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Figure 3.
Figure 3: RNA degradation by RNase II.
Figure 3 : RNA
degradation by RNase II. Unfortunately we are unable to
provide accessible alternative text for this. If you
require assistance to access this image, or to obtain a
text description, please contact npg@nature.com-
a, Stereo view of RNase II D209N mutant active site; bonds
are shown as sticks (oxygen in red, nitrogen in blue, phosphorus
in orange), waters as red spheres, Mg as a green sphere and its
coordination as dashed orange lines, and hydrogen bonds as
dashed green lines, superposed with sigma-A corrected Fourier
synthesis electron density map (brown mesh) contoured at 1  .
Additionally, N1 and N6 of nucleotide 13 are in the vicinity of
the carboxylate oxygens of Glu 542, at 3.2 Å (hydrogen
bond as dashed green lines) and at 4.3 Å (distance as
dotted orange line), respectively. b, Magnified view of the Mg
ion and its coordinating environment (distances in Å)
superposed with the positive 3 sigma-A
corrected Fourier difference map (green mesh) calculated with
the Mg and coordinating waters omitted from the model. c, Stereo
view of the superposition of the RNase II D209N mutant (yellow)
and RNase H (grey) with magnesium coordinating spheres (opposite
view to Fig. 3a). RNase H displays two magnesium ions ligated by
Glu 109, D132N, Glu 188 and Asp 192 that correspond in RNase II
to Asp 201, Asp 210, D209N and Asp 207, respectively. d,
Proposed catalytic mechanism for RNase II, showing the
postulated second Mg (Mg II) and the attacking hydroxyl group
(grey). e, Model for RNA degradation by RNase II. ssRNA (red) is
threaded into the catalytic cavity and clamped between Tyr 253
and Phe 358. The additional stabilization of RNA inside the
cavity drives the RNA translocation after each cleavage, up to a
final four-nucleotide fragment.
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