BIOINORGANIC CHEMISTRY A Short Course Second Edition

MAGNESIUM AND CATALYTIC RNA 253

Another base triple between the bulged - out A218 in P6 and the P3 domain
base pair C102 – G272 ties together the two major domains of the Tetrahymena
ribozyme using a type II base triple (see magenta lines in Figure 3A of refer-
ence 24 ).
In the P7 domain G binding site, the 3 ′ - terminal guanosine ( ω G, G414 in
PDB: 1X8W) is part of a base triple with the G264 – C311 pair. Since a con-
served G – C pair has been shown to be important in establishing the G binding
site in group I introns, the authors believe that the particular G264 – C311 pair
can be specifi ed as the G binding site facilitator. Three interactions form
betweenω G and the G264 – C311 pair: ω G N 1 – G 264 O 6 = 3.3 Å , ω G N 2 – G 264 N 7
= 3.0 Å , and ω G O 6 – C 311 N 4 = 4.0 Å. The ω G – G264 – C311 base triple is sand-
wiched by three other layers of base triples. Above ω G – G264 – C311 is a base
triple composed of the C262 – G312 pair with A263, while below are two base
triples: the A265 – U310 pair with A261 and the C266 – G309 pair with A306
(see Figure 4 of of reference 24 , and Figures 6.5 and 6.6 ).
The resolution of the PDB: 1X8W crystal structure does not allow identifi -
cation of magnesium ions. However, heavy atom [europium (Eu) and iridium,

Figure 6.5 Triple base pair for the Tetrahymena ribozyme (PDB: 1X8W). Visualized
using CambridgeSoft Chem3D Ultra 10.0 with notations in ChemDraw Ultra 10.0.
(Printed with permission of CambridgeSoft Corporation.)

A105

C216

N 3 O 2

O 6

N 4

N 3

N 1

N 1 N^2

G257

3.1 A

3.3 A

3.0 A

2.8 A

O2’

O5’

O5’

O5’

P

P

P

O 2 ’

O 2 ’