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Figure 1.
Figure 1. The overall structure of A. pleuropneumoniae SOD (ApSOD). (a) Schematic diagram of ApSOD subunit
connectivity. The eight antiparallel b-strands are numbered based on their three-dimensional order of appearance
around the b-barrel, and the sequence order is indicated with lower-case letters. The connections are afforded by a
Greek-key loop from b3c to b6d and a Greek-key helix from b4f to b7g. Extra-barrel loops form the metal-containing
active-site and the electrostatic attraction loop. (b) C
a
trace of the SOD dimer, colored by thermal factor (gradual
change from dark blue <20 Å
2
to red >95 Å
2
), shows that the disorder is much higher in Sub(unit)1, in particular the
extended loops from residues 20-25 and 70-75 (upper right). These loops border the large solvent channel in the crys-
tals, whereas in Sub2, the loops form crystal contacts with a neighboring molecule and are well-ordered, with no
ambiguity in the interpretation of the map. (c) Schematic ribbon rendering of the molecule showing dimer interface
side-chains (green) and water molecules (red) as well as the disulfide bond (yellow) and metals (orange sphere, cop-
per and silver sphere, zinc) and side-chains in the active-site (colored by atom type). Interface water molecules obey
the non-crystallographic 2-fold symmetry. The charged residues (orange side-chains, top left, shown only for Sub2) at
the tip of the electrostatic loop, together with the catalytic copper, form an electrostatically favorable pathway for
substrate superoxide ions. The active-site channel is formed between loops on the side of the b-barrel. Copper ligands
His60 N
d1
, His62 N
e2
, and His141 N
e2
are 1.99-2.13 Å from the Cu(II) ion, which is exposed at the bottom of the
active-site channel. The structural zinc is buried 6.4 Å under the copper and ligated by His85 N
d1
, His94 N
d1
, His103
N
d1
and Asp106 O
d1
, with bond distances of 2.00 Å for the Asp residue and 2.07-2.12 Å for the histidine residues.
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