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. 2012 Jul 6;13(7):8398–8429. doi: 10.3390/ijms13078398

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© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.

This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

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(a) The side-chain torsions of Asn297 of the Fc fragment. Torsion angles of the Asn297 side chain are measured by MolProbity [52]. We excluded Fc with high-mannose type glycan (PDB code 2wah) from this inspection, since this structure contains high-mannose type glycans. (b) Comparison of glycosidic torsions of N-glycan attached on Asn297 of Fc fragment. Dihedral angles of each linkage are calculated with CARP [15]. The vertical and horizontal axes indicate ϕ and φ angles, respectively. The residues with errors are carefully excluded from this analysis. In many cases, a β1-6 linkage is erroneously used between core Fuc and GlcNAc instead of an α1-6 bond [53]. Eight entries are plotted in Fuc-GlcNAc-1 (PDB code; 1h3w, 3ave, 3d6g, 2rgs, chain-A in 1e4k, and chain-B in 3sgj).

(a) The side-chain torsions of Asn297 of the Fc fragment. Torsion angles of the Asn297 side chain are measured by MolProbity [52]. We excluded Fc with high-mannose type glycan (PDB code 2wah) from this inspection, since this structure contains high-mannose type glycans. (b) Comparison of glycosidic torsions of N-glycan attached on Asn297 of Fc fragment. Dihedral angles of each linkage are calculated with CARP [15]. The vertical and horizontal axes indicate ϕ and φ angles, respectively. The residues with errors are carefully excluded from this analysis. In many cases, a β1-6 linkage is erroneously used between core Fuc and GlcNAc instead of an α1-6 bond [53]. Eight entries are plotted in Fuc-GlcNAc-1 (PDB code; 1h3w, 3ave, 3d6g, 2rgs, chain-A in 1e4k, and chain-B in 3sgj).