Sidebar
mm:parameters:zinc:hdc_fp
Table of Contents
Zinc (II) - HDC[fP]
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 |  |
| OD2 | OK | 15.9994 | |
| SG | SK | 32.065 | |
| NE2 | NK | 14.0067 | |
| SG | SL | 32.065 |
Bond Parameters
| BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
| ZK-OK | 85.3 | 1.977 | [Sousa, 2007] |
| ZK-SK | 108.3 | 2.280 | |
| ZK-NK | 84.8 | 2.055 | |
| ZK-SL | 26.6 | 2.660 | |
| C-OK | 656.0 | 1.331 | |
| CT-SK | 227.0 | 1.901 | |
| NK-CV | 427.0 | 1.405 | |
| CR-NK | 477.0 | 1.338 | |
| CT-SL | 227.0 | 1.930 |
Angles Parameters
| ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
| OK-ZK-NK | 18.8 | 108.2 | [Sousa, 2007] |
| OK-ZK-SK | 15.2 | 127.6 | |
| OK-ZK-SL | 24.6 | 92.3 | |
| SK-ZK-NK | 12.6 | 118.7 | |
| SK-ZK-SL | 16.8 | 101.6 | |
| NK-ZK-SL | 22.1 | 99.1 | |
| C-OK-ZK | 10.0 | 114.5 | |
| CT-SK-ZK | 18.9 | 101.5 | |
| CV-NK-ZK | 20.0 | 124.3 | |
| CR-NK-ZK | 20.0 | 128.4 | |
| CT-SL-ZK | 18.9 | 106.8 | |
| O2-C-OK | 80.0 | 122.0 | |
| CT-C-OK | 70.0 | 115.4 | |
| NK-CV-H4 | 35.0 | 119.8 | |
| H5-CR-NK | 35.0 | 125.8 | |
| CR-NK-CV | 70.0 | 107.1 | |
| NA-CR-NK | 70.0 | 109.9 | |
| CC-CV-NK | 70.0 | 109.2 | |
| CT-CM-CT | 70.0 | 113.8 | |
| CM-CM-CM | 70.0 | 122.8 | |
| CM-CT-SL | 50.0 | 109.1 | |
| CT-SL-CT | 62.0 | 101.6 | |
| H1-CT-SK | 50.0 | 109.5 | |
| CT-CT-SK | 50.0 | 114.7 | |
| H1-CT-SL | 50.0 | 109.5 | |
| CT-CT-SL | 50.0 | 114.7 |
Van der Waals Parameters
| ATOM TYPE | Ri / Å | εi / kcal mol-1 | REFERENCE |
| ZK | 1.7000 | 0.0125 | [Ryde, 1995] |
| OK | 1.6612 | 0.2100 | |
| SK | 2.0000 | 0.2500 | |
| SL | 2.0000 | 0.2500 | |
| NK | 1.8240 | 0.1700 |
Validation of Parameters from MD Simulations
Bond Parameters
| BOND | l0 crystal | ‹l›MD ± σ(l) Product Complex |
| ZK-OK | 2.06 | 1.95 ± 0.06 |
| ZK-SL | 2.66 | 2.60 ± 0.10 |
| ZK-SK | 2.27 | 2.28 ± 0.06 |
| ZK-NK | 2.18 | 2.08 ± 0.06 |
Angle Parameters
| ANGLE | θ0 crystal | ‹θ›MD ± σ(θ) Product Complex |
| OK-ZK-NK | 124 | 111 ± 6 |
| OK-ZK-SK | 108 | 118 ± 6 |
| OK-ZK-SL | 87 | 87 ± 5 |
| SK-ZK-NK | 120 | 125 ± 5 |
| SK-ZK-SL | 114 | 101 ± 6 |
| NK-ZK-SL | 98 | 103 ± 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_fp.txt · Last modified: 2013/08/05 14:53 by joaocoimbra
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
