Conserved positions for ribose recognition: Importance of water bridging interactions among ATP, ADP and FAD-protein complexes

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand–protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein–ligand com-plexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved pos-ition. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose–protein complexes