Example of complicated links involving residues in alternate conformations. In the crystal structure of β-mannanase in complex with 2,4-dinitrophenyl 2-deoxy-2-fluoro-β-mannotrioside the unhydrolysed substrate and a covalent intermediate are present simultaneously (Ducros et al., 2002). In the unhydrolysed form the substrate the sugar moiety MAF is bound to BEN, whereas in the covalent intermediate MAF is bound a glutamate residue. The links and modifications needed to refine this complex are given in Fig. 7.