mm:parameters:manganese:hhdh_ho_o
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mm:parameters:manganese:hhdh_ho_o [2013/07/26 08:14] ruineves created |
mm:parameters:manganese:hhdh_ho_o [2013/10/03 18:56] (current) ruineves |
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| ====== Manganese(III) - HHDH[HO]O ====== | ====== Manganese(III) - HHDH[HO]O ====== | ||
| - | + | ### | |
| - | + | Electronic spectroscopy studies on the resting and enzyme-substrates states of Manganese Superoxide Dismutase support the hypothesis of a side-on peroxo complex with the superoxide anion. The superoxide anion coordinates to the manganese ion between two histidines. The spin multiplicity of the coordination sphere has been reported as a quartet, due to an antiferromagnetic coupling between the superoxide and manganese species. | |
| - | + | ### | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 4 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :mm:parameters:manganese:non-parameterized_hhdhhoo_.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.)) | | + | | {{ :mm:parameters:manganese:non-parameterized_hhdhhoo_.png?120 |}} | \\ **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 4 | |
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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 | 93.41 | 91.0663 | [[#references | [Neves, 2013]]] | | | NI-M1-NJ | 93.41 | 91.0663 | [[#references | [Neves, 2013]]] | | ||
| | NI-M1-NK | 96.11 | 86.5034 | ::: | | | NI-M1-NK | 96.11 | 86.5034 | ::: | | ||
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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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| | O | 1.6612 | 0.2100 | | | O | 1.6612 | 0.2100 | | ||
| | W1 | 1.7210 | 0.2104 | | | W1 | 1.7210 | 0.2104 | | ||
| - | | 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 | 1.80 | 2.06 | 2.09 ± 0.05 | [2.038; 2.142] | | | M1-D1 | 1.80 | 2.06 | 2.09 ± 0.05 | [2.038; 2.142] | | ||
| | M1-NI | 2.15 | 2.19 | 2.20 ± 0.06 | [2.141; 2.254] | | | M1-NI | 2.15 | 2.19 | 2.20 ± 0.06 | [2.141; 2.254] | | ||
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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 | 92.4 | 91.1 | 92 ± 2 | [86.9; 96.6] | | | NI-M1-NJ | 92.4 | 91.1 | 92 ± 2 | [86.9; 96.6] | | ||
| | NI-M1-NK | 90.3 | 86.5 | 89 ± 2 | [84.3; 93.7] | | | NI-M1-NK | 90.3 | 86.5 | 89 ± 2 | [84.3; 93.7] | | ||
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| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | + | | //Parameter File// | {{:mm:parameters:manganese:hhdh_ho_o-frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[ho]o_mn-iii.zip| .off}} | |
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} | | + | | //Manganese Superoxide Dismutase’s PDB File (1MNG.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase-oh-oo.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/hhdh_ho_o.1374822893.txt.gz · Last modified: 2013/07/26 08:14 by ruineves
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