Table 2.
Distances of the Molecular Dynamics Simulations
| Atomsa | 16-Ib Å | 16-IIc Å | 16-IIId Å | 16 Restraints Radiie | 16 REDORf Å | 15-IVg Å | 15 Restraints Radiih | 15REDORi Å | 15 X-Rayj Å |
|---|---|---|---|---|---|---|---|---|---|
| NZ LysA92-P | 9.6k | 5.3 | 8.2 k | (3.8) 4.5 - 5.0 (6.0) | 3.8 or >8 | 7.3 | (5.7) 6.2 - 7.4 (7.8) | 6.2 | 7.4 |
| NZ LysB92-P | 5.7 | 10.3 k | 10.1 k | (3.8) 4.5 - 5.0 (6.0) | 3.8 or >8 | 7.6 | (5.7) 6.2 - 7.4 (7.8) | 6.2 | 7.4 |
| NZ LysC92-P | 5.4 | 5.5 | 9.7k | (3.8) 4.5 - 5.0 (6.0) | 3.8 or >8 | 7.3 | (5.7) 6.2 - 7.4 (7.8) | 6.2 | 7.4 |
| NZ LysD92-P | 5.4 | 13.6k | 9.0k | (3.8) 4.5 - 5.0 (6.0) | 3.8 or >8 | 7.5 | (5.7) 6.2 - 7.4 (7.8) | 6.2 | 7.4 |
| NZ LysE92-P | 8.6k | 5.5 | 8.7k | (3.8) 4.5 - 5.0 (6.0) | 3.8 or >8 | 7.5 | (5.7) 6.2 - 7.4 (7.8) | 6.2 | 7.4 |
| NE2 HisA97-P | 4.7 | 5.3 | 5.3 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 5.8 | (4.7) 5.0 - 5.9 (7.3) | 5.4 | 7.2 |
| NE2 HisB97-P | 5.2 | 5.0 | 5.1 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 5.7 | (4.7) 5.0 - 5.9 (7.3) | 5.4 | 7.2 |
| NE2 HisC97-P | 4.6 | 5.3 | 5.2 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 5.8 | (4.7) 5.0 - 5.9 (7.3) | 5.4 | 7.2 |
| NE2 HisD97-P | 5.4 | 5.2 | 5.0 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 5.9 | (4.7) 5.0 - 5.9 (7.3) | 5.4 | 7.2 |
| NE2 HisE97-P | 5.1 | 4.9 | 4.8 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 5.8 | (4.7) 5.0 - 5.9 (7.3) | 5.4 | 7.2 |
| NE ArgA136-P | 4.0 | 4.6 | 4.2 | (3.5) 4.0 - 4.5 (5.0) | 4.0 | 3.9 | (3.5) 4.0 - 4.5 (5.0) | 4.5 | 3.8 |
| NE ArgB136-P | 4.4 | 3.8 | 3.8 | (3.5) 4.0 - 4.5 (5.0) | 4.0 | 4.0 | (3.5) 4.0 - 4.5 (5.0) | 4.5 | 3.8 |
| NE ArgC136-P | 4.7 | 3.8 | 4.4 | (3.5) 4.0 - 4.5 (5.0) | 4.0 | 3.8 | (3.5) 4.0 - 4.5 (5.0) | 4.5 | 3.8 |
| NE ArgD136-P | 3.9 | 3.9 | 3.6 | (3.5) 4.0 - 4.5 (5.0) | 4.0 | 3.6 | (3.5) 4.0 - 4.5 (5.0) | 4.5 | 3.8 |
| NE ArgE136-P | 4.4 | 4.0 | 3.8 | (3.5) 4.0 - 4.5 (5.0) | 4.0 | 4.0 | (3.5) 4.0 - 4.5 (5.0) | 4.5 | 3.8 |
| NH1 ArgA136-P | 4.5 | 4.3 | 4.3 | (3.5) 3.9 - 4.5 (5.0) | 3.9 | 5.2 | (3.5) 3.9 - 4.9 (5.6) | 3.8 | 5.6 |
| NH1 ArgB136-P | 3.8 | 5.6 | 5.2 | (3.5) 3.9 - 4.5 (5.0) | 3.9 | 5.2 | (3.5) 3.9 - 4.9 (5.6) | 3.8 | 5.6 |
| NH1 ArgC136-P | 4.1 | 4.7 | 3.9 | (3.5) 3.9 - 4.5 (5.0) | 3.9 | 5.4 | (3.5) 3.9 - 4.9 (5.6) | 3.8 | 5.6 |
