MAGNESIUM AND CATALYTIC RNA 299
and A 14. As mentioned many times before, X 1.1 and A 9 are important metal ion
binding sites. With the catalytic core, only U 7 appears to have no essential
functional group.
Next, the reference 61 authors attempted to defi ne some structure – function
relationships, based on defi ned charge – charge, van der Waals stacking, and
hydrogen - bonding crystal structure interactions in concert with biochemical
and spectroscopic experimental results. They believe that far away, domain II
essential functional groups cannot be intimately involved at the active site but
rather are important for structural interactions. This means that the hammer-
head global fold must be more critical for catalysis than for most other enzymes.
One can place hammerhead functional groups in three categories of struc-
ture – function correlation: (1) structure and function data that agree; (2) inter-
actions predicted by structural information that cannot be confi rmed by
functional data; and (3) deleterious functional group modifi cations that have
no apparent basis in structural details. Of course, the last is the most disturbing
factor. For instance, G 5.0 in domain I exhibits three essential functional groups
at N 2 , N 1 , and O 6 , although it appears to have no interaction partner in the
crystal structures. Note, however, that these G 5.0 functional groups do show
interactions with metal ions in the crystal structures represented by PDB:
300D, 301D, 1NYI, and 1Q29. In domain II, 10 different essential functional
groups on six different nucleotides have no apparent partner in the crystal
structures. A consistent metal ion bonding site appearing in most crystal struc-
tures involves the pro - R p - oxygen of A 9 and the N 7 essential atom of G 10.1 , but
little metal ion interaction is seen for residues C 11.1 , G 12 , A 13 , A 14 , or A 15.1. The
PDB: 1NYI structure shows an interaction between Co 2+ and the essential 2 ′ -
OH of U 16.1 , and several interactions with G 16.2 just outside domain II are noted
in Table 6.3. In category (1), in which structure and function agree, one can
site several hydrogen - bonding interactions that appear in the crystal structure
between essential functional groups. One of these is between O2 ′ of G 8 and
the N 2 of G 12 with a bonding distance of 2.4 – 3.0 Å in most crystal structures.
Examples of category (2) include hydrogen - bonding partners found in the
crystal structure that have only one essential functional group as part of the
hydrogen bond. For instance, the O2 ′ of G 5.0 (essential) forms an H - bond with
O2′ of U 15.2 (non - essential) in crystal structures. Lastly, it should be noted that
structural – functional agreement for the essential nature of the pro - R p - oxygen
of A 9 and the N 7 atom of G 10.1 (many crystal structures show metal ion bonding
at this location), along with the fact that this site resides approximately 20 Å
from the cleavage site in every crystal structure and never gets closer to the
cleavage site, raises unanswered questions as to what role is played by this
domain II location.
Blount and Uhlenbeck^61 next discuss the progression of crystal structures
published by the Scott group that have been extensively discussed previously
in this section. They agree that the structures show a progression of conforma-
tion changes at the cleavage site, especially in changes in orientation of the
C 17 nucleotide and achievement of a proper angle for the inline attack needed