This methyltransferase catalyzes the formation of m2G966 in the loop of hairpin 31 of 16S rRNA within a pre-30S ribosome. A purified complex containing stoichiometric amounts of proteins S7, S9, and S19 bound to 16S rRNA possess the same RsmD methylation properties as 30S subunits. Structure of E.coli RsmD methyltransferase was determined and compared with the one of the M. jannaschii RsmC ortholog, specific for m2G1207 of the same 16S rRNA. RsmD and RsmC both posses a common MTase domain in the C-terminus (Rossmann-fold) and a variable region in the N-terminus that is related to the YbiN family of MTases (formation of m6A1618 by RlmF). Sequence/structure comparison suggests that both rRNA:m2G MTases are very closely related to RNA and DNA:m6A MTases and that these two enzyme families share common architecture of the active site and presumably a similar mechanism of methyl group transfer onto the exocyclic amino group of their target bases. Notice, adjacent to G966, a m5C967 has been found. The corresponding E. coli RsmB enzyme catalyzing m5C967 synthesis works in vitro only on free 16S rRNA; the presence of ribosomal proteins S7, S9 and S19 inhibit formation of m5C967 in vitro.