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Figure 2.
Structure of the C cluster, putative substrate channels, and
proposed mechanism of C-O bond formation. (A) Stick diagram of
the C cluster and surrounding residues together with surface
diagram highlighting internal cavities. The atoms of the C
cluster including the bound CO and putative H[2]O are colored by
atom with Fe in violet, Ni in slate, carbon in gray, and sulfur
in CPK. The protein is shown in stick with the carbon atoms
depicted in cyan and the remaining atoms in CPK. The Ni and FCII
iron that bind CO and H[2]O/OH, respectively, are labeled as are
residues Ile-641 and His-117, which may help CO adopt its bent
geometry. (B) Stick diagram highlighting putative proton/water
channel. The conserved His residues that line one side of this
channel are labeled. (C) The CO/CO[2] channel of methanogenic
CODH component depicted as a transparent molecular surface
component colored by subunit according to the color scheme in
Fig. 1. The protein atoms have been omitted for clarity, but the
metal clusters are shown as spheres with Fe atoms colored in
violet, Ni atoms in slate, and the remaining atoms in CPK. The
Xe-binding sites that map the channel are shown as pink spheres.
A small molecule modeled as a portion of a PEG group is shown in
stick and colored in CPK. This PEG molecule marks the channel
exit from the ε-subunit. (D) Proposed coupling of the CO and
H[2]O species via intermediate observed in this structure. The
loss of the proton required for CO + OH^− bond formation may
account for the stability of the current intermediate, which was
crystallized at low pH. All other Ni-CODH structures have been
determined at neutral pH.
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