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mm:parameters:zinc:hdc
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Zinc (II) - HDC
The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided, together with the parameter files for the FPP molecule.
| Coordination Sphere | Oxidation state: Zn(II) Spin multiplicity: 1 |
 | 1) |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | Farnesyltransferase |
| PDB Code | 1FT1 |
| Crystallographic Resolution | 2.25 Å |
| Organism | Rattus norvegicus |
| [Park, 1997] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| ZN | ZF | 65.409 | |
| NE2 | NF | 14.0067 | |
| OD2 | OF | 15.9994 | |
| OD1 | OG | 15.9994 | |
| SG | SF | 32.065 |
Bond Parameters
| BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
| ZF-NF | 88.3 | 2.043 | [Sousa, 2007] |
| ZF-OF | 62.3 | 2.094 | |
| ZF-OG | 43.8 | 2.159 | |
| ZF-SF | 115.8 | 2.258 | |
| C-OF | 656.0 | 1.308 | |
| C-OG | 656.0 | 1.306 | |
| CT-SF | 227.0 | 1.903 | |
| NF-CR | 477.0 | 1.338 | |
| NF-CV | 427.0 | 1.401 |
Angles Parameters
| ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
| OF-ZF-OG | 318.9 | 63.5 | [Sousa, 2007] |
| OF-ZF-NF | 16.7 | 107.3 | |
| OF-ZF-SF | 16.5 | 126.6 | |
| OG-ZF-NF | 19.4 | 97.0 | |
| OG-ZF-SF | 15.4 | 136.9 | |
| NF-ZF-SF | 16.2 | 114.5 | |
| C-OF-ZF | 10.0 | 90.8 | |
| C-OG-ZF | 10.0 | 88.0 | |
| CT-SF-ZF | 18.9 | 101.7 | |
| CV-NF-ZF | 20.0 | 127.9 | |
| CR-NF-ZF | 20.0 | 124.8 | |
| OF-C-OG | 80.0 | 117.8 | |
| CT-C-OF | 70.0 | 120.8 | |
| CT-C-OG | 70.0 | 121.5 | |
| H1-CT-SF | 50.0 | 109.5 | |
| CT-CT-SF | 50.0 | 114.7 | |
| NF-CV-H4 | 35.0 | 125.2 | [Sousa, 2007] |
| H5-CR-NF | 35.0 | 121.0 | |
| CR-NF-CV | 70.0 | 107.3 | |
| NA-CR-NF | 70.0 | 109.5 | |
| CC-CV-NF | 70.0 | 109.5 | |
| CR-NF-CV | 70.0 | 107.3 | |
| NA-CR-NF | 70.0 | 109.5 | |
| CC-CV-NF | 70.0 | 109.5 | |
| 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 |
| ZF | 1.7000 | 0.0125 | [Babu, 2006] |
| OF | 1.6612 | 0.2100 | |
| OG | 1.6612 | 0.2100 | |
| SF | 2.0000 | 0.2500 | |
| NF | 1.8240 | 0.1700 |
Validation of Parameters from MD Simulations
Bond Parameters
| BOND | l0 crystal | ‹l›MD ± σ(l) (Resting State) | ‹θ›MD ± σ(θ) (Binary Complex) |
| ZF-OF | 2.06 ± 0.06 | 2.09 ± 0.06 | |
| ZF-OG | 2.15 ± 0.07 | 2.13 ± 0.07 | |
| ZF-SF | 2.23 ± 0.05 | 2.24 ± 0.05 | |
| ZF-NF | 2.02 ± 0.06 | 2.03 ± 0.06 |
Angle Parameters
| ANGLE | θ0 crystal | ‹θ›MD ± σ(θ) (Resting State) | ‹θ›MD ± σ(θ) (Binary Complex) |
| NF-ZF-SF | 119 ± 5 | 114 ± 6 | |
| OF-ZF-NF | 101 ± 6 | 102 ± 7 | |
| OF-ZF-OG | 64 ± 1 | 63 ± 1 | |
| OF-ZF-SF | 124 ± 6 | 124 ± 6 | |
| OG-ZF-NF | 81 ± 4 | 80 ± 5 | |
| SF-ZF-OG | 84 ± 6 | 83 ± 6 |
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.1375112167.txt.gz · Last modified: 2013/07/29 16:36 by joaocoimbra
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