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Figure 2.
Figure 2. Sequences, Foldings, and DNA Recognition(A) Amino
acid sequences of CBFα and CBFβ with indications of their
secondary structures; the nucleotide sequence of the 26 bp
double-stranded DNA fragment used for determining the structures
of the CBFα-β-C/EBPβ-DNA and CBFα-C/EBPβ-DNA complexes; and
the sequence of the 16 bp DNA fragment used for determining the
structure of the CBFα-DNA complex.(B and C) Topology diagrams
of the structures of CBFα (B) and CBFβ (C). The first and last
residue numbers of each secondary structure are indicated. The
notations A, B, C, C′, E, F, and G correspond to the β
strands classified as being within the immunoglobulin fold. In
(B), cyan, green, and yellow circles depict the residues
involved in specific DNA base recognition, nonspecific DNA
backbone interactions, and water-mediated interactions,
respectively. In (C), the electron density of a section of L3
(residues 71 to 81) was not observed (dotted line).(D) Schematic
representation of DNA recognition by CBFα. Dashed and solid
lines depict intermolecular hydrogen bonds and van der Waals
contacts, respectively. DNA base labels involved in direct
interactions with amino acids are colored red. A DNA base label
involved in water-mediated base recognitions is colored green.
DNA recognitions by the peptide backbone amide are noted as NH.
Minor groove recognitions are circled with magenta.(E) A stereo
view of the specific interactions between CBFα and DNA. Pink
tubes show the CBFα peptide backbone. Dotted lines depict
intermolecular hydrogen bonds and water molecules are shown as
red balls
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