====== Manganese(III) - HHDH[HO] ======
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The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions.
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:manganese:non-parameterized_hhdhho_.png?120 |}} | \\ **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 |
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===== Structure chosen to parameterize =====
| **TEST PROTEIN** ||
| //Protein// | Manganese Superoxide Dismutase |
| //PDB Code// | 1N0J |
| //Crystallographic Resolution// | 2.20 Å |
| //Organism// | Homo sapiens |
| [[http://www.sciencedirect.com/science/article/pii/009286749290270M | [Borgstahl, 1992]]] ||
===== Parameters Determined =====
==== Atom Types ====
| **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** |
| MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_hhdhho_.png?120 |}} |
| OD1 | D1 | 15.9994 | ::: |
| NE2 | NI | 14.0067 | ::: |
| NE2 | NJ | 14.0067 | ::: |
| NE2 | NK | 14.0067 | ::: |
| OW | W1 | 15.9994 | ::: |
| HO | HM | 1.00794 | ::: |
==== Bond Parameters ====
| **BOND** | **Kl** / **kcal mol-1 Å-2** | **l / Å** | **REFERENCE** |
| M1-NI | 106.65 | 2.1265 | [[#references | [Neves, 2013]]] |
| M1-NJ | 95.00 | 2.1147 | ::: |
| M1-NK | 81.69 | 2.1238 | ::: |
| M1-D1 | 129.13 | 1.9569 | ::: |
| M1-W1 | 247.2 | 1.7776 | ::: |
| NI-CR | 488.0 | 1.335 |
| NI-CV | 410.0 | 1.394 |
| NJ-CR | 488.0 | 1.335 |
| NJ-CV | 410.0 | 1.394 |
| NK-CR | 488.0 | 1.335 |
| NK-CV | 410.0 | 1.394 |
| D1-C | 656.0 | 1.25 |
| W1-HM | 553.0 | 0.9572 |
==== Angle Parameters ====
| **ANGLE** | **K?** / **kcal mol-1 rad-2** | **θ / deg** | **REFERENCE** |
| NI-M1-NJ | 88.01 | 91.6707 | [[#references | [Neves, 2013]]] |
| NI-M1-NK | 86.76 | 88.725 | ::: |
| NI-M1-D1 | 131.4 | 82.9759 | ::: |
| NI-M1-W1 | 75.8 | 176.7937 | ::: |
| NJ-M1-NK | 30.68 | 136.3174 | ::: |
| NJ-M1-D1 | 23.09 | 110.6038 | ::: |
| NJ-M1-W1 | 89.71 | 91.1769 | ::: |
| NK-M1-D1 | 20.64 | 112.8695 | ::: |
| NK-M1-W1 | 89.03 | 90.3375 | ::: |
| D1-M1-W1 | 100.0 | 94.5712 | ::: |
| M1-NI-CR | 53.671 | 126.4370 | ::: |
| M1-NI-CV | 53.671 | 126.4370 | ::: |
| M1-NJ-CR | 40.495 | 123.3813 | ::: |
| M1-NJ-CV | 40.495 | 123.3813 | ::: |
| M1-NK-CR | 31.220 | 112.3780 | ::: |
| M1-NK-CV | 31.220 | 112.3780 | ::: |
| M1-D1-C | 47.094 | 135.5495 | ::: |
| M1-W1-HM | 18.57 | 116.025 | ::: |
| 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 |
| NK-CR-NA | 70.0 | 120.0 |
| NK-CR-H5 | 50.0 | 120.0 |
| NK-CV-CC | 70.0 | 120.0 |
| CV-NK-CR | 70.0 | 117.0 |
| H4-CV-NK | 50.0 | 120.0 |
| D1-C-CT | 70.0 | 117.0 |
| D1-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 |
| NJ | 1.824 | 0.17 |
| NK | 1.824 | 0.17 |
| D1 | 1.6612 | 0.21 |
| W1 | 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-D1 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] |
| M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] |
| M1-NJ | 2.08 | 2.12 | 2.11 ± 0.06 | [2.053; 2.163] |
| N1-NK | 2.09 | 2.12 | 2.14 ± 0.06 | [2.080; 2.197] |
| M1-W1 | 2.02 | 1.78 | 1.76 ± 0.04 | [1.722; 1.792] |
==== Angle Parameters ====
| **ANGLE** | **θ0 crystal** | **θ0 QM** | **‹θ›MD ± σ(θ)** | **‹θ›MD ± 2σ(θ)** |
| NI-M1-NJ | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] |
| NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] |
| NI-M1-D1 | 82.4 | 83.0 | 83 ± 2 | [79.0; 87.6] |
| NI-M1-W1 | 166.1 | 176.8 | 174 ± 2 | [169.9; 179.1] |
| NJ-M1-NK | 137.7 | 136.4 | 138 ± 5 | [128.8; 146.9] |
| NJ-M1-D1 | 110.4 | 110.4 | 111 ± 5 | [100.1; 121.9] |
| NJ-M1-W1 | 91.8 | 91.1 | 91 ± 3 | [85.8; 96.4] |
| NK-M1-D1 | 106.4 | 112.9 | 111 ± 6 | [99.6; 122.2] |
| NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] |
| D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] |
===== Downloads =====
| //Parameter File// | {{:mm:parameters:manganese:hhdh_ho-frcmod.zip| .frcmod}} |
| //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[ho]_mn-iii.zip| .off}} |
| //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase-oh.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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