mm:parameters:manganese:ed_py2_wawa
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mm:parameters:manganese:ed_py2_wawa [2013/07/26 08:13] ruineves created |
mm:parameters:manganese:ed_py2_wawa [2013/10/03 18:55] (current) ruineves |
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| ====== Manganese(II) - ED[PY2]WaWa ====== | ====== Manganese(II) - ED[PY2]WaWa ====== | ||
| + | ### | ||
| + | In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate. | ||
| + | Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand. | ||
| + | A water molecule is referred as participating in the octahedral coordination of manganese(II). | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:manganese:non-parameterized_edpy2ww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | + | |
| - | | {{ :mm:parameters:manganese:non-parameterized_edpy2ww_.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** | |
| | D1-M1-E1 | 38.27 | 96.6209 | [[#references | [Neves, 2013]]] | | | D1-M1-E1 | 38.27 | 96.6209 | [[#references | [Neves, 2013]]] | | ||
| | D1-M1-R1 | 23.41 | 104.8054 | ::: | | | D1-M1-R1 | 23.41 | 104.8054 | ::: | | ||
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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]]] | | ||
| | D1 | 1.6612 | 0.21 | | | D1 | 1.6612 | 0.21 | | ||
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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-D1 | 1.97 | 2.09 | 2.16 ± 0.06 | [2.095; 2.225] | | | M1-D1 | 1.97 | 2.09 | 2.16 ± 0.06 | [2.095; 2.225] | | ||
| | M1-E1 | 1.96 | 2.14 | 2.22 ± 0.06 | [2.153; 2.281] | | | M1-E1 | 1.96 | 2.14 | 2.22 ± 0.06 | [2.153; 2.281] | | ||
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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 | 97.0 | 96.6 | 99 ± 5 | [89.0; 108.1] | | | D1-M1-E1 | 97.0 | 96.6 | 99 ± 5 | [89.0; 108.1] | | ||
| | D1-M1-R1 | 90.8 | 104.8 | 103 ± 5 | [93.1; 112.4] | | | D1-M1-R1 | 90.8 | 104.8 | 103 ± 5 | [93.1; 112.4] | | ||
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| ===== Downloads ===== | ===== Downloads ===== | ||
| - | + | | //Parameter File// | {{:mm:parameters:manganese:ed_py2_ww-frcmod.zip| .frcmod}} | | |
| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:ed[py2]ww_mn-ii.zip| .off}} | |
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | + | | //Pyruvate Kinase’s PDB File (2G50.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:pyruvate_kinase.zip| .pdb, leaprc}} | |
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .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/ed_py2_wawa.1374822824.txt.gz · Last modified: 2013/07/26 08:13 by ruineves
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