mm:parameters:manganese:dedwawawa
Differences
This shows you the differences between two versions of the page.
|
mm:parameters:manganese:dedwawawa [2013/07/26 13:29] ruineves |
mm:parameters:manganese:dedwawawa [2013/10/03 18:51] (current) ruineves |
||
|---|---|---|---|
| Line 2: | Line 2: | ||
| ====== Manganese(II) - DEDWaWaWa ====== | ====== Manganese(II) - DEDWaWaWa ====== | ||
| + | ### | ||
| + | Muconate Cycloisomerase shows preference on manganese(II) over the magnesium ion to perform. | ||
| + | Its coordination sphere is similar to the one found in chloromuconate cycloisomerase, with two aspartates and a glutamate. | ||
| + | ### | ||
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :mm:parameters:manganese:non-parameterized_dedwww_.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.)) | | + | | {{ :mm:parameters:manganese:non-parameterized_dedwww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | |
| Line 60: | Line 64: | ||
| ==== 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-D2 | 34.80 | 166.2571 | [[#references | [Neves, 2013]]] | | | D1-M1-D2 | 34.80 | 166.2571 | [[#references | [Neves, 2013]]] | | ||
| | D1-M1-E1 | 36.67 | 98.6591 | ::: | | | D1-M1-E1 | 36.67 | 98.6591 | ::: | | ||
| Line 95: | Line 99: | ||
| ==== 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 | | ||
| Line 103: | Line 107: | ||
| | 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]]] | |
| Line 112: | Line 116: | ||
| ==== 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 | 2.10 | 2.11 | 2.22 ± 0.06 | [2.162; 2.279] | | | M1-D1 | 2.10 | 2.11 | 2.22 ± 0.06 | [2.162; 2.279] | | ||
| | M1-D2 | 2.16 | 2.14 | 2.26 ± 0.06 | [2.194; 2.324] | | | M1-D2 | 2.16 | 2.14 | 2.26 ± 0.06 | [2.194; 2.324] | | ||
| Line 123: | Line 127: | ||
| ==== 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-D2 | 175.3 | 166.3 | 168 ± 4 | [160.5; 174.6] | | | D1-M1-D2 | 175.3 | 166.3 | 168 ± 4 | [160.5; 174.6] | | ||
| | D1-M1-E1 | 89.4 | 98.7 | 98 ± 4 | [90.0; 106.0] | | | D1-M1-E1 | 89.4 | 98.7 | 98 ± 4 | [90.0; 106.0] | | ||
| Line 145: | Line 149: | ||
| | //Parameter File// | {{:mm:parameters:manganese:dedwww-frcmod.zip| .frcmod}} | | | //Parameter File// | {{:mm:parameters:manganese:dedwww-frcmod.zip| .frcmod}} | | ||
| | //Coordination Sphere Charges// | {{:mm:parameters:manganese:dedwww_mn-ii.zip| .off}} | | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:dedwww_mn-ii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (3CT2.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:muconate_cycloisomerase.zip| .pdb, leaprc}} | | + | | //Muconate Cycloisomerase’s PDB File (3CT2.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:muconate_cycloisomerase.zip| .pdb, leaprc}} | |
| Line 151: | Line 155: | ||
| ===== 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/dedwawawa.1374841749.txt.gz · Last modified: 2013/07/26 13:29 by ruineves
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
