Table 1.
Increase in hydrogen-bonding distance after His → Asn
| PDB ID | Allele–peptide residue | d(His) | d(Asn) (PyMol) | Change |
|---|---|---|---|---|
| 1DLH | DR1–Lys2 | 2.69Å | 3.86Å (3.75) | 1.17Å |
| 1A6A | DR3–Lys2 | 3.03Å | 3.80Å (3.75) | 0.77Å |
| 1AQD | DR1–Asp4 | 2.68Å | 3.67Å (3.48) | 0.99Å |
| 1H15 | DR2–Val3 | 2.77Å | 3.85Å (3.74) | 1.07Å |
| 1HQR | DR2–Phe3 | 3.27Å | 4.14Å (4.10) | 1.17Å |
| 1HXY | DR1–Lys2 | 2.66Å | 3.73Å (3.66) | 1.08Å |
| 1J8H | DR1–Lys2 | 2.57Å | 3.65Å (3.55) | 1.08Å |
| 1KLU | DR1–Leu3 | 3.00Å | 4.17Å (4.13) | 1.17Å |
| 1KT2 | I-Ek–Leu4 | 3.03Å | 4.20Å (4.02) | 1.17Å |
| 1KTD | I-Ek–Leu4 | 2.88Å | 4.04Å (3.86) | 1.16Å |
| 1IEA | I-Ek–Val4 | 2.72Å | 4.11Å (3.98) | 1.39Å |
Modeling of His→Asn substitution with Swiss PDBviewer or PyMol41 for various human and mouse MHC class II molecule crystal structures. All structures have the conserved histidine residue; however, the side chains of the peptides whose carbonyl group potentially form a hydrogen bond with that histidine residue vary (column 2). d(His), distance between the conserved histidine and the oxygen atom of carbonyl group, as in the structure; d(Asn), distance between closest allowed 'conformer' of asparagine (after the substitution) and that same carbonyl group; change, d(Asn) – d(His). The potential hydrogen-bonding distance consistently increases by an average of 1.1Å; hence, the bond is weaker for the asparagine mutant models for all structures analyzed. PDB ID, Protein Data Bank accession number.