====== Manganese(II) - HHEWaWa ======
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Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same.
Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions.
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:manganese:non-parameterized_hheww_.png?120 |}} | \\ **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 5 |
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===== Structure chosen to parameterize =====
| **TEST PROTEIN** ||
| //Protein// | Homoprotocatechuate 2,3-Dioxygenase |
| //PDB Code// | 1F1U |
| //Crystallographic Resolution// | 1.50 Å |
| //Organism// | Arthrobacter globiformis |
| [[http://jb.asm.org/content/186/7/1945.long | [Vetting, 2004]]] ||
===== Parameters Determined =====
==== Atom Types ====
| **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** |
| MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_hheww_.png?120 |}} |
| OE1 | E1 | 15.9994 | ::: |
| NE2 | NI | 14.0067 | ::: |
| NE2 | NJ | 14.0067 | ::: |
| OW | W1 | 15.9994 | ::: |
| OW | W2 | 15.9994 | ::: |
| HW | HM | 1.00794 | ::: |
==== Bond Parameters ====
| **BOND** | **Kl** / **kcal mol-1 Å-2** | **l / Å** | **REFERENCE** |
| M1-NI | 81.53 | 2.1862 | [[#references | [Neves, 2013]]] |
| M1-NJ | 78.93 | 2.1763 | ::: |
| M1-E1 | 90.87 | 2.0648 | ::: |
| M1-W1 | 43.45 | 2.2506 | ::: |
| M1-W2 | 45.59 | 2.2237 | ::: |
| NI-CR | 488.0 | 1.335 |
| NI-CV | 410.0 | 1.394 |
| NJ-CR | 488.0 | 1.335 |
| NJ-CV | 410.0 | 1.394 |
| E1-C | 656.0 | 1.25 |
| W1-HM | 553.0 | 0.9572 |
| W2-HM | 553.0 | 0.9572 |
==== Angle Parameters ====
| **ANGLE** | **Kθ** / **kcal mol-1 rad-2** | **θ / deg** | **REFERENCE** |
| NI-M1-NJ | 35.670 | 106.2009 | [[#references | [Neves, 2013]]] |
| NI-M1-E1 | 66.76 | 90.0029 | ::: |
| NI-M1-W1 | 27.91 | 89.1764 | ::: |
| NI-M1-W2 | 27.25 | 152.3584 | ::: |
| NJ-M1-E1 | 58.53 | 100.4401 | ::: |
| NJ-M1-W1 | 8.378 | 121.3184 | ::: |
| NJ-M1-W2 | 30.649 | 101.1859 | ::: |
| E1-M1-W1 | 8.825 | 136.6245 | ::: |
| E1-M1-W2 | 64.45 | 88.6732 | ::: |
| W1-M1-W2 | 41.88 | 73.2308 | ::: |
| M1-NI-CR | 46.273 | 126.3998 | ::: |
| M1-NI-CV | 46.273 | 126.3998 | ::: |
| M1-NJ-CR | 31.467 | 118.1041 | ::: |
| M1-NJ-CV | 31.467 | 118.1041 | ::: |
| M1-E1-C | 49.84 | 127.7223 | ::: |
| M1-W1-HM | 7.881 | 110.4316 | ::: |
| M1-W2-HM | 26.41 | 109.0419 | ::: |
| 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 |
| NJ-CR-NA | 70.0 | 120.0 |
| NJ-CR-H5 | 50.0 | 120.0 |
| NJ-CV-CC | 70.0 | 120.0 |
| CV-NJ-CR | 70.0 | 117.0 |
| H4-CV-NJ | 50.0 | 120.0 |
| 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 |
| HM-W1-HM | 100.0 | 104.52 |
| HM-W2-HM | 100.0 | 104.52 |
==== 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 |
| NJ | 1.824 | 0.17 |
| E1 | 1.6612 | 0.21 |
| W1 | 1.7683 | 0.152 |
| W2 | 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 | 2.21 | 2.19 | 2.15 ± 0.06 | [2.086; 2.205] |
| M1-NJ | 2.03 | 2.18 | 2.15 ± 0.06 | [2.086; 2.212] |
| M1-E1 | 2.11 | 2.06 | 2.08 ± 0.06 | [2.017; 2.133] |
| M1-W1 | 2.38 | 2.25 | 2.18 ± 0.08 | [2.098; 2.266] |
| M1-W2 | 2.18 | 2.22 | 2.17 ± 0.08 | [2.095; 2.255] |
==== Angle Parameters ====
| **ANGLE** | **θ0 crystal** | **θ0 QM** | **‹θ›MD ± σ(θ)** | **‹θ›MD ± 2σ(θ)** |
| NI-M1-NJ | 95.6 | 106.2 | 110 ± 4 | [102.1; 117.0] |
| NI-M1-E1 | 86.7 | 90.0 | 94 ± 3 | [86.9; 100.5] |
| NI-M1-W1 | 91.4 | 89.2 | 80 ± 4 | [71.5; 89.3] |
| NI-M1-W2 | 151.4 | 152.4 | 152 ± 4 | [143.9; 159.7] |
| NJ-M1-E1 | 97.3 | 100.4 | 102 ± 4 | [93.6; 110.1] |
| NJ-M1-W1 | 93.4 | 121.3 | 122 ± 7 | [108.5; 135.2] |
| NJ-M1-W2 | 109.2 | 101.2 | 97 ± 4 | [88.6; 104.7] |
| E1-M1-W1 | 169.3 | 136.6 | 135 ± 7 | [121.3; 148.7] |
| E1-M1-W2 | 103.5 | 88.7 | 89 ± 4 | [82.0; 96.6] |
| W1-M1-W2 | 73.6 | 73.2 | 78 ± 4 | [69.5; 86.8] |
===== Downloads =====
| //Parameter File// | {{:mm:parameters:manganese:hheww-frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:manganese:hheww_mn-ii.zip| .off}} |
| //Homoprotocatechuate-2,3-dioxygenase’s PDB File (1F1U.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:homoprotocatechuate-2,3-dioxygenase.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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