From the secondary cloverleaf structure to the tertiary L-shaped structure of
Nomenclature of domains is recalled and positions of nucleotides
are numbered according to conventional rules (Sprinzl et al., 1998).
Notice especially numbering in the D- loop where the two conserved G residues
are always referred to as G18 and G19. Variation in size of this loop is very
frequent and additional nucleotides are indicated as 17:a, 17:b, ... or 20:a,
20:b, etc. The number of nucleotides forming the Variable region goes from 3
to more than 20 with additional nucleotides referred to as 47:a, 47:b, etc.
Conserved nucleotides in the cloverleaf are given and their involvement in tertiary
interactions leading to the L-shaped structure indicated by thin lines. Y stands
for pyrimidine, R for purine,