Figure 3.
Figure 3. Proposed reaction pathway. (a) Mixed trans (80%)
and cis (20%) structures of AMA-A. Maps were calculated before
inclusion of the minor cis conformation in the model. 2F[o] -
F[c] (silver) and F[o] - F[c] (blue) maps are contoured at 1.0
and 2.0 r.m.s.
deviation, respectively. Final refined coordinates for the two
partially occupied conformations are shown in orange (trans) and
green (cis). (b) Top view of AMA-A trans (orange, 80% occupied)
and cis (green, 20% occupied) conformations. Series of red and
orange/green spheres show path of CA^N Ala89 O and C atoms
for intermediate conformations. This path would keep the Ala89
side chain clear of CypA protein and maintains a staggered
conformation. White dashed line; contact between the side chain
of CA^N Ala89 and CypA Arg55 that prevents CA^N Pro90 from
binding fully into the active site when in the trans
conformation. Black dashed lines represent the hydrogen bonds
between CypA Arg55 and CA^N Pro90 O that prevents propagation of
conformational changes to C-terminal residues and the hydrogen
bond to CA^N Pro90 N that promotes catalysis.
r.m.s.
deviation, respectively. Final refined coordinates for the two
partially occupied conformations are shown in orange (trans) and
green (cis). (b) Top view of AMA-A trans (orange, 80% occupied)
and cis (green, 20% occupied) conformations. Series of red and
orange/green spheres show path of CA^N Ala89 O and C 
atoms
for intermediate conformations. This path would keep the Ala89
side chain clear of CypA protein and maintains a staggered
conformation. White dashed line; contact between the side chain
of CA^N Ala89 and CypA Arg55 that prevents CA^N Pro90 from
binding fully into the active site when in the trans
conformation. Black dashed lines represent the hydrogen bonds
between CypA Arg55 and CA^N Pro90 O that prevents propagation of
conformational changes to C-terminal residues and the hydrogen
bond to CA^N Pro90 N that promotes catalysis.