To map out the heavy metal binding sites of iduronic acid containing oligosaccharides isolated from human kidneys, we studied Zn (II) binding by nuclear magnetic resonance (NMR) and molecular modeling to two disaccharides isolated after nitrous acid depolymerization of heparin and two synthetic disaccharides representative of the heparin structure, namely, IdopA2S(α1,4) AnManOH, 1a, IdopA2S(α1,4)AnManOH6S, 1b, IdopA2S-(α1,4) GlcNSαMe, 2a, and IdopA2S(α1,4)GlcNS6SαMe, 2b (see previous article in this series). A conformational analysis of the metal free and metal bound solutions was made by comparing calculated 〈(NOE)〉s, 〈T1〉s, and 〈J〉s to experimental values. The 1C4, 4C1, and 2S0 conformations of the L-idopyranosiduronate ring and the 4E and 4T3 of the anhydro-D-mannitol ring are evaluated as are rotations about the C5–C6 hydroxymethylene of the AnManOH (6S) or GlcNS(6S) residues. The NOE between IdopA2S H1 and H3 and the known NOE between H2 and H5, as well as the T1 of IdopA2S H3, are introduced as NMR observables sensitive to the IdopA2S ring conformation. Similarly, a NOE between IdopA2S H5 and AnManOH (6S) or GlcNS (6S) H3 was observed that directly restricts the allowed interglycosidic conformational space. For all disaccharides, the Zn(II) bound spectral data are consistent with models in which these motions are partially “frozen” such that the 1C4 conformation of the IdopA2S is stabilized along with the 4T3 conformation of the AnManOH (6S) ring. The interglycosidic conformation is also stabilized in one of two minima. Electrostatic potential energy calculations gave the best overall agreement with experiment and suggest metal binding conformations with the carboxylate and ring oxygen of the IdopA2S residues (1C4 conformation) and either O3 of the GlcNS (6S) residues or the sulfate oxygens of the 6-sulphate for 2b providing additional chelating sites. These chelation models concur with the observation of marked 13C and 1H NMR chemical shifts for the IdopA2S resonances and of GlcNS H3 for 2a and GlcNS6S C6 for 2b. This study of model compounds implicates the IdopA2S(α1,4) GlcNS6S group as part of the heavy metal binding site in biologically important acidic oligosaccharides such as heparin.