MAGNESIUM AND CATALYTIC RNA 257
tide forms the only interaction holding the 5 ′ - exon in place because any cova-
lent bond between it and the intron has been broken during the fi rst step of
the splicing sequence (chem.1 step of Figure 6.1 , parts ii – iii). In the pre - 2S
structure the 3 ′ - splice site is formed primarily by interactions with the Ω G,
PDB: 1U6B G206 residue that is in turn bound into a pocket created by four
nucleotides: A127, G128, A129, and G130. A127 stacks under Ω G, G128, and
A129 stack overΩ G, and G130 is coplanar and makes a Hoogsteen base pair
with it. A129 resides at the P7 helix apex and makes a base triple with the
G128 – C178 base pair. J6/7 residues U126, A127, and G128 span 22 Å across
the active site, whereas the usual distance between three stacked bases would
be approximately 9 Å. These residues are important in that they stack with Ω G
(A127, G128) and the extended backbones of A127 and G128 coordinate an
active site metal ion (3 ′ O G128 – K + = 2.7 Å ).
The Strobel research group compared the metal ions found in the PDB:
1U6B crystal structure to those found using biochemical methods, specifi cally
the metal ions M A , M B , and M C described by the Herschlag group using sulfur
or amino substitutions rescued with soft divalent metal ions.^27 As described
previously, the metal ions have specifi c purposes: (1) M A activates the nucleo-
phile — the O3 ′ of U − 1 or dt − 1 in the PDB: 1U6B nomenclature; (2) M B stabilizes
the leaving group — the O3 ′ of Ω G; and (3) M C helps neutralize the negative
charge on the trigonal bipyramidal phosphorus transition state as well as coor-
dinating to theΩ G O2 ′. In the PDB: 1U6B structure, only two metal ions are
positioned near the scissile phosphate (the a +1 phosphate). The metal ion
labeled as M 1 was found to be a magnesium ion through heavy metal substitu-
tion experiments. This Mg 2+ coordinated to the nonbridging oxygens of four
phosphates and had an outer sphere contact with a fi fth. In Figure 6.7 , this
magnesium ion is identifi ed as M 1. In the PDB: 1U6B structure, M 1 coordinated
to the pro - R p - oxygen of dt − 1 at a distance of 2.4 Å. M 1 also coordinated to the
O3′ - oxygen of dt − 1 (Mg 2+ – O3 ′ dt − 1 = 2.4 Å ), leading these researchers to identify
it as comparable to the biochemically defi ned M A described in reference 27b.
A second metal ion in the PDB: 1U6B structure was defi ned as a K + ion, again
using heavy metal substitution experiments. The potassium ion coordinates to
a modeled - in O2 ′ of Ω G (K + – O2 ′ d Ω g = 2.7 Å ) and therefore was compared
to the biochemically identifi ed M C. In biochemical experiments, M C was found
to coordinate to the pro - S p - oxygen of the scissile phosphate; however, this
coordination is not found in the PDB: 1U6B structure. The closest approach
of the potassium ion to the scissile phosphate occurs with the pro - R p nonbridg-
ing oxygen with a bonding distance of approximately 5 Å. The authors believe
that the absence of O2 ′ in the Ω G deoxy nucleotide may have contributed to
the metal ion positions found in the PDB: 1U6B crystal structure, a proposal
to keep in mind during analysis of the PDB: 1ZZN crystal structure to be dis-
cussed next. Importantly, the magnesium ion identifi ed as M 1 in the PDB: 1U6B
structure is bringing the scissile phosphate and O3 ′ oxygens of Ω G and dt − 1
into alignment for a S N 2 nucleophilic attack — that is, the O3 ′ - Ω G – P – O3 ′ - dt − 1
bond angle is equal to 150 ° and the O3 ′ - dt − 1 – scissile P distance equals 3.4 Å.