I-CreI/DNA binding interface. (A) Natural I-CreI target site with all positions indexed with respect to the center of the site from -11 to 11. -11NNNN and -5NNN are the reverse-complements of 11N4 and 5N3. (B) 3D structure of the I-CreI/DNA complex (PDB code: 1g9y). (C) I-CreI/DNA interaction map. Columns correspond to position on the DNA, rows correspond to positions of protein residues. Colors in the table are used to describe the nature of interaction between residues and nucleotides: dark green – backbone interactions, blue – water mediated, red – base specific. Residues N30-S40 and Q44-D75 are clustered together to indicate that they contact separate regions 11N4 and 5N3 on the DNA target.