====== Manganese(II) - DED[CL] ======
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The metal atom of Chloromuconate Cycloisomerase is shown to be bonded to two aspartates, a glutamate and chloride ion.
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:manganese:non-parameterized_dedcl_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 |
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===== Structure chosen to parameterize =====
| **TEST PROTEIN** ||
| //Protein// | Chloromuconate Cycloisomerase |
| //PDB Code// | 2CHR |
| //Crystallographic Resolution// | 3.00 Å |
| //Organism// | Cupriavidus necator |
| [[http://www.ncbi.nlm.nih.gov/pubmed/15299651?dopt=Abstract | [Kleywegt, 1996]]] ||
===== Parameters Determined =====
==== Atom Types ====
| **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** |
| MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_dedcl_.png?120 |}} |
| OD2 | D1 | 15.9994 | ::: |
| OD2 | D2 | 15.9994 | ::: |
| OE2 | E1 | 15.9994 | ::: |
==== Bond Parameters ====
| **BOND** | **Kl** / **kcal mol-1 Å-2** | **l / Å** | **REFERENCE** |
| M1-D1 | 86.71 | 2.0770 | [[#references | [Neves, 2013]]] |
| M1-D2 | 72.61 | 2.0834 | ::: |
| M1-E1 | 75.79 | 2.0710 | ::: |
| M1-R1 | 69.25 | 2.4005 | ::: |
| D1-C | 656.0 | 1.25 |
| D2-C | 656.0 | 1.25 |
| E1-C | 656.0 | 1.25 |
==== Angle Parameters ====
| **ANGLE** | **Kθ** / **kcal mol-1 rad-2** | **θ / deg** | **REFERENCE** |
| D1-M1-D2 | 18.812 | 124.2299 | [[#references | [Neves, 2013]]] |
| D1-M1-E1 | 35.39 | 100.9790 | ::: |
| D1-M1-R1 | 23.76 | 106.7074 | ::: |
| D2-M1-E1 | 38.51 | 102.8186 | ::: |
| D2-M1-R1 | 23.73 | 108.1030 | ::: |
| E1-M1-R1 | 19.27 | 113.6328 | ::: |
| M1-D1-C | 10.075 | 144.1664 | ::: |
| M1-D2-C | 45.967 | 141.6861 | ::: |
| M1-E1-C | 20.462 | 135.2443 | ::: |
| D1-C-CT | 70.0 | 117.0 |
| D1-C-O2 | 80.0 | 126.0 |
| D2-C-CT | 70.0 | 117.0 |
| D2-C-O2 | 80.0 | 126.0 |
| E1-C-CT | 70.0 | 117.0 |
| E1-C-O2 | 80.0 | 126.0 |
==== Van der Waals Parameters ====
| **ATOM TYPE** | **Ri / Å** | **εi / kcal mol-1** | **REFERENCE** |
| M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] |
| D1 | 1.6612 | 0.21 |
| D2 | 1.6612 | 0.21 |
| E1 | 1.6612 | 0.21 |
| R1 | 1.948 | 0.265 |
===== Validation of Parameters from MD Simulations =====
==== Bond Parameters ====
| **BOND** | **l0 crystal** | **l0 opt** | **‹l›MD ± σ(l)** | **‹l›MD ± 2σ(l)** |
| M1-D1 | 3.08 | 2.08 | 2.10 ± 0.06 | [2.042; 2.161] |
| M1-D2 | 2.10 | 2.08 | 2.08 ± 0.07 | [2.016; 2.148] |
| M1-E1 | 2.05 | 2.07 | 2.07 ± 0.06 | [2.011; 2.137] |
| M1-R1 | 2.95 | 2.40 | 2.38 ± 0.07 | [2.316; 2.451] |
==== Angle Parameters ====
| **ANGLE** | **θ0 crystal** | **θ0 QM** | **‹θ›MD ± σ(θ)** | **‹θ›MD ± 2σ(θ)** |
| D1-M1-D2 | 173.5 | 124.2 | 138 ± 5 | [127.1; 148.5] |
| D1-M1-E1 | 80.0 | 101.0 | 107 ± 5 | [96.8; 116.8] |
| D1-M1-R1 | 87.2 | 106.7 | 80 ± 7 | [66.5; 93.4] |
| D2-M1-E1 | 99.4 | 102.8 | 105 ± 5 | [95.9; 114.8] |
| D2-M1-R1 | 87.1 | 108.1 | 79 ± 6 | [65.8; 91.4] |
| E1-M1-R1 | 112.9 | 113.6 | 85 ± 7 | [71.7; 98.4] |
===== Downloads =====
| //Parameter File// | {{:mm:parameters:manganese:ded_cl-frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:manganese:ded[cl]_mn-ii.zip| .off}} |
| //Chloromuconate Cycloisomerase’s PDB File (2CHR.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:chloromuconate_cycloisomerase.zip| .pdb, leaprc}} |
===== References =====
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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
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