PortoBioComp

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== Zinc (II) - HDCC ======

The metal center of Farnesyltransferase for the ternary complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 2 cysteine residues (1 from the peptide inhibitor) and to 1 aspartate (monodentate). 

|  **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//  |  1JCR  |
|  //Crystallographic Resolution//  |  2.00 Å  |
|  //Organism//  |  //Rattus norvegicus//  |
|  [[http://www.ncbi.nlm.nih.gov/pubmed/11687658 | [Long, 2001]]]  ||


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

==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  ZN  |  ZJ  |  65.409  |  {{ :mm:parameters:zinc:image.png?120 |}}  |
|  NE2  |  NJ  |  14.0067  | ::: |
|  OD2  |  OJ  |  15.9994  | ::: |
|  OD1  |  SJ  |  32.065  | ::: |
|  SG  |  SR  |  32.065  | ::: |

==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  ZJ-OJ  |  88.3  |  1.999  |  [[#references | [Sousa, 2007]]]  |
|  ZJ-SJ  |  81.2  |  2.352  | ::: |
|  ZJ-NJ  |  62.6  |  2.129  | ::: |
|  ZJ-SR  |  69.3  |  2.373  | ::: |
|  C-OJ  |  656.0  |  1.311  | ::: |
|  CT-SJ  |  227.0  |  1.900  | ::: |
|  NJ-CV  |  427.0  |  1.401  | ::: |
|  CR-NJ  |  477.0  |  1.334  | ::: |
|  CT-SR  |  227.0  |  1.896  | ::: |

==== Angles Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  OJ-ZJ-NJ  |  27.8  |  100.2  |  [[#references | [Sousa, 2007]]]  |  
|  OJ-ZJ-SJ  |  23.0  |  114.0  | ::: |
|  OJ-ZJ-SR  |  24.1  |  115.1  | ::: |
|  SJ-ZJ-NJ  |  20.7  |  110.1  | ::: |
|  SJ-ZJ-SR  |  27.3  |  116.0  | ::: |
|  NJ-ZJ-SR  |  39.1  |  98.8  | ::: |
|  C-OJ-ZJ  |  10.0  |  134.0  | ::: |
|  CT-SJ-ZJ  |  18.9  |  101.9  | ::: |
|  CR-NJ-ZJ  |  20.0  |  130.0  | ::: |  
|  CV-NJ-ZJ  |  20.0  |  122.2  | ::: |
|  CT-SR-ZJ  |  18.9  |  101.6  | ::: |
|  O2-C-OJ  |  80.0  |  126.2  | ::: |
|  CT-C-OJ  |  70.0  |  114.2  |  |
|  H1-CT-SJ  |  50.0  |  109.5  | [[#references | [Sousa, 2007]]] |
|  CT-CT-SJ  |  50.0  |  114.7  | ::: |
|  NJ-CV-H4  |  35.0  |  119.2  | ::: |
|  H5-CR-NJ  |  35.0  |  124.0  | ::: |
|  CR-NJ-CV  |  70.0  |  107.5  | ::: |
|  NA-CR-NJ  |  70.0  |  109.7  | ::: |
|  CC-CV-NJ  |  70.0  |  109.3  | ::: |
|  H1-CT-SR  |  50.0  |  109.5  | [[#references | [Sousa, 2007]]] |
|  CT-CT-SR  |  50.0  |  114.7  | ::: |
|  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**  |
|  ZJ  |  1.7000  |  0.0125  |  [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]]  |
|  OJ  |  1.6612  |  0.2100  |    |
|  SJ  |  2.0000  |  0.2500  | ::: |
|  SR  |  2.0000  |  0.2500  | ::: |
|  NJ  |  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>Ternary Complex</sup>**  |
|  ZJ-OJ  |    |  1.95 ± 0.06  | 
|  ZJ-SR  |    |  2.44 ± 0.07  |
|  ZJ-SJ  |    |  2.36 ± 0.06  |
|  ZJ-NJ  |    |  2.19 ± 0.07  |

==== Angle Parameters ====

|  **ANGLE**  |  **θ<sub>0 crystal</sub>**  |  **‹θ›<sub>MD</sub> ± σ(θ) <sup>Ternary Complex</sup>**  |
|  NJ-ZJ-SR  |    |  99 ± 4  |
|  OJ-ZJ-NJ  |    |  110 ± 5  |
|  OJ-ZJ-SJ  |    |  113 ± 5  |
|  OJ-ZJ-SR  |    |  102 ± 7  | 
|  SJ-ZJ-NJ  |    |  118 ± 5  |
|  SJ-ZJ-SR  |    |  112 ± 5  | 

===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:zinc:hdc-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:zinc:hdc_mn-ii.zip| .lib}}  |
|  //FTase PDB File (1JCR.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
PortoBioComp

User Tools

Site Tools

Page Tools
