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1aay.A1 1zaa.C1 1p47.A1 1jk1.A1 1f2i.K1 1p47.B1 1a1j.A1 1a1i.A1 1jk2.A1 1a1l.A1 1a1g.A1 1f2i.H1 1f2i.L1 1f2i.G1 1f2i.J1 1f2i.I1 1a1h.A1 1a1k.A1 1a1f.A1 Zif268 ZF1 (a) RDER:GCG RAER:GCG RDER:GCG RADR:GCG RADR:GCA RAER:GCT RDER:GCA DSNR:GCG RDER:GCG QGSR:GCA RADR:GAC DSNR:GAC

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1aay.A2 1a1h.A2 1jk2.A2 1jk1.A2 1p47.A2 1llm.D2 1a1g.A2 1a1k.A2 1a1l.A2 1a1j.A2 1a1i.A2 1a1f.A2 1zaa.C2 1p47.B2 1llm.C2 1f2i.J2 1f2i.H2 1f2i.L2 1f2i.G2 1f2i.K2 1f2i.I2 Zif268 ZF2 (b) RDHT:TGG

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1aay.A3 1zaa.C3 1a1k.A3 1jk1.A3 1a1f.A3 1a1i.A3 1a1l.A3 1a1h.A3 1jk2.A3 1p47.A3 1a1g.A3 1llm.D3 1a1j.A3 1p47.B3 1llm.C3 Zif268 ZF3 (c) RDER:GCG

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1g2d.C1 1g2d.F1 1g2f.C1 1g2f.F1 1g2d.C2 1g2d.F2 1g2f.C2 1g2f.F2 1g2d.C3 1g2d.F3 1g2f.C3 1g2f.F3 1mey.C1 1mey.F1 1mey.C2 1mey.F2 1mey.C3 1mey.F3 Designed Zinc Fingers (d) QTNT:AAA QTGQ:ATA QASA:ATA THTR:TCG QSNK:GAA QSDK:GCA RDHR:GAG

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1ubd.C1 1ubd.C2 1ubd.C3 1ubd.C4 2drp.A1 2drp.D1 2drp.A2 2drp.D2 2gli.A2 2gli.A3 2gli.A4 2gli.A5 1tf6.A1 1tf6.D1 1tf6.A2 1tf6.D2 1tf6.A3 1tf6.D3 1tf6.A5 1tf6.D5 YY1, Tramtrack, GLI, TFIIIA (e) YY1 Tramtrack GLI TFIIIA DSAK:AGA ESKR:GGA LFNT:AAT QTNS:CAA HSNR:GAT RDNA:AAG AYMV:ACG RENT:CAA NSDK:CCC DSSK:ACC KWKA:AGA SHHR:GGG TANK:GAT LSRR:GTT

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Figure S1. Detailed view of regions along the diagonal of the docking- comparison matrix shown in Figure 1. Pair-wise IAS values are shown as in Figure 1. Scores below 5.0 are in white (not shown). IAS values between domains with a wild-type-docking geometry (see text) in each of the three Zif268 groups are delineated with a heavy dashed line. PDB identifier, chain ID and ZF domain number (as in Table 1) for each complex are indicated at the far left. Amino acid identities for the canonical ZF helix positions -1, 2, 3 and 6 (as in Figure 2), and base identities for the recognized base triplet (e.g. bases 4-6, 4’-6’ for ZF2 in Figure 2) are indicated for each complex.

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