Table 1.
Summary of major direct protein-GMP/GDP substrate interactions
| OGMP |
CGMP |
CGMP, ATP |
CGDP,ADP |
|||
|---|---|---|---|---|---|---|
| Protein residue | Domain | GMP/GDP | (GMP binding) | (Closure) | (ATP binding) | (P transfer) |
| Strong interactions | ||||||
| Glu88 (OE1,2) | GMP-BD | GMP/GDP (N1,2) | >100% | >100% | >100% | >100% |
| Arg57 (NE, NH1) | GMP-BD | GMP/GDP (Pα,β) | >100% | 46% | >100% | >100% |
| Ser53 (OG) | GMP-BD | GMP/GDP (O6, N7) | 87% | 66% | 95% | 96% |
| Tyr69 (OH) | GMP-BD | GMP/GDP (Pα) | 97% | >100% | >100% | 48% |
| Arg166 (NH1,2) | LID | GMP/GDP (Pα) | — | >100% | >100% | — |
| LID | GDP (Pβ) | >100% | ||||
| Arg155 (NH1,2) | LID | GDP (Pβ) | >100% | |||
| Ser30 (OG) | CORE | GDP (Pβ) | 100% | |||
| Weaker interactions | ||||||
| Arg60 (NH1,2) | GMP-BD | GMP/GDP (Pα) | 60% | >100% | 28% | >100% |
| Thr101 (OG1) | GMP-BD | GMP/GDP (O6) | <5% | 71% | <5% | <5% |
| Asp121 (OD2) | CORE | GMP/GDP (N2) | — | 57% | 15% | 40% |
| Lys34 (NZ) | CORE | GMP/GDP (O3′,Pα) | — | 53% | 43% | — |
| CORE | GDP (Pβ) | 86% | ||||
Hydrogen-bonding and salt-bridge contact frequency in the catalytic site during the MD simulations of enzymatic substates 2–5 (see Fig. 2). Contacts are sorted from the strongest to the weakest interaction. Atoms or groups involved in the interaction are indicated in parentheses. Frequencies over 70% are shown in boldface. Percentages over 100% take into account multiple interactions from different groups of the same residue (such as bidentate contacts).