Dear Hailiang, as Herman Schreuder already wrote sugars are quite likely to contain errors. We are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group to help crystallographers locating problems in sugars. There will be an update soon, which includes checks for potentially missing LINK records and indicates the atoms that should be linked (and also checks, if linkages result in proper residues, i.e. if there are residues linked to a protein that are not known to occur in glycoproteins, such as NDG (a-D-GlcpNAc) in N-glycan chains). A beta version of the upcoming update is now available at http://www.glycosciences.de/tools/pdbcare2/ - it might help you to identify the atoms that are to be linked and to find potential issues before publishing the structure.
Best regards, Thomas
