mm:parameters:manganese:hhewawa
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mm:parameters:manganese:hhewawa [2013/07/26 13:43] ruineves |
mm:parameters:manganese:hhewawa [2013/10/03 18:58] (current) ruineves |
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| ====== Manganese(II) - HHEWaWa ====== | ====== Manganese(II) - HHEWaWa ====== | ||
| + | ### | ||
| + | Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same. | ||
| + | Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions. | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:manganese:non-parameterized_hheww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 5 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 5 | | + | |
| - | | {{ :mm:parameters:manganese:non-parameterized_hheww_.png?200 |}} | IMAGE2 ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | + | |
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| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **ANGLE** | **K<sub>?</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **? / deg** | **REFERENCE** | | + | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | |
| | NI-M1-NJ | 35.670 | 106.2009 | [[#references | [Neves, 2013]]] | | | NI-M1-NJ | 35.670 | 106.2009 | [[#references | [Neves, 2013]]] | | ||
| | NI-M1-E1 | 66.76 | 90.0029 | ::: | | | NI-M1-E1 | 66.76 | 90.0029 | ::: | | ||
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| ==== Van der Waals Parameters ==== | ==== Van der Waals Parameters ==== | ||
| - | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **?<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** | |
| | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | ||
| | NI | 1.824 | 0.17 | | | NI | 1.824 | 0.17 | | ||
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| | W1 | 1.7683 | 0.152 | | | W1 | 1.7683 | 0.152 | | ||
| | W2 | 1.7683 | 0.152 | | | W2 | 1.7683 | 0.152 | | ||
| - | | HM | 0.6000 | 0.0157 | [[LINK | [Cornel, 1995]]] | | + | | HM | 0.6000 | 0.0157 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
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| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± ?(l)** | **‹l›<sub>MD</sub> ± 2?(l)** | | + | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | |
| | M1-NI | 2.21 | 2.19 | 2.15 ± 0.06 | [2.086; 2.205] | | | M1-NI | 2.21 | 2.19 | 2.15 ± 0.06 | [2.086; 2.205] | | ||
| | M1-NJ | 2.03 | 2.18 | 2.15 ± 0.06 | [2.086; 2.212] | | | M1-NJ | 2.03 | 2.18 | 2.15 ± 0.06 | [2.086; 2.212] | | ||
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| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **ANGLE** | **?<sub>0 crystal</sub>** | **?<sub>0 QM</sub>** | **‹?›<sub>MD</sub> ± ?(?)** | **‹?›<sub>MD</sub> ± 2?(?)** | | + | | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | |
| | NI-M1-NJ | 95.6 | 106.2 | 110 ± 4 | [102.1; 117.0] | | | NI-M1-NJ | 95.6 | 106.2 | 110 ± 4 | [102.1; 117.0] | | ||
| | NI-M1-E1 | 86.7 | 90.0 | 94 ± 3 | [86.9; 100.5] | | | NI-M1-E1 | 86.7 | 90.0 | 94 ± 3 | [86.9; 100.5] | | ||
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| | //Parameter File// | {{:mm:parameters:manganese:hheww-frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:manganese:hheww-frcmod.zip| .frcmod}} | | ||
| | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hheww_mn-ii.zip| .off}} | | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hheww_mn-ii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (1F1U.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:homoprotocatechuate-2,3-dioxygenase.zip| .pdb, leaprc}} | | + | | //Homoprotocatechuate-2,3-dioxygenase’s PDB File (1F1U.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:homoprotocatechuate-2,3-dioxygenase.zip| .pdb, leaprc}} | |
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| ===== References ===== | ===== References ===== | ||
| + | ### | ||
| Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | ||
| + | ### | ||
mm/parameters/manganese/hhewawa.1374842603.txt.gz · Last modified: 2013/07/26 13:43 by ruineves
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