====== 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**  ||
|  {{ :mm:parameters:manganese:non-parameterized_dedwww_.png?120 |}} |  \\ **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |


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===== Structure chosen to parameterize =====


|  **TEST PROTEIN**  ||
|  //Protein//  |  Muconate Cycloisomerase  |
|  //PDB Code//  |  3CT2  |
|  //Crystallographic Resolution//  |  1.80 Å  |
|  //Organism//  |  Pseudomonas protegens Pf-5  |
|  [[http://pubs.acs.org/doi/abs/10.1021/bi802277h | [Sakai, 2009]]]  ||



===== Parameters Determined =====



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_dedwww_.png?120 |}}  |
|  OD2  |  D1  |  15.9994  | ::: |
|  OD2  |  D2  |  15.9994  | ::: |
|  OE2  |  E1  |  15.9994  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  OW  |  W2  |  15.9994  | ::: |
|  OW  |  W3  |  15.9994  | ::: |
|  HW  |  HM  |  1.00794  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-D1  |  87.24  |  2.1060  | [[#references | [Neves, 2013]]] |
|  M1-D2  |  67.69  |  2.1358  | ::: |
|  M1-E1  |  64.66  |  2.1182  | ::: |
|  M1-W1  |  37.55  |  2.2668  | ::: |
|  M1-W2  |  21.70  |  2.3891  | ::: |
|  M1-W3  |  26.88  |  2.3509  | ::: |
|  D1-C  |  656.0  |  1.25  |
|  D2-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**  |  **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-E1  |  36.67  |  98.6591  | ::: |
|  D1-M1-W1  |  64.83  |  84.6089  | ::: |
|  D1-M1-W2  |  28.655  |  100.2850  | ::: |
