mm:parameters:zinc:hdc_prod
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mm:parameters:zinc:hdc_prod [2013/07/30 19:39] joaocoimbra [Bond Parameters] |
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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: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// | 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:image.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 | | 111 ± 6 | | ||
| - | | OK-ZK-SK | | 118 ± 6 | | ||
| - | | OK-ZK-SL | | 87 ± 5 | | ||
| - | | SK-ZK-NK | | 125 ± 5 | | ||
| - | | SK-ZK-SL | | 101 ± 6 | | ||
| - | | NK-ZK-SL | | 103 ± 5 | | ||
| - | |||
| - | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:zinc:hdcx_Zn-II.frcmod.zip| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:ASK.lib.zip| Asp.lib}} {{:mm:parameters:zinc:HIK.lib.zip| His.lib}} {{:mm:parameters:zinc:CZK.lib.zip| Cys.lib}} {{:mm:parameters:zinc:CZL.lib.zip| Product.lib}} {{:mm:parameters:zinc:ZNK.lib.zip| Zn.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 | ||
mm/parameters/zinc/hdc_prod.1375209576.txt.gz · Last modified: 2013/07/30 19:39 by joaocoimbra
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