====== Manganese(II) - HDEWaWaWa ======
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In Citochrome //c// Oxidase the manganese ion has a nonredox role.
Manganese(II) is bonded to residues from different subunits: a glutamate, an aspartate and histidine ligands and possibly one to three water molecules. The glutamate ligand is also coordinated to a copper atom and the histidine is hydrogen bonded to a heme //a3// propionate.
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:manganese:non-parameterized_hdewww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 |
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===== Structure chosen to parameterize =====
| **TEST PROTEIN** ||
| //Protein// | Citochrome //c// Oxidase |
| //PDB Code// | 3HB3 |
| //Crystallographic Resolution// | 2.25 Å |
| //Organism// | Paracoccus denitrificans |
| [[http://www.sciencedirect.com/science/article/pii/S0005272809001315 | [Koepke, 2009]]] ||
===== Parameters Determined =====
==== Atom Types ====
| **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** |
| MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_hdewww_.png?120 |}} |
| OD1 | D1 | 15.9994 | ::: |
| OE1 | E1 | 15.9994 | ::: |
| NE2 | NI | 14.0067 | ::: |
| OW | W1 | 15.9994 | ::: |
| OW | W2 | 15.9994 | ::: |
| OW | W3 | 15.9994 | ::: |
| HW | HM | 1.00794 | ::: |
==== Bond Parameters ====
| **BOND** | **Kl** / **kcal mol-1 Å-2** | **l / Å** | **REFERENCE** |
| M1-NI | 63.17 | 2.242 | [[#references | [Neves, 2013]]] |
| M1-D1 | 77.67 | 2.141 | ::: |
| M1-E1 | 68.41 | 2.147 | ::: |
| M1-W1 | 31.5 | 2.3664 | ::: |
| M1-W2 | 31.4 | 2.325 | ::: |
| M1-W3 | 64.37 | 2.1601 | ::: |
| NI-CR | 488.0 | 1.335 |
| NI-CV | 410.0 | 1.394 |
| D1-C | 656.0 | 1.25 |
| E1-C | 656.0 | 1.25 |
| W1-HM | 553.0 | 0.9572 |
| W2-HM | 553.0 | 0.9572 |
| W3-HM | 553.0 | 0.9572 |
==== Angle Parameters ====
| **ANGLE** | **Kθ** / **kcal mol-1 rad-2** | **θ / deg** | **REFERENCE** |
| NI-M1-D1 | 55.1 | 90.0153 | [[#references | [Neves, 2013]]] |
| NI-M1-E1 | 41.458 | 159.9206 | ::: |
| NI-M1-W1 | 24.19 | 94.3889 | ::: |
| NI-M1-W2 | 31.3 | 89.0778 | ::: |
| NI-M1-W3 | 34.86 | 98.8181 | ::: |
| D1-M1-E1 | 50.26 | 103.9094 | ::: |
| D1-M1-W1 | 42.6 | 73.0866 | ::: |
| D1-M1-W2 | 12.075 | 162.4957 | ::: |
| D1-M1-W3 | 56.22 | 90.7127 | ::: |
| E1-M1-W1 | 37.25 | 76.4231 | ::: |
| E1-M1-W2 | 54.4 | 73.2795 | ::: |
| E1-M1-W3 | 37.25 | 95.45 | ::: |
| W1-M1-W2 | 12.36 | 89.5541 | ::: |
| W1-M1-W3 | 32.47 | 159.1053 | ::: |
| W2-M1-W3 | 11.975 | 106.6994 | ::: |
| M1-NI-CR | 34.139 | 123.4259 | ::: |
