BIOINORGANIC CHEMISTRY A Short Course Second Edition

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

(Ir)] models were used to place magnesium ions in the fi nal native structural

model. Each of the four molecules in the PDB: 1X8W asymmetric unit showed

a magnesium ion in close contact with at least one of the two ribose hydroxyl

groups ofω G, G414 in PDB: 1X8W. The PDB: 1X8W model shown in Figure

6.6 shows a Mg 2+ – G414 O3 ′ bond equal to 2.7 Å and a Mg 2+ – G414 O2 ′ bond

equal to 4.4 Å. G414 is rendered in ball - and - stick format with CPK atom color-

ing — red, oxygen; blue, nitrogen; gray, carbon; magenta, phosphorus. As stated

previously, the ω G 3 ′ - OH is the attacking nucleophile in the cleavage reaction

and the 2 ′ - OH is believed to coordinate one of the magnesium ions involved

in the three - metal mechanism for group I introns.^27 The same magnesium ion

contacts nonbridging phosphate oxygens of orange - brown C262 (3.6 Å ), green

U305 (2.5 Å ), and magenta A306 (2.5 Å ). These specifi c oxygen atoms were

previously identifi ed in biochemical experiments as important to the guano-

sine addition step (Figure 6.1 , parts ii – iii; Figure 6.3 ). As will be seen in the

paragraphs below, similar positions for magnesium ions are found in the PDB:

1U6B and 1ZZN structures. In Figure 6.6 , one sees a stack of base triples sur-

rounding theω G base (G414 in PDB: 1X8W) with G414 itself as part of a base

triple with the G264 – C311 base pair. The coloring system in Figure 6.6 is

similar to that of the informative Figure 4 of reference 24.

Another X - ray crystallographic structure, at 3.1 - Å resolution, of the purple

bacteriumAzoarcus sp. group I self - splicing intron was published in 2004 by

Figure 6.6 Base triples surrounding ω G in PDB: 1X8W. Magnesium ions in position to

facilitate nucleophilic attack. Visualized using Chem3D Ultra and ChemDraw Ultra,

version 10.0. (Printed with permission of CambridgeSoft Corporation) (See color plate)

C262

A261

A263

C311

A265

U310

C266

A306

Mg

Mg

U305

G312

G264

G309

ωG O 2 ’

ωG O 3 ’

non-bridging

phosphate O

non-bridging
phosphate O

ωG, G414

PDB: 1X8W numbering