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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  |
|  {{ :mm:parameters:zinc:image.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//  |  1FT1  |
|  //Crystallographic Resolution//  |  2.25 Å  |
|  //Organism//  |  //Rattus norvegicus//  |
|  [[http://www.ncbi.nlm.nih.gov/pubmed/9065406 | [Park, 1997]]]  ||


===== Parameters Determined =====

==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  ZN  |  ZF  |  65.409  |  {{ :mm:parameters:zinc:image.png?120 |}}  |
|  NE2  |  NF  |  14.0067  | ::: |
|  OD2  |  OF  |  15.9994  | ::: |
|  OD1  |  OG  |  15.9994  | ::: |
|  SG  |  SF  |  32.065  | ::: |

==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  ZF-NF  |  88.3  |  2.043  |  [[#references | [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**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  OF-ZF-OG  |  318.9  |  63.5  |  [[#references | [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  | [[#references | [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**  |  **R<sub>i</sub> / Å**  |  **ε<sub>i</sub> / kcal mol<sup>-1</sup>**  |  **REFERENCE**  |
|  ZF  |  1.7000  |  0.0125  |  [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [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**  |  **l<sub>0 crystal</sub>**  |  **‹l›<sub>MD</sub> ± σ(l) <sup>(Resting State)</sup>**  |  **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Binary Complex)</sup>**  |
|  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**  |  **θ<sub>0 crystal</sub>**  |  **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Resting State)</sup>**  |  **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Binary Complex)</sup>**  |
|  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 =====
|  //Parameter File//  |  {{:mm:parameters:zinc:hdc-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:zinc:hdc_mn-ii.zip| .lib}}  |
|  //Integrase’s PDB File (1A5V.pdb)\\ LEAPRC file//  |  {{:mm:parameters:zinc:integrase.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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