Figure 2.

Arg¹⁸⁷ of RelA binds 4- and 5-bp half-sites differently. A, top panel, close-up view of the amino acid residues of each subunit of the two RelA homodimers in contact with the 21-mer DNA sequence containing tandem κB sites. The dotted lines denote hydrogen bonds. Amino acid residues are shown in different colors according to the RelA subunit coloring in Fig. 1. DNA nucleotides participating in RelA–DNA contacts are also highlighted. Bottom panel, base-contacting residues are mapped on the DNA sequence in the complex. B, a cartoon highlighting how RelA interacts with half κB sites spanning 5 bp (left panel) or 4 bp (right panel), respectively. Amino acids involved in these contacts are colored in magenta and cyan, because these contacts correspond to subunit C and subunit B, respectively. Arrows indicate interaction, whereas X indicates no contact.