BIOINORGANIC CHEMISTRY A Short Course Second Edition

248 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II

tetraloop and its receptor. The end result is that a number of riboses of the
isolated P4 – P6 domain are inaccessible to Fe(II) - EDTA cleavage — that is,
they are protected from solvent. Free radicals produced by Fe(II) - EDTA in
solution attack the C4 ′ ribose carbons at each unprotected — exposed to
solvent — nucleotide residue and therefore probe the solvent accessibility of
domains within folded RNA.^23 Close packing of phosphates is relieved by
outer - sphere contacts with hydrated magnesium ions (at distances < 4 Å ) at
several locations — between P4 and J6/6a, between P5 and P5a, and between
P5b and P6a. The reference 13 authors believe that the divalent magnesium
ions fulfi ll a role in intron (and other RNA ribozyme) folding. The following
conclusions can be derived from the PDB: 1GID crystal structure observa-
tions: (1) Catalytic RNA appears to require a closely packed structure much
different from the classical view of stringlike messenger RNA; (2) metal –
phosphate interactions are abundant in the structure, allowing polyanionic
helices to come into close contact; and (3) ribose 2 ′ - OH groups appear to be
important players in the intron structure, as a donor or acceptor of hydrogen
bonds or in forming metal ion – ribose interactions.
The Cech group described an X - ray crystallographic structure of the group
I intron fromTetrahymena thermophila in a Science magazine research article
published in 1998 (PDB: 1GRZ).^15 The 5.0 - Å resolution crystal structure
included 247 nucleotides comprising most of theTetrahymena thermophila
intron. At this resolution, clear density for the ribozyme backbone was seen,
and stacked bases were visualized as continuous tubes of electron density.

TABLE 6.1 Selected Distances for Group I Intron PDB: 1GID

Nucleotide
(PDB: 1GID
Residue
Number)

Structural

Element

Ligand Atom (PDB:

1GID Symbol, Atom

Number)

Bond Distance ( Å ) to

Mg 12 +() 6799 ,Mg 22 +() 6800 ,

Mg 32 +() 6804 , Mg 42 +() 6806 ,

Mg 52 +() 6808 , Mg 62 +() 6797

A183 a A - rich bulge pro - S p - O (O2P, 1729) Mg 22 +−O 21.
pro - R p - O (01P, 1728) Mg 12 +−O 37.
A184 b A - rich bulge pro - S p - O (02P, 1751) Mg 22 +−O 21.
pro - R p - O (01P, 1750) Mg 12 +−O 23.
A186 b A - rich bulge pro - S p - O (02P, 1793) Mg 22 +−O 23.
pro - R p - O (01P, 1792) Mg 12 +−O 25.
A187 A - rich bulge pro - R p - O (01P, 1814) Mg 22 +−O 21.
G163 P5bc connector N 7 (1309) Mg 32 +−N 26.
G164 P5bc connector O 6 (1335) Mg 32 +−O 21.
A171 L5c (loop 5c) pro - R p - O (01P, 1465) Mg 42 +−O 23.
A173 L5c (loop 5c) pro - R p - O (01P, 1509) Mg 52 +−O 24.
G188 A - rich bulge O 6 (1852) Mg 62 +−O 20.
a Conserved in group I intron ribozymes.
b Invariant in group I intron ribozymes.