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Figure 5.
Figure 5 Schematic surface and ball-and-stick diagrams
illustrating the 6[1] packing interactions of hinged
hairpin-ribozyme constructs. (a) Comparison of C3L (blue) and
S9L (magenta) unit cells. The perspective represents the
interaction of molecules about the 6[1] screw axis. (For twofold
and 2[1] operations, refer to Fig. 6-a.) Superposition of C3L
onto S9L initiates at the third molecule from the bottom (i.e.
the `reference' molecule), represented in bold magenta and blue
overlay. Symmetry operations used to generate the remaining
molecules demonstrate the degeneration of the superposition as a
result of the 15 Å elongated unit cell of the C3L
structure. C3L molecules are shown in blue and green, with S9L
structures shown in pink. The dashed box denotes the inset for
(b) and (c). (b) Expanded view of the 6[1] packing scheme for
the S9L structure. Atoms engaged in potential hydrogen bonds are
depicted as white spheres. Helices are labeled as in Fig. 1-(c)
and primes (') denote symmetry-related molecules. An additional
H3'' helix that is packed in a blunt-ended base stack with H4
has been omitted for clarity. The asymmetric unit (H4) is
colored magenta, with symmetry molecules in red (H3') or light
pink (H4'). (c) The C3L 6[1] packing scheme as described in (b),
but the asymmetric unit is colored blue and symmetry mates are
coloured teal (H3') or green (H4'). White spheres identify
equivalent atoms in the C3L structure that are engaged in
hydrogen bonding in the S9L structure. (d)-(g) Detailed view of
hydrogen-bond interactions with each of four H4 residues. The
A31 and U31 residues are base-paired; A31 ends the linker
strand, while U31 begins the S-turn strand. (h)-(k) Equivalent
distances in the C3L structure demonstrate the loss of 6[1]-fold
packing interactions.
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