mm:parameters:manganese:hhe_d2
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mm:parameters:manganese:hhe_d2 [2013/07/26 13:42] ruineves |
mm:parameters:manganese:hhe_d2 [2013/10/03 18:57] (current) ruineves |
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| ====== Manganese(II) - HHE[D2] ====== | ====== Manganese(II) - HHE[D2] ====== | ||
| + | ### | ||
| + | During the crystallographic refinements of Pneumococcal Surface Antigen Adhesin A the metal ion was modeled as zinc, with attempts to model manganese(II) failed. | ||
| + | The metal atom is expected to be tetrahedral bonded to two histidines, a glutamate and an aspartate, with angles ranging from 93<sup>o</sup> to 131<sup>o</sup>. | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:manganese:non-parameterized_hhed2_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | + | |
| - | | {{ :mm:parameters:manganese:non-parameterized_hhed2_.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 | 34.37 | 107.8506 | [[#references | [Neves, 2013]]] | | | NI-M1-NJ | 34.37 | 107.8506 | [[#references | [Neves, 2013]]] | | ||
| | NI-M1-D1 | 18.529 | 105.7841 | ::: | | | NI-M1-D1 | 18.529 | 105.7841 | ::: | | ||
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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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| ==== 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 | 2.00 | 2.20 | 2.12 ± 0.07 | [2.059; 2.190] | | | M1-NI | 2.00 | 2.20 | 2.12 ± 0.07 | [2.059; 2.190] | | ||
| | M1-NJ | 2.01 | 2.19 | 2.17 ± 0.06 | [2.105; 2.229] | | | M1-NJ | 2.01 | 2.19 | 2.17 ± 0.06 | [2.105; 2.229] | | ||
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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 | 106.9 | 107.9 | 105 ± 5 | [95.1; 114.6] | | | NI-M1-NJ | 106.9 | 107.9 | 105 ± 5 | [95.1; 114.6] | | ||
| | NI-M1-D1 | 109.9 | 105.8 | 102 ± 6 | [90.7; 113.6] | | | NI-M1-D1 | 109.9 | 105.8 | 102 ± 6 | [90.7; 113.6] | | ||
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| | //Parameter File// | {{:mm:parameters:manganese:hhe_d2-frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:manganese:hhe_d2-frcmod.zip| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhe[d2]_mn-iii.zip| .off}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhe[d2]_mn-ii.zip| .off}} | |
| - | | //Integrase’s PDB File (1PSZ.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:pneumococcal_surface_antigen_adhesin_a.zip| .pdb, leaprc}} | | + | | //Pneumococcal Surface Antigen Adhesin A’s PDB File (1PSZ.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:pneumococcal_surface_antigen_adhesin_a.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/hhe_d2.1374842525.txt.gz · Last modified: 2013/07/26 13:42 by ruineves
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