mm:parameters:manganese:hhdh_ho
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mm:parameters:manganese:hhdh_ho [2013/07/26 13:37] ruineves |
mm:parameters:manganese:hhdh_ho [2013/10/03 18:55] (current) ruineves |
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| ====== Manganese(III) - HHDH[HO] ====== | ====== Manganese(III) - HHDH[HO] ====== | ||
| - | + | ### | |
| - | + | The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions. | |
| - | + | ### | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :mm:parameters:manganese:non-parameterized_hhdhho_.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_hhdhho_.png?120 |}} | \\ **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 | |
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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>?</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | |
| | NI-M1-NJ | 88.01 | 91.6707 | [[#references | [Neves, 2013]]] | | | NI-M1-NJ | 88.01 | 91.6707 | [[#references | [Neves, 2013]]] | | ||
| | NI-M1-NK | 86.76 | 88.725 | ::: | | | NI-M1-NK | 86.76 | 88.725 | ::: | | ||
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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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| | D1 | 1.6612 | 0.21 | | | D1 | 1.6612 | 0.21 | | ||
| | W1 | 1.7683 | 0.152 | | | W1 | 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 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] | | | M1-D1 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] | | ||
| | M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] | | | M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] | | ||
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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 | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] | | | NI-M1-NJ | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] | | ||
| | NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] | | | NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] | | ||
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| | NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] | | | NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] | | ||
| | D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] | | | D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] | | ||
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| ===== Downloads ===== | ===== Downloads ===== | ||
| + | |||
| | //Parameter File// | {{:mm:parameters:manganese:hhdh_ho-frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:manganese:hhdh_ho-frcmod.zip| .frcmod}} | | ||
| | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[ho]_mn-iii.zip| .off}} | | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[ho]_mn-iii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (1N0J.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase.zip| .pdb, leaprc}} | | + | | //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase-oh.zip| .pdb, leaprc}} | |
| ===== 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.1374842246.txt.gz · Last modified: 2013/07/26 13:37 by ruineves
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