252 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II
PDB: 1GID structure. (See Table 6.1 .) The PDB: 1HR2 bond length data are
collected in Table S1 of reference 29. The majority of the directly coordinated
magnesium ions were found near the A - rich bulge ( Mg 12 +, Mg 22 +, and Mg 62 +)
or the three - helix junction ( Mg 32 +, Mg 42 +, and Mg 52 +). The metal ions appear to
help fold important structural motifs, stabilize the structures formed by P5a
and P5c, and facilitate the group I intron ’ s tertiary structure. Other fully
hydrated magnesium ions, with six aquo ligands, also stabilize the intron ’ s
tertiary structure mainly in the major groove of an A - form helix. The majority
of ordered water molecules found in the structure, whether or not they are
attached to magnesium ions, appear in the group I intron ’ s interior. The authors
believe that the water molecules may work independently or cooperatively
with magnesium ions, but in either case they assist the RNA bases to extend
their hydrogen bonding capability and further stabilize the intron ’ s tertiary
structure. In conclusion, the reference 29 researchers believe that the higher -
resolution model established for PDB: 1HR2 provided new, important details
of metal ion – RNA interactions as well as identifying a core of ordered water
molecules. Both of these could be integral to RNA tertiary structure
formation.
In 2004, the Cech group published the 3.8 - Å resolution X - ray crystallo-
graphic structure of a catalytically activeTetrahymena ribozyme containing
stabilizing mutations that helped achieve greater thermal stability and better
diffracting crystals (PDB: 1X8W).^24 In solution tests on the enzymatic form of
the mutant, the ribozyme ’ s ability to cleave its RNA substrate remained intact.
However, the crystallized species did not contain the exon but corresponded
to the enzymatic form in the absence of its exon substrate. Even though the
crystal structure did not include the ribozyme ’ s RNA substrate, it did yield
more information about the ribozyme ’ s tertiary structure both close to and
away from the catalytic pocket. Many of the interactions found in the P6
domain involved base triples. Base triples are a common stabilizing motif in
RNA tertiary structures and have been described fully in an article by Jennifer
Doudna and co - workers.^30 Essentially, base triples most often involve an ade-
nosine nucleotide interacting with a traditional base pair and are found in two
forms — Type I and Type II. In the P4 – P6 domain of the Tetrahymena group I
intron, Type I base triples involve the N 1 , C 2 , N 3 , and 2 ′ - OH atoms or groups
along the minor groove face of the adenosine contacting the minor groove
surface of a base pair (including its sugars) burying∼ 195 Å^2 of molecular
surface area. Type II base triples involve the N 1 , C 2 , N 3 , and 2 ′ - OH atoms or
groups along the minor groove face of the adenosine contacting about one - half
of the minor groove surface of a base pair burying less surface area ( ∼ 145 Å^2 ).
One PDB: 1X8W structure type I base triple in the P6 domain uses the minor
groove side of the A105 base and ribose to contact the entire minor groove
surface of the C216 – G257 pair This is shown in Figure 6.5 as adapted from
Figure 3D of reference 24. Note that in Figure 6.5 , Watson – Crick base pairing
between C216 and G257 are shown in dashed bond format, while the triple
base interactions with A105 are shown in hashed bond format.