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mm:parameters:zinc:hdc_prod
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Zinc (II) - HDC[Prod]
The metal center of Farnesyltransferase for the product complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine, 1 aspartate (monodentate), and to the product.
| Coordination Sphere | Oxidation state: Zn(II) Spin multiplicity: 1 |
 | 1) |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | Farnesyltransferase |
| PDB Code | 1KZP |
| Crystallographic Resolution | 2.10 Å |
| Organism | Rattus norvegicus |
| [Long, 2002] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| ZN | ZK | 65.409 | |
| NE2 | OK | 14.0067 | |
| OD2 | SK | 15.9994 | |
| OD1 | NK | 32.065 | |
| SG | SL | 32.065 |
Bond Parameters
| BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
| ZJ-OJ | 88.3 | 1.999 | [Sousa, 2007] |
| ZJ-SJ | 81.2 | 2.352 | |
| ZJ-NJ | 62.6 | 2.129 | |
| ZJ-SR | 69.3 | 2.373 | |
| C-OJ | 656.0 | 1.311 | |
| CT-SJ | 227.0 | 1.900 | |
| NJ-CV | 427.0 | 1.401 | |
| CR-NJ | 477.0 | 1.334 | |
| CT-SR | 227.0 | 1.896 |
Angles Parameters
| ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
| OJ-ZJ-NJ | 27.8 | 100.2 | [Sousa, 2007] |
| OJ-ZJ-SJ | 23.0 | 114.0 | |
| OJ-ZJ-SR | 24.1 | 115.1 | |
| SJ-ZJ-NJ | 20.7 | 110.1 | |
| SJ-ZJ-SR | 27.3 | 116.0 | |
| NJ-ZJ-SR | 39.1 | 98.8 | |
| C-OJ-ZJ | 10.0 | 134.0 | |
| CT-SJ-ZJ | 18.9 | 101.9 | |
| CR-NJ-ZJ | 20.0 | 130.0 | |
| CV-NJ-ZJ | 20.0 | 122.2 | |
| CT-SR-ZJ | 18.9 | 101.6 | |
| O2-C-OJ | 80.0 | 126.2 | |
| CT-C-OJ | 70.0 | 114.2 | |
| H1-CT-SJ | 50.0 | 109.5 | [Sousa, 2007] |
| CT-CT-SJ | 50.0 | 114.7 | |
| NJ-CV-H4 | 35.0 | 119.2 | |
| H5-CR-NJ | 35.0 | 124.0 | |
| CR-NJ-CV | 70.0 | 107.5 | |
| NA-CR-NJ | 70.0 | 109.7 | |
| CC-CV-NJ | 70.0 | 109.3 | |
| H1-CT-SR | 50.0 | 109.5 | [Sousa, 2007] |
| CT-CT-SR | 50.0 | 114.7 | |
| CT-CM-CT | 70.0 | 113.8 | |
| CM-CM-CM | 70.0 | 122.8 |
Van der Waals Parameters
| ATOM TYPE | Ri / Å | εi / kcal mol-1 | REFERENCE |
| ZJ | 1.7000 | 0.0125 | [Babu, 2006] |
| OJ | 1.6612 | 0.2100 | |
| SJ | 2.0000 | 0.2500 | |
| SR | 2.0000 | 0.2500 | |
| NJ | 1.8240 | 0.1700 |
Validation of Parameters from MD Simulations
Bond Parameters
| BOND | l0 crystal | ‹l›MD ± σ(l) Ternary Complex |
| ZJ-OJ | 1.95 ± 0.06 | |
| ZJ-SR | 2.44 ± 0.07 | |
| ZJ-SJ | 2.36 ± 0.06 | |
| ZJ-NJ | 2.19 ± 0.07 |
Angle Parameters
| ANGLE | θ0 crystal | ‹θ›MD ± σ(θ) Ternary Complex |
| NJ-ZJ-SR | 99 ± 4 | |
| OJ-ZJ-NJ | 110 ± 5 | |
| OJ-ZJ-SJ | 113 ± 5 | |
| OJ-ZJ-SR | 102 ± 7 | |
| SJ-ZJ-NJ | 118 ± 5 | |
| SJ-ZJ-SR | 112 ± 5 |
Downloads
References
Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism . Theoretical Chemistry Accounts, 2007, 117, 171-181
1)
The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.
mm/parameters/zinc/hdc_prod.1375112471.txt.gz · Last modified: 2013/07/29 16:41 by joaocoimbra
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