Table 1. Hydrogen bonds formed between the fingers domain loop aspartic acid or its equivalent (the amino acid shown in green and arrowed in Figure 1) and amino acids (shown in blue) in the subsequent α-helix.
| DNA polymerase | Data source | Number of H bonds | Hydrogen bonding partnersa |
|---|---|---|---|
| Sce-Pol α | pdb, 4FVM | 3 | D929-H931 |
| D929-K932 | |||
| D929-R933 | |||
| Sce-Pol δ | pdb, 3IAY | 3 | D686-F688 |
| D686-K689 | |||
| D686-R690 | |||
| Sce-Pol ϵb | pdb, 4M8O | 1 | D807-K811 |
| Sce-Pol ζb | ‘Phyre2’ model | 2 | D1070-T1073 |
| D1070-K1075 | |||
| Pfu-Pol | pdb, 2JGU | 2 | D473-I475 |
| D473-K477 | |||
| Pfu-Pol D473Gb | ‘Phyre2’ model | 1 | G473-K477 |
| Tgo-Pol | pdb, 1TGO | 3 | D472-I474 |
| D472-E475 | |||
| D472-K476 | |||
| Tgo-Pol Z1b | ‘Phyre2’ model | 3 | D473-T476 |
| D473-K478 | |||
| D473-R479 | |||
| Eco-Pol IIc | pdb, 3K5O | 3 | N485-L488 |
| N485-S489 | |||
| N485-A491 |
aThe first residue shown is the aspartic acid (asparagine in the case of Eco-Pol II) in the loop region, the second the amino acids in the following α-helix. The underlined hydrogen bonds were found with a distance constraint <0.4 Å and an angle constraint <20°. The other hydrogen bonds had more relaxed constraints of <1 Å and <30°.
bThese DNA polymerases possess a fingers loop that is longer than three amino acids.
cWith Eco-Pol II the third residue in the loop is asparagine rather than aspartic acid.