Figure 5.
Figure 5. Ligand-binding sites in the structures of Mth and
Pae 14-mers bound to UMP. The two Mth heptamers (red, blue) in
the asymmetric unit of the P2[1] form are shown in (A). A single
molecule of MPD binds identically to each monomer
(space-filling, colored by atom type with yellow carbons).
Space-filling models of the 14 UMP ligands show that they bind
in the pore region (colored by atom type, gray carbons).
Electron density for a UMP binding site is shown in (B). The
2|F[o]| - |F[c]| density is contoured at +1.2 (green) and
|F[o]| - |F[c]| maps are contoured at -3.2 (red) or +3.2
(blue).
Conserved residues that form the UMP binding sites are labeled,
and residues from different monomers are distinguished by
primes. Hydrogen-bond distances are not shown, for the sake of
clarity (see Fig. 6 Go-).
Orthogonal views are shown in (C) for the Pae SmAP1 14-mer in
the C222[1] lattice (heptamer per a.u.). Ten glycerol molecules
bind to each heptamer (space-filling, green-colored carbons),
and seven of them occupy identical sites. Only the uridine
fragments of UMP were modeled (space-filling, gray-colored
carbons), at identical sites distal to the pore region.
The above figure is reprinted
by permission from the Protein Society:
Protein Sci
(2003,
12,
832-847)
copyright 2003.
(green) and
|F[o]| - |F[c]| maps are contoured at -3.2 
).
Orthogonal views are shown in (C) for the Pae SmAP1 14-mer in
the C222[1] lattice (heptamer per a.u.). Ten glycerol molecules
bind to each heptamer (space-filling, green-colored carbons),
and seven of them occupy identical sites. Only the uridine
fragments of UMP were modeled (space-filling, gray-colored
carbons), at identical sites distal to the pore region.