Table 1. Summary of RNA systems.

RNA	PDB ID	Structural Features	RMSD (Å)a	Length (nt)
Human telomerase pseudoknot	2K96	Pseudoknot, Hoogsteen pairs	4.25	47
Murine leukemia virus pseudoknot	2LC8	Pseudoknot	4.29	56
Mouse mammary tumor virus pseudoknot	1KAJ	Pseudoknot	5.13	32
HIV-2 TAR hairpin kissing dimer	1KIS	Kissing interaction	2.39	16+16
Guanosine binding site of Group I intron from Tetrahymena thermophile	1K2G	GCG base triple	3.73	22
Aquifex aeolicus tmRNA pseudoknot PK1	2G1W	Pseudoknot	5.00	22
Bacilus subtilis PreQ1 riboswitch class I aptamer	2L1V	Pseudoknot, small molecule ligand	5.53	36
Pea enation mosaic virus P1-P2 pseudoknot	2RP0	Pseudoknot, Hoogsteen pairs	5.28	27
Sugarcane yellow leaf virus mRNA pseudoknot	1YG3	Pseudoknot	4.85	28
Kluyveromyces lactis telomerase RNA pseudoknot	2M8K	Pseudoknot	4.46	48
Neurospora Varkud satellite ribozyme stem I-V kissing-loop interaction	2MI0	Kissing interaction	4.51	22+21
Streptococcus pneumonia PreQ1 class II riboswitch	2MIY	Pseudoknot, Hoogsteen pairs, small molecule	6.47	59
Neurospora VS ribozyme II-III-VI three-way junction	2N3R	Three-way junction	13.44	62
Neurospora VS ribozyme III-IV-V three-way junction	2MTJ	Three-way junction	7.60	47
Bacillus cereus fluoride riboswitch aptamer	4ENCb	Pseudoknot, Hoogsteen pairs	5.84	47