BIOINORGANIC CHEMISTRY A Short Course Second Edition

MAGNESIUM AND CATALYTIC RNA 259

by the Cech group in 2004, one metal ion (possibly Mg 22 +) coordinated to the

O2′ and O3 ′ of ω G.^24 Although this structure included ω G, it did not include

the scissile phosphate, the 3 ′ - or 5 ′ - exons, or the internal guide sequence (IGS)

to which the exons bind. The PDB: 1Y0Q group I intron crystal structure

published in 2005 also included a single metal ion that appeared to be equiva-

lent to Mg 12 +.^32 This metal coordinated the O3 ′ of U − 1. The construct in the

latter structure included the nucleophile O3 ′ and the ω G but not the scissile

phosphate or the 3 ′ - exon.

The following conclusions were made by Stahley and Strobel for group I

intron studies: (1) The group I intron reaction is reversible from that seen in

the PDB: 1ZZN structure, with U − 1 becoming the leaving group and the exog-

enous G O3 ′ becoming the nucleophile (see Figures 6.1 and 6.3 ); (2) the two -

TABLE 6.2 Selected Distances for Group I Intron PDB: 1ZZN

Nucleotide (PDB: 1ZZN
Residue Number)

Intron or Exon

(Structural Element)

Bonding Atoms

(PDB Symbol,

Atom Number)

Bond Distance to

Mg 22 +() 5550 or

Mg 12 +()() 5552 Å

G128 Intron (P9.0) part of
base triple
G128 – C178 – A129

pro - S p - O (01P,

3655)

Mg 22 +−O 20.

A172 Intron (J8/7) stacks
with U173 – A134
base pair

Two nonbridging

phosphate

oxygens (4603,

4604)

Mg 22 +−O 22.

Mg 12 +−O 22.

G170 Intron (J8/7) stacks
with U173 – A134
base pair

pro - S p - O (O1P,

4559)

Mg 12 +−O 21.

C88 Intron (P4) base pair
with G56

pro - S p - O (O1P,

2590)

Mg 12 +−O 22.

A +1 3 ′ - Exon scissile
phosphate

pro - R p - O (O2P,

5360)

Mg 22 +−O 20.

Mg 12 +−O 22.

5MU1 5 ′ - Exon O3 ′ – O (5540) Mg 12 +−O3′ 21.

U − 1 (dt − 1 in PDB: 1U6B) Nucleophile O3 ′ – O (5540) – P
A+1 (5358)

O3 ′ – O – P 3.2

G206 ( ω G) Intron terminus,
leaving group
O3′ – O

O3 ′ – O (5343) Mg^22 +−O3′ 21.

O2 ′ – OH (5345) Mg^22 +−O2′ 22.

Bond Angle and Distances for S N 2 reaction at Catalytic Site

O3 ′ – O (nucleophile,
U − 1 ) – P (A +1 ) – O3 ′ – O
(leaving group, ω G)

Bond angle = 175 °

O3 ′ – O (nucleophile,
U − 1 ) – P (A +1 )

3.2

Mg 22 ++() () 5550 −Mg^215552 3.9