mm:parameters:zinc:hdcc
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mm:parameters:zinc:hdcc [2013/07/30 19:17] joaocoimbra [Van der Waals Parameters] |
mm:parameters:zinc:hdcc [2013/10/03 18:57] (current) joaocoimbra |
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| ====== Zinc (II) - HDCC ====== | ====== Zinc (II) - HDCC ====== | ||
| + | ### | ||
| 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). | 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). | ||
| + | ### | ||
| - | | **Coordination Sphere** | **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :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:set2.png?120 |}} | \\ **Oxidation state:** Zn(II) \\ **Spin multiplicity:** 1 | |
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| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | ZN | ZJ | 65.409 | {{ :mm:parameters:zinc:image.png?120 |}} | | + | | ZN | ZJ | 65.409 | {{ :mm:parameters:zinc:set2_molecule.png?120 |}} | |
| | NE2 | NJ | 14.0067 | ::: | | | NE2 | NJ | 14.0067 | ::: | | ||
| | OD2 | OJ | 15.9994 | ::: | | | OD2 | OJ | 15.9994 | ::: | | ||
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| | 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-SJ | 50.0 | 109.5 | | | + | | 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 | ::: | | | CT-CT-SJ | 50.0 | 114.7 | ::: | | ||
| | H1-CT-SR | 50.0 | 109.5 | ::: | | | H1-CT-SR | 50.0 | 109.5 | ::: | | ||
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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** | | ||
| | ZJ | 1.7000 | 0.0125 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | | | ZJ | 1.7000 | 0.0125 | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | | ||
| - | | OJ | 1.6612 | 0.2100 | | | + | | OJ | 1.6612 | 0.2100 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
| | SJ | 2.0000 | 0.2500 | ::: | | | SJ | 2.0000 | 0.2500 | ::: | | ||
| | SR | 2.0000 | 0.2500 | ::: | | | SR | 2.0000 | 0.2500 | ::: | | ||
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| | **BOND** | **l<sub>0 crystal</sub>** | **‹l›<sub>MD</sub> ± σ(l) <sup>Ternary Complex</sup>** | | | **BOND** | **l<sub>0 crystal</sub>** | **‹l›<sub>MD</sub> ± σ(l) <sup>Ternary Complex</sup>** | | ||
| - | | ZJ-OJ | | 1.95 ± 0.06 | | + | | ZJ-OJ | 2.08 | 1.95 ± 0.06 | |
| - | | ZJ-SR | | 2.44 ± 0.07 | | + | | ZJ-SR | 2.41 | 2.44 ± 0.07 | |
| - | | ZJ-SJ | | 2.36 ± 0.06 | | + | | ZJ-SJ | 2.33 | 2.36 ± 0.06 | |
| - | | ZJ-NJ | | 2.19 ± 0.07 | | + | | ZJ-NJ | 2.21 | 2.19 ± 0.07 | |
| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| | **ANGLE** | **θ<sub>0 crystal</sub>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>Ternary Complex</sup>** | | | **ANGLE** | **θ<sub>0 crystal</sub>** | **‹θ›<sub>MD</sub> ± σ(θ) <sup>Ternary Complex</sup>** | | ||
| - | | NJ-ZJ-SR | | 99 ± 4 | | + | | NJ-ZJ-SR | 104 | 99 ± 4 | |
| - | | OJ-ZJ-NJ | | 110 ± 5 | | + | | OJ-ZJ-NJ | 119 | 110 ± 5 | |
| - | | OJ-ZJ-SJ | | 113 ± 5 | | + | | OJ-ZJ-SJ | 106 | 113 ± 5 | |
| - | | OJ-ZJ-SR | | 102 ± 7 | | + | | OJ-ZJ-SR | 102 | 102 ± 7 | |
| - | | SJ-ZJ-NJ | | 118 ± 5 | | + | | SJ-ZJ-NJ | 118 | 118 ± 5 | |
| - | | SJ-ZJ-SR | | 112 ± 5 | | + | | SJ-ZJ-SR | 106 | 112 ± 5 | |
| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:zinc:hdc-frcmod.zip| .frcmod}} | | + | | //Parameter File// | {{:mm:parameters:zinc:hdcc_zn-II.frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:hdc_mn-ii.zip| .lib}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:zinc:lib_files_3.zip| .lib}} | |
| - | | //FTase PDB File (1JCR.pdb)\\ LEAPRC file// | {{:mm:parameters:zinc:integrase.zip| leaprc}} | | + | | //Additional Charges// | {{:mm:parameters:zinc:fpp.zip| .lib}} | |
| + | | //FTase PDB File (1JCR.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/hdcc.1375208267.txt.gz · Last modified: 2013/07/30 19:17 by joaocoimbra
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