mm:parameters:zinc:hdc_prod
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mm:parameters:zinc:hdc_prod [2013/07/29 16:41] joaocoimbra created |
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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]]] || | ||
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| - | |||
| - | ===== Parameters Determined ===== | ||
| - | |||
| - | ==== Atom Types ==== | ||
| - | |||
| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | ZN | ZK | 65.409 | {{ :mm:parameters:zinc:image.png?120 |}} | | ||
| - | | NE2 | OK | 14.0067 | ::: | | ||
| - | | OD2 | SK | 15.9994 | ::: | | ||
| - | | OD1 | NK | 32.065 | ::: | | ||
| - | | SG | SL | 32.065 | ::: | | ||
| - | |||
| - | ==== Bond Parameters ==== | ||
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| - | | **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 | ::: | | ||
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| - | |||
| - | ==== 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 | ||
mm/parameters/zinc/hdc_prod.1375112471.txt.gz · Last modified: 2013/07/29 16:41 by joaocoimbra
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