====== Zinc (II) - HDCC ======
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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).
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:zinc:set2.png?120 |}} | \\ **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 |
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===== 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:set2_molecule.png?120 |}} |
| NE2 | NJ | 14.0067 | ::: |
| OD2 | OJ | 15.9994 | ::: |
| SG | SJ | 32.065 | ::: |
| SG | SR | 32.065 | ::: |
==== Bond Parameters ====
| **BOND** | **Kl** / **kcal mol-1 Å-2** | **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** | **Kθ** / **kcal mol-1 rad-2** | **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 | ::: |
| 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 | ::: |
| CT-CM-CT | 70.0 | 113.8 | ::: |
| CM-CM-CM | 70.0 | 122.8 | ::: |
| H1-CT-SJ | 50.0 | 109.5 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] |
| CT-CT-SJ | 50.0 | 114.7 | ::: |
| H1-CT-SR | 50.0 | 109.5 | ::: |
| CT-CT-SR | 50.0 | 114.7 | ::: |
==== Van der Waals Parameters ====
| **ATOM TYPE** | **Ri / Å** | **εi / kcal mol-1** | **REFERENCE** |
| ZJ | 1.7000 | 0.0125 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] |
| OJ | 1.6612 | 0.2100 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] |
| SJ | 2.0000 | 0.2500 | ::: |
| SR | 2.0000 | 0.2500 | ::: |
| NJ | 1.8240 | 0.1700 | ::: |
===== Validation of Parameters from MD Simulations =====
==== Bond Parameters ====
| **BOND** | **l0 crystal** | **‹l›MD ± σ(l) Ternary Complex** |
| ZJ-OJ | 2.08 | 1.95 ± 0.06 |
| ZJ-SR | 2.41 | 2.44 ± 0.07 |
| ZJ-SJ | 2.33 | 2.36 ± 0.06 |
| ZJ-NJ | 2.21 | 2.19 ± 0.07 |
==== Angle Parameters ====
| **ANGLE** | **θ0 crystal** | **‹θ›MD ± σ(θ) Ternary Complex** |
| NJ-ZJ-SR | 104 | 99 ± 4 |
| OJ-ZJ-NJ | 119 | 110 ± 5 |
| OJ-ZJ-SJ | 106 | 113 ± 5 |
| OJ-ZJ-SR | 102 | 102 ± 7 |
| SJ-ZJ-NJ | 118 | 118 ± 5 |
| SJ-ZJ-SR | 106 | 112 ± 5 |
===== Downloads =====
| //Parameter File// | {{:mm:parameters:zinc:hdcc_zn-II.frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_3.zip| .lib}} |
| //Additional Charges// | {{:mm:parameters:zinc:fpp.zip| .lib}} |
| //FTase PDB File (1JCR.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:leaprc.zip| leaprc}} |
===== References =====
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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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