mm:parameters:zinc:hdc
Differences
This shows you the differences between two versions of the page.
|
mm:parameters:zinc:hdc [2013/07/29 16:36] joaocoimbra [Downloads] |
mm:parameters:zinc:hdc [2013/08/06 15:33] (current) ruineves |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ====== Zinc (II) - HDC ====== | ====== Zinc (II) - HDC ====== | ||
| - | The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided, together with the parameter files for the FPP molecule. | + | The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided. |
| | **Coordination Sphere** | **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 | | | **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.)) | | + | | {{ :mm:parameters:zinc:set1.png?120 |}} | JMOL | |
| Line 24: | Line 24: | ||
| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | ZN | ZF | 65.409 | {{ :mm:parameters:zinc:image.png?120 |}} | | + | | ZN | ZF | 65.409 | {{ :mm:parameters:zinc:set1_molecule.png?120 |}} | |
| | NE2 | NF | 14.0067 | ::: | | | NE2 | NF | 14.0067 | ::: | | ||
| | OD2 | OF | 15.9994 | ::: | | | OD2 | OF | 15.9994 | ::: | | ||
| Line 60: | Line 60: | ||
| | CT-C-OF | 70.0 | 120.8 | ::: | | | CT-C-OF | 70.0 | 120.8 | ::: | | ||
| | CT-C-OG | 70.0 | 121.5 | ::: | | | CT-C-OG | 70.0 | 121.5 | ::: | | ||
| - | | H1-CT-SF | 50.0 | 109.5 | | | + | | NF-CV-H4 | 35.0 | 125.2 | ::: | |
| - | | CT-CT-SF | 50.0 | 114.7 | ::: | | + | |
| - | | NF-CV-H4 | 35.0 | 125.2 | [[#references | [Sousa, 2007]]] | | + | |
| | H5-CR-NF | 35.0 | 121.0 | ::: | | | H5-CR-NF | 35.0 | 121.0 | ::: | | ||
| | CR-NF-CV | 70.0 | 107.3 | ::: | | | CR-NF-CV | 70.0 | 107.3 | ::: | | ||
| Line 72: | Line 70: | ||
| | CT-CM-CT | 70.0 | 113.8 | ::: | | | CT-CM-CT | 70.0 | 113.8 | ::: | | ||
| | CM-CM-CM | 70.0 | 122.8 | ::: | | | CM-CM-CM | 70.0 | 122.8 | ::: | | ||
| - | + | | H1-CT-SF | 50.0 | 109.5 | | | |
| + | | CT-CT-SF | 50.0 | 114.7 | ::: | | ||
| ==== Van der Waals Parameters ==== | ==== Van der Waals Parameters ==== | ||
| | **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** | | ||
| - | | ZF | 1.7000 | 0.0125 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | + | | ZF | 1.7000 | 0.0125 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | |
| | OF | 1.6612 | 0.2100 | | | | OF | 1.6612 | 0.2100 | | | ||
| | OG | 1.6612 | 0.2100 | ::: | | | OG | 1.6612 | 0.2100 | ::: | | ||
| | SF | 2.0000 | 0.2500 | ::: | | | SF | 2.0000 | 0.2500 | ::: | | ||
| | NF | 1.8240 | 0.1700 | ::: | | | NF | 1.8240 | 0.1700 | ::: | | ||
| - | |||
| ===== Validation of Parameters from MD Simulations ===== | ===== Validation of Parameters from MD Simulations ===== | ||
| Line 88: | Line 85: | ||
| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| - | | **BOND** | **l<sub>0 crystal</sub>** | **‹l›<sub>MD</sub> ± σ(l) <sup>(Resting State)</sup>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Binary Complex)</sup>** | | + | | **BOND** | **l<sub>0 crystal</sub>** | **‹l›<sub>MD</sub> ± σ(l) <sup>(Resting State)</sup>** | **‹l›<sub>MD</sub> ± σ(l) <sup>(Binary Complex)</sup>** | |
| - | | ZF-OF | | 2.06 ± 0.06 | 2.09 ± 0.06 | | + | | ZF-OF | 2.00 | 2.06 ± 0.06 | 2.09 ± 0.06 | |
| - | | ZF-OG | | 2.15 ± 0.07 | 2.13 ± 0.07 | | + | | ZF-OG | 2.56 | 2.15 ± 0.07 | 2.13 ± 0.07 | |
| - | | ZF-SF | | 2.23 ± 0.05 | 2.24 ± 0.05 | | + | | ZF-SF | 2.22 | 2.23 ± 0.05 | 2.24 ± 0.05 | |
| - | | ZF-NF | | 2.02 ± 0.06 | 2.03 ± 0.06 | | + | | ZF-NF | 2.48 | 2.02 ± 0.06 | 2.03 ± 0.06 | |
| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| | **ANGLE** | **θ<sub>0 crystal</sub>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Resting State)</sup>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Binary Complex)</sup>** | | | **ANGLE** | **θ<sub>0 crystal</sub>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Resting State)</sup>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>(Binary Complex)</sup>** | | ||
| - | | NF-ZF-SF | | 119 ± 5 | 114 ± 6 | | + | | NF-ZF-SF | 118 | 119 ± 5 | 114 ± 6 | |
| - | | OF-ZF-NF | | 101 ± 6 | 102 ± 7 | | + | | OF-ZF-NF | 120 | 101 ± 6 | 102 ± 7 | |
| - | | OF-ZF-OG | | 64 ± 1 | 63 ± 1 | | + | | OF-ZF-OG | 56 | 64 ± 1 | 63 ± 1 | |
| - | | OF-ZF-SF | | 124 ± 6 | 124 ± 6 | | + | | OF-ZF-SF | 104 | 124 ± 6 | 124 ± 6 | |
| - | | OG-ZF-NF | | 81 ± 4 | 80 ± 5 | | + | | OG-ZF-NF | 90 | 81 ± 4 | 80 ± 5 | |
| - | | SF-ZF-OG | | 84 ± 6 | 83 ± 6 | | + | | SF-ZF-OG | 80 | 84 ± 6 | 83 ± 6 | |
| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:zinc:hdc-frcmod.zip| .frcmod}} | | + | | //Parameter File// | {{:mm:parameters:zinc:hdc_zn-II.frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:hdc_mn-ii.zip| .lib}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_1.zip| .lib}} | |
| - | | //FTase PDB File (1FT1.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:integrase.zip| leaprc}} | | + | | //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.1375112167.txt.gz · Last modified: 2013/07/29 16:36 by joaocoimbra
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
