mm:parameters:manganese:denwawawa
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mm:parameters:manganese:denwawawa [2013/07/26 13:31] ruineves |
mm:parameters:manganese:denwawawa [2013/10/03 18:53] (current) ruineves |
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| ====== Manganese(II) - DENWaWaWa ====== | ====== Manganese(II) - DENWaWaWa ====== | ||
| + | ### | ||
| + | D-Glutarate Dehydratase is analogous to mandelate racemase and enolase. | ||
| + | The manganese coordination sphere has a manganese(II) atom bonded to a glutamate, an aspartate and an asparagine from the same subunit. | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:manganese:non-parameterized_denwww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | + | |
| - | | {{ :mm:parameters:manganese:non-parameterized_denwww_.png?200 |}} | {{ :mm:parameters:manganese:octahedral_highspin_d5.png?400|}} ((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** | |
| | NW-M1-D1 | 50.31 | 168.8916 | [[#references | [Neves, 2013]]] | | | NW-M1-D1 | 50.31 | 168.8916 | [[#references | [Neves, 2013]]] | | ||
| | NW-M1-E1 | 36.14 | 92.7969 | ::: | | | NW-M1-E1 | 36.14 | 92.7969 | ::: | | ||
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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]]] | | ||
| | NW | 1.6612 | 0.21 | | | NW | 1.6612 | 0.21 | | ||
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| | W2 | 1.7683 | 0.152 | | | W2 | 1.7683 | 0.152 | | ||
| | W3 | 1.7683 | 0.152 | | | W3 | 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-D1 | 2.28 | 2.15 | 2.16 ± 0.06 | [2.095; 2.224] | | | M1-D1 | 2.28 | 2.15 | 2.16 ± 0.06 | [2.095; 2.224] | | ||
| | M1-E1 | 2.45 | 2.06 | 2.13 ± 0.06 | [2.066; 2.186] | | | M1-E1 | 2.45 | 2.06 | 2.13 ± 0.06 | [2.066; 2.186] | | ||
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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)** | |
| | D1-M1-E1 | 100.8 | 100.6 | 98 ± 4 | [89.3; 106.1] | | | D1-M1-E1 | 100.8 | 100.6 | 98 ± 4 | [89.3; 106.1] | | ||
| | D1-M1-NW | 154.1 | 168.9 | 165 ± 3 | [158.6; 172.1] | | | D1-M1-NW | 154.1 | 168.9 | 165 ± 3 | [158.6; 172.1] | | ||
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| | //Parameter File// | {{:mm:parameters:manganese:denwww-frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:manganese:denwww-frcmod.zip| .frcmod}} | | ||
| | //Coordination Sphere Charges// | {{:mm:parameters:manganese:denwww_mn-ii.zip| .off}} | | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:denwww_mn-ii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (3NXL.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:d-glutarate_dehydratase.zip| .pdb, leaprc}} | | + | | //D-Glutarate Dehydratase’s PDB File (3NXL.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:d-glutarate_dehydratase.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/denwawawa.1374841880.txt.gz · Last modified: 2013/07/26 13:31 by ruineves
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