| NH1 ArgD136-P | 4.0 | 4.7 | 5.5 | (3.5) 3.9 - 4.5 (5.0) | 3.9 | 5.4 | (3.5) 3.9 - 4.9 (5.6) | 3.8 | 5.6 |
| NH1 ArgE136-P | 4.7 | 4.2 | 3.5 | (3.5) 3.9 - 4.5 (5.0) | 3.9 | 4.5 | (3.5) 3.9 - 4.9 (5.6) | 3.8 | 5.6 |
| NH2 ArgA136-P | 4.1 | 4.6 | 4.6 | (3.5) 3.9 - 4.5 (5.0) | 3.8 | 3.5 | (3.5) 3.8 - 4.3 (4.5) | 3.8 | 3.8 |
| NH2 ArgB136-P | 4.8 | 3.8 | 3.9 | (3.5) 3.9 - 4.5 (5.0) | 3.8 | 3.6 | (3.5) 3.8 - 4.3 (4.5) | 3.8 | 3.8 |
| NH2 ArgC136-P | 4.0 | 4.1 | 3.9 | (3.5) 3.9 - 4.5 (5.0) | 3.8 | 3.5 | (3.5) 3.8 - 4.3 (4.5) | 3.8 | 3.8 |
| NH2 ArgD136-P | 4.8 | 4.1 | 3.3 | (3.5) 3.9 - 4.5 (5.0) | 3.8 | 3.7 | (3.5) 3.8 - 4.3 (4.5) | 3.8 | 3.8 |
| NH2 ArgE136-P | 4.5 | 4.2 | 3.5 | (3.5) 3.9 - 4.5 (5.0) | 3.8 | 4.3 | (3.5) 3.8 - 4.3 (4.5) | 3.8 | 3.8 |
| NE2 HisA148-P | 5.1 | 5.2 | 4.5 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 4.5 | (3.7) 4.1 - 4.6 (5.6) | 4.1 | 6.8 |
| NE2 HisB148-P | 5.1 | 5.0 | 4.8 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 4.6 | (3.7) 4.1 - 4.6 (5.6) | 4.1 | 6.8 |
| NE2 HisC148-P | 5.0 | 5.1 | 4.6 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 4.2 | (3.7) 4.1 - 4.6 (5.6) | 4.1 | 6.8 |
| NE2 HisD148-P | 5.0 | 5.2 | 4.8 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 4.5 | (3.7) 4.1 - 4.6 (5.6) | 4.1 | 6.8 |
| NE2 HisE148-P | 5.4 | 4.9 | 5.0 | (4.0) 4.7 - 5.0 (7.3) | 4.7 | 4.8 | (3.7) 4.1 - 4.6 (5.6) | 4.1 | 6.8 |
Atoms whose distances are calculated or determined at the five binding sites A, B, C, D, and E.
Distance between atoms calculated from molecular dynamics simulation of the enzyme-16 complex starting from docked conformer I.
Distance between atoms calculated from molecular dynamics simulation of the enzyme-16 complex starting from docked conformer II.
Distance between atoms calculated from molecular dynamics simulation of the enzyme-16 complex starting from docked conformer III.
REDOR restraint radii (r1) r2-r3 (r4) used in the molecular dynamics simulation involving 16.
Distance determined by 15N{31P} REDOR NMR on the enzyme-16 complex.
Distance between atoms calculated from molecular dynamics simulation of the enzyme-15 complex starting from docked conformer IV.
REDOR restraint radii (r1) r2-r3 (r4) used in the molecular dynamics simulation involving 15.
Distance determined by 15N{31P} REDOR NMR on the enzyme-15 complex.
Distances determined by crystallography on the enzyme-15 complex.
Italicized: not restrained.