Table 2.
Mean distances between the sidechain of R177 and potential hydrogen-bonding partners in structures of actin monomers and filaments and in MD simulations
| Filament subunits (except monomer) | Nucleotide | R177- N111 SC |
R177-P109 C = O |
R177-H161 SC | R177-H73 C = O |
R177-D179 SC |
Gate |
|---|---|---|---|---|---|---|---|
| Monomer | ATP | 8.6 Å | 6.6 Å | 5.9 Å | 4.8, 4.5 Å | 3.2, 3.5 Å | Open |
| Internal | ADP | 2.9, 3.0 Å | 2.5 Å | 7.2 Å | 2.9 Å | 3.8 Å | Closed |
| Pointed end P-1 | ADP | 9.6, 10.6 Å | 6.8 Å | 5.5 Å | 3.3 Å | 3.0 Å | Open |
| Barbed end | ADP | 5.4 Å | 4.2 Å | 8.6 Å | 2.4 Å | 4.6 Å | Open |
| MD closed | ADP-Pi | 2.8 Å | 2.8 Å | 4.20 Å | 3.5 Å | 8.4 Å | Closed |
| MD occluded | ADP-Pi | 8.2 Å | 4.0 Å | 5.1 Å | 4.9 Å | 7.4 Å | Occluded |
| MD open | ADP-Pi | 10.3 Å | 6.5 Å | 7.3 Å | 4.9 Å | 2.79 Å | Open |
| MD wide-open | ADP-Pi | 16.1 Å | 10.8 Å | 8.6 Å | 9.9 Å | 3.2 Å | Wide-open |
Distances smaller than 4.0 Å are bold. Measurements were taken from the following structures. Monomer: PDB 2V52. Internal: PDB 8A2T. P-1: Chou and Pollard. https://biorxiv.org/cgi/content/short/2023.05.12.540494v1. Barbed end: PDB 8F8R.