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| organism | PDB-ID | sequence identity (%) | r.m.s.d. (Å) (number of matched residues) |
| Entamoeba histolytica EhMeth (this study) | 3QV2 | 100 | 0 |
| Homo sapiens DNMT2 | 1G55 | 27.6 | 1.03 (260) |
| Haemophilus haemolyticus M. Hha I (closed conformation) | 1MHT | 20.5 | 1.66 (237) |
| Haemophilus haemolyticus M. Hha I (open conformation) | 1HMY | 20.5 | 1.59 (224) |
