Table 2.
Superpositions of the structures of substrate-bound XMRV and HIV-1 RTs
| Superimposed domain (Total number of traced Cα atoms in each XMRV RT domain given in parentheses) | RMSD (Å) calculated for: |
||||
|---|---|---|---|---|---|
| Substrate | Fingers | Palm | Thumb | Connection | |
| RNA/DNA complex, 1HYS | |||||
| Substrate 30 pairs of atomsa | 0.5 | 5.8 | 2.3 | 3.1 | 4.1 |
| Fingers 84 pairs of Cα atoms (of 106) | 7.3 | 1.7 | 8.2 | 14.9 | 17.1 |
| Palm 91 pairs of Cα atoms (of 136) | 1.1 | 4.6 | 1.3 | 3.1 | 3.1 |
| Thumb 53 pairs of Cα atoms (of 79) | 2.9 | 6.1 | 5.3 | 1.6 | 2.3 |
| Connection 54 pairs of Cα atoms (of 120) | 4.7 | 8.1 | 5.7 | 3.1 | 1.6 |
| dsDNA complex, 1RTD | |||||
| Substrate 24 pairs of atomsa | 0.4 | 2.4 | 1.8 | 3.0 | 3.4 |
| Fingers 84 pairs of Cα atoms (of 106) | 1.6 | 1.2 | 3.6 | 3.7 | 6.2 |
| Palm 91 pairs of Cα atoms (of 136) | 0.7 | 2.7 | 1.3 | 3.0 | 3.2 |
| Thumb 53 pairs of Cα atoms (of 79) | 2.7 | 3.5 | 4.4 | 1.5 | 2.8 |
| Connection 54 pairs of Cα atoms (of 120) | 5.2 | 7.3 | 5.8 | 3.1 | 1.6 |
The individual subdomains were superimposed [the resulting root mean square deviations (RMSDs) of pairs of C−α atoms are shown in bold] and the RMSD values for the other subdomains are given.
aPhophodiester backbone atoms of nucleotides −1, −2 and −3 of the primer and template strands were used for superposition.