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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  |
|  {{ :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.)) |


----

===== 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**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **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**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **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**  |  **R<sub>i</sub> / Å**  |  **ε<sub>i</sub> / kcal mol<sup>-1</sup>**  |  **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**  |  **l<sub>0 crystal</sub>**  |  **‹l›<sub>MD</sub> ± σ(l) <sup>Product Complex</sup>**  |
|  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**  |  **θ<sub>0 crystal</sub>**  |  **‹θ›<sub>MD</sub> ± σ(θ) <sup>Product Complex</sup>**  |
|  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
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