn-anti
base-pairing conformation of U-5 modeled for the 2.05 Å
resolution junctionless ribozyme (PDB code 1zfr ). Alternate
conformations were modeled with equal occupancy and are colored
green or cyan. A single set of hydrogen bonds is indicated; the
symmetry-related hydrogen bonds and labels were omitted for
clarity. A  [A]-weighted
simulated-annealing omit electron-density map calculated for the
U-5 residue and nearby solvent molecules is shown contoured at
3.5 with
coefficients mF[o] - DF[c]. (d) The revised 2.05 Å
resolution minimal hairpin-ribozyme structure of this study
depicting the new anti-anti or `Calcutta' model for U-5 fitted
into an omit map as described in (c).
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