====== 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 |
| {{ :mm:parameters:zinc:set3.png?200 |}} | {{ :mm:parameters:zinc:image.png?400|}} ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) |
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===== Structure chosen to parameterize =====
| **TEST PROTEIN** ||
| //Protein// | Farnesyltransferase |
| //PDB Code// | 1KZP |
| //Crystallographic Resolution// | 2.10 Å |
| //Organism// | //Rattus norvegicus// |
| [[http://www.ncbi.nlm.nih.gov/pubmed/12374986 | [Long, 2002]]] ||
===== Parameters Determined =====
==== Atom Types ====
| **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** |
| ZN | ZK | 65.409 | {{ :mm:parameters:zinc:set3_molecule.png?120 |}} |
| 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 | [[#references | [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 | [[#references | [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 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [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 =====
| //Parameter File// | {{:mm:parameters:zinc:hdcx_Zn-II.frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_3.zip| .lib}} |
| //FTase PDB File (1KZP.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:leaprc.zip| leaprc}} |
===== References =====
Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://link.springer.com/article/10.1007%2Fs00214-006-0170-9 | 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