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Figure 5.
Figure 5. DNA Contacts by I-CeuI
(A) The numbering of
bases, extending from the center of the four base cleavage site,
and the corresponding numbering of the bases in the deposited
pdb file. Unambiguous noncovalent contacts to individual bases
are shown below. The scissile phosphate groups are red. Base
pairs that are conserved between the left and right half-sites,
and enzyme residues that are engaged in identical contacts to
bases in each half-site, are shaded. Structured water molecules
involved in contacts between the DNA target and the enzyme are
indicated with circles; the single observed bound metal ion
(calcium) is indicated by a circled “M.” This single metal
ion is indicated twice in the figure, and it is shared between
the scissile phosphates and the enzyme active sites. Residue 93,
which is a conserved glutamine in the wild-type enzyme, is
present in the structure as a catalytically inactivating
arginine (Q93R); this side chain is in contact with the
phosphate in each half-site directly 5′ to the scissile
phosphate. In structures of I-CreI and I-MsoI, the wild-type
glutamine residue participates in coordination of a metal bound
water molecule.
(B) Ribbon diagram of the β sheet DNA
binding platform and additional elaborations (α-2 and loop 5/6)
from I-CeuI; residues participating in DNA-contacts are shown
and labeled. The same view of the DNA binding elements of the
enzyme with the bound target site is shown below. Figure 5.
DNA Contacts by I-CeuI(A) The numbering of bases, extending from
the center of the four base cleavage site, and the corresponding
numbering of the bases in the deposited pdb file. Unambiguous
noncovalent contacts to individual bases are shown below. The
scissile phosphate groups are red. Base pairs that are conserved
between the left and right half-sites, and enzyme residues that
are engaged in identical contacts to bases in each half-site,
are shaded. Structured water molecules involved in contacts
between the DNA target and the enzyme are indicated with
circles; the single observed bound metal ion (calcium) is
indicated by a circled “M.” This single metal ion is
indicated twice in the figure, and it is shared between the
scissile phosphates and the enzyme active sites. Residue 93,
which is a conserved glutamine in the wild-type enzyme, is
present in the structure as a catalytically inactivating
arginine (Q93R); this side chain is in contact with the
phosphate in each half-site directly 5′ to the scissile
phosphate. In structures of I-CreI and I-MsoI, the wild-type
glutamine residue participates in coordination of a metal bound
water molecule.(B) Ribbon diagram of the β sheet DNA binding
platform and additional elaborations (α-2 and loop 5/6) from
I-CeuI; residues participating in DNA-contacts are shown and
labeled. The same view of the DNA binding elements of the enzyme
with the bound target site is shown below.
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