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Figure 1.
Figure 1. Ribosomal RNA and L11 sequences used for NMR studies and a comparison of L11-RNA and homeodo-
main-DNA contact sites. (a) A 58 nucleotide fragment of E. coli 23 S rRNA, modified at position 1061 (E. coli number-
ing) by a U to A substitution. Bases which are protected by native L11 in hydroxyl radical footprinting experiments
are indicated by gray shading (Rosendahl & Douthwaite, 1993). (b) A primary sequence alignment of the Oct-1
(Klemm et al., 1994) and MAT-a2 (Li et al., 1995) homeodomains. Homeodomain residues are numbered according
the convention previously established (Li et al., 1995). The helical boundaries and amino acid residues which contact
the DNA, are those reported for the Oct-1 (Klemm et al., 1994) and MAT-a2 (Li et al., 1995) homeodomain-DNA com-
plexes, respectively. The three helical regions are indicated symbolically above the amino acid sequences, whereas the
protein-DNA contact sites are identified by residue shading. Residues shaded black correspond to those which
engage in base-specific contacts, whereas those shaded gray correspond to those which exhibit either phosphate or
ribose contacts. (c) Primary sequence, deduced secondary structure,and sites of protein-RNA contacts for the C-term-
inal fragment (75 residues plus N-terminal initiator methionine) of Bacillus stearothermophilus L11. The secondary
structure is indicated schematically above the amino acid sequence, whereas the protein-RNA contact sites are indi-
cated by residue shading. The latter were identified on the basis of filtered NOE experiments, as described in
Materials and Methods.
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