present in the holo structure only — a base pair that appears on binding. The headline Base pairs formed on binding counts the canonical (Watson–Crick / G·U wobble) formed pairs — the secondary-structure rewiring.
present in the apo structure only — a base pair lost on binding.
present in both states — unchanged by binding.
Click any bar to view that subset in the gallery.
x3dna-dssr also reports many non-canonical Leontis–Westhof pairs (imino, cis-WW A·A/U·U, base triples, single-H-bond contacts). These are geometrically labile and flip in and out between apo and holo structures of differing resolution, so counting them would let threshold noise dominate the reported rewiring.
Some short fragments (e.g. the aminoglycoside A-site RNAs, ~9–23 nt) are self-complementary duplexes whose base pairs run between two separate strands. x3dna-dssr still resolves these inter-strand pairs, so their counts here are full structure-derived base pairs (canonical foregrounded as above).
On the pair page they are summarised as counts — marked with a “?” — rather than drawn as a single-chain arc diagram.
The base pairs are structure-derived (read from each 3D model with x3dna-dssr); the apo–holo mapping is geometric (the pairwise sequence alignment). It compares two experimentally determined endpoint structures, not a binding pathway.