Figure 2

Sequence alignment of the ferredoxin domains: a) PSI-BLAST alignment of a bacterial ferredoxin domain (2pda, chain A: 679–767) with a α-helical ferredoxin domain (1kf6). The cluster-binding residues are boxed in black. Small residues near the ligand-binding site are colored red. Similar residues are colored yellow. b) Multiple structure-based sequence alignment of bacterial ferredoxins and α-helical ferredoxins. The consensus secondary structures for the two types of ferredoxins are shown: α-helices as cylinders and β-strands as arrows. The multiple alignment was made by manually defining equivalent residues for the structurally similar regions of the ferredoxin domains. Sequences shown in capitals correspond to the structurally superimposed regions. Regions that are not superimposable due to structural differences are shown in italics. The PDB code and the domain range are shown. The structures of 1feh (red) and 1kf6 (black) correspond to the superposition in figure 1e. Residues are colored according to figure 2a.