Chemistry Reference
In-Depth Information
Figure 15.2
Preferred coordination geometry of divavlent cations (Me
2+
): (A) Mg
2+
prefers
octahedral coordination with six ligands; (B) Zn
2+
prefers tetrahedral confi guration with four
ligands. In protein structures, both Mg
2+
and Zn
2+
have been observed with fi ve ligands in
nonstandard geometry
or ligand. Therefore ionic (Shannon) radii
17
are inapplicable. The most common
ligand coordination geometry is octahedral or tetrahedral
18
(Figure 15.2 ). Mg
2+
prefers to have six inner-sphere ligands arranged in an octahedral confi guration, and
so does Fe
2+
.
18
Ca
2+
and Zn
2+
can have octahedral coordination, but Zn
2+
is fre-
quently coordinated by four ligands in a tetrahedron,
19
and Ca
2+
by seven, eight or
even nine ligands.
20
The number and length of ligand bonds are empirically determined and shown
to vary within a very narrow range.
18
These metal ions are far more sensitive to the
ligand type and geometry than hydrogen bonds or salt bridges between oxygen and
nitrogen atoms. Each of these divalent cations has been found to be essential for
catalysis by at least one enzyme, e.g. Fe
2+
in nonheme iron enzymes (oxygenases and
demethylases),
21
Zn
2+
in deacetylase and protease,
22,23
Ni
2+
in urease,
24
but the Mg
2+
ion is most frequently associated with nucleic acid enzymes.
13
This is perhaps because
of its abundance and solubility, stability in redox potentials compared with Mn
2+
,
Fe
2+
and Cu
2+
, its small size relative to Ca
2+
and its rigid coordination geometry
compared to the transition metals Fe
2+
, Cu
2+
, Ni
2+
and Zn
2+
.
16
The ligand bond of the
Mg
2+
ion is empirically determined to be 2.07 Å.
18
The unusual hydration property of
Mg
2+
ions may also be a factor for its catalytic role. Mg
2+
ions exhibit extremely slow
exchange rates of inner-shell water molecules
16,25
and often retain a couple of water
ligands when coordinated by organic or macromolecules.
18
The p
K
a value of a water
molecule is reduced from 16.0 in free solution to 11.4 when associated with Mg
2+
.
26
15.2 All DNA and RNA Polymerases Require Two Mg
2+
Ions for Catalysis
To date, six families of DNA polymerases have been identifi ed, and each contains
a number of conserved sequence motifs.
27,28
The
fi rst four families, A to D,
