Table 2. A list of virus species having RdRp structures in the PDB, observed non-catalytic ion types, and distances of non-catalytic ions from the catalytic site.
| Family | Genus | Species1,2 | Observed non-catalytic iontypes(PDBid)3,4 | Distance (Å) of non-catalytic ions from the catalytic position5 |
| Caliciviridae | Lagovirus | RHV | Lu2+(1KHV) | 6.0 |
| Norovirus | Norwalk virus | Mg2+(1SH3), Mn2+ (3H5Y, 3H5X) | 6.6 | |
| Sapovirus | Sapporo virus | – | – | |
| Flaviviridae | Flavivirus | Dengue virus | Mg2+(2J7U) | 5.8 |
| West Nile virus | Ca2+(2HCN), Mg2+ (2HFZ) | 5.7 | ||
| Hepacivirus | hepatitis C virus | – | – | |
| Pestivirus | BVDV | – | – | |
| Leviviridae | Allolevivirus | Qβ | Ca2+ (3AGP), Mg2+ (3AGQ) | 4.0 |
| Picornaviridae | Aphthovirus | FMDV | Mg2+(1WNE, 2EC0, 2E9Z, 2E9T,2E9R, 3KOA, 3KNA, 3KLV, 3KMS) | 6.1 |
| Enterovirus | coxsackie virus | – | – | |
| poliovirus | Ca2+(1RDR) | 4.9 | ||
| human rhinovirus | – | – | ||
| Birnaviridae | Avibirnavirus | IBDV | Mg2+(2R72) | 5.5 |
| Cystoviridae | Cystovirus | φ6 | Mg2+(1HI8), Mn2+ (1HI0, 1HHS,1HHT, 1UVI, 1UVJ, 1UVK, 1UVL,1UVN, 1UVM, 2JLF) | 6.4 |
| Reoviridae | Orthoreovirus | reovirus | Mn2+(1MWH) | 6.1 |
| Rotavirus | simian rotavirus | – | – |
1
Abbreviations used: RHV, rabbit hemorrhagic virus; BVDV, bovine viral diarrhea virus; Qβ, enterobacteria virus Qβ; FMDV, foot-and-mouth disease virus; coxsackie virus, human enterovirus B; IBDV, infectious bursal disease virus; φ6, pseudomonas phage φ6; reovirus, mammalian orthoreovirus.
2
The viral species for which a non-catalytic metal was found are in bold.
3
PDBids are given only for structures that include a non-catalytic ion.
4
Structures used for the determination of the distances are in bold.
5
Structures were structurally aligned with the hepatitis C virus RdRp structure (PDBid: 2WHO). Distances were measured from catalytic ion A of the hepatitis C virus RdRp.