| M1-NI-CV | 34.139 | 123.4259 | ::: |
| M1-D1-C | 46.237 | 123.2712 | ::: |
| M1-E1-C | 44.53 | 121.9953 | ::: |
| M1-W1-HM | 8.322 | 99.514 | ::: |
| M1-W2-HM | 9.174 | 99.3627 | ::: |
| M1-W3-HM | 33.538 | 97.246 | ::: |
| NI-CR-NA | 70.0 | 120.0 |
| NI-CR-H5 | 50.0 | 120.0 |
| NI-CV-CC | 70.0 | 120.0 |
| CV-NI-CR | 70.0 | 117.0 |
| H4-CV-NI | 50.0 | 120.0 |
| HM-W1-HM | 100.0 | 104.52 |
| HM-W2-HM | 100.0 | 104.52 |
| HM-W3-HM | 100.0 | 104.52 |
| D1-C-CT | 70.0 | 117.0 |
| D1-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]]] |
| NI | 1.824 | 0.17 |
| D1 | 1.6612 | 0.21 |
| E1 | 1.6612 | 0.21 |
| W1 | 1.7683 | 0.152 |
| W2 | 1.7683 | 0.152 |
| W3 | 1.7683 | 0.152 |
| HM | 0.6000 | 0.0157 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] |
===== Validation of Parameters from MD Simulations =====
==== Bond Parameters ====
| **BOND** | **l0 crystal** | **l0 opt** | **‹l›MD ± σ(l)** | **‹l›MD ± 2σ(l)** |
| M1-NI | 1.98 | 2.24 | 2.17 ± 0.06 | [2.111; 2.238] |
| M1-D1 | 2.17 | 2.14 | 2.18 ± 0.06 | [2.117; 2.245] |
| M1-E1 | 2.19 | 2.15 | 2.18 ± 0.07 | [2.112; 2.245] |
| M1-W1 | 2.20 | 2.37 | 2.3 ± 0.1 | [2.189; 2.383] |
| M1-W2 | 2.14 | 2.33 | 2.3 ± 0.1 | [2.170; 2.371] |
| M1-W3 | 2.11 | 2.16 | 2.14 ± 0.07 | [2.070; 2.215] |
==== Angle Parameters ====
| **ANGLE** | **θ0 crystal** | **θ0 QM** | **‹θ›MD ± σ(θ)** | **‹θ›MD ± 2σ(θ)** |
| NI-M1-D1 | 74.7 | 90.0 | 84 ± 4 | [76.5; 90.8] |
| NI-M1-E1 | 171.1 | 159.9 | 159 ± 3 | [151.8; 165.4] |
| NI-M1-W1 | 87.0 | 94.4 | 88 ± 4 | [81.0; 95.7] |
| NI-M1-W2 | 99.9 | 89.1 | 82 ± 4 | [73.3; 90.8] |
| NI-M1-W3 | 98.0 | 98.8 | 96 ± 5 | [86.6; 105.4] |
| D1-M1-E1 | 113.6 | 103.9 | 100 ± 4 | [92.0; 107.2] |
| D1-M1-W1 | 72.3 | 73.1 | 76 ± 4 | [68.2; 83.2] |
| D1-M1-W2 | 166.7 | 162.5 | 135 ± 6 | [123.2; 146.7] |
| D1-M1-W3 | 86.4 | 90.7 | 84 ± 4 | [76.2; 91.5] |
| E1-M1-W1 | 86.4 | 76.4 | 73 ± 4 | [64.6; 81.0] |
| E1-M1-W2 | 71.3 | 73.3 | 81 ± 4 | [73.5; 89.0] |
| E1-M1-W3 | 79.7 | 95.5 | 105 ± 5 | [95.1; 114.4] |
| W1-M1-W2 | 120.1 | 89.6 | 62 ± 6 | [50.6; 72.9] |
| W1-M1-W3 | 156.1 | 159.1 | 158 ± 4 | [149.5; 166.0] |
| W2-M1-W3 | 82.2 | 106.7 | 139 ± 6 | [127.5; 151.4] |
===== Downloads =====
| //Parameter File// | {{:mm:parameters:manganese:hdewww-frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:manganese:hdewww_mn-ii.zip| .off}} |
| //Citochrome //c// Oxidase’s PDB File (3HB3.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:citochrome_c_oxidase.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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