mm:parameters:zinc:hdc_czl
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mm:parameters:zinc:hdc_czl [2013/08/05 15:12] joaocoimbra [Angles Parameters] |
mm:parameters:zinc:hdc_czl [2013/10/03 18:59] (current) joaocoimbra |
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| ====== Zinc (II) - HDC[CZL] ====== | ====== Zinc (II) - HDC[CZL] ====== | ||
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| 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 (CZL). | 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 (CZL). | ||
| + | ### | ||
| - | | **Coordination Sphere** | **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :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.)) | | + | | {{ :mm:parameters:zinc:set3.png?120 |}} | \\ **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 | |
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| | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | | **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]]] | | | ZK | 1.7000 | 0.0125 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | | ||
| - | | OK | 1.6612 | 0.2100 | | | + | | OK | 1.6612 | 0.2100 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
| | SK | 2.0000 | 0.2500 | ::: | | | SK | 2.0000 | 0.2500 | ::: | | ||
| | SL | 2.0000 | 0.2500 | ::: | | | SL | 2.0000 | 0.2500 | ::: | | ||
| | NK | 1.8240 | 0.1700 | ::: | | | NK | 1.8240 | 0.1700 | ::: | | ||
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| ===== Validation of Parameters from MD Simulations ===== | ===== Validation of Parameters from MD Simulations ===== | ||
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| | //Parameter File// | {{:mm:parameters:zinc:hdcx_Zn-II.frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:zinc:hdcx_Zn-II.frcmod.zip| .frcmod}} | | ||
| | //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_3.zip| .lib}} | | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_3.zip| .lib}} | | ||
| + | | //Additional Charges// | {{:mm:parameters:zinc:far_prk.zip| .lib}} | | ||
| | //FTase PDB File (1KZP.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:leaprc.zip| leaprc}} | | | //FTase PDB File (1KZP.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:leaprc.zip| leaprc}} | | ||
| ===== References ===== | ===== 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 | 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_czl.1375711949.txt.gz · Last modified: 2013/08/05 15:12 by joaocoimbra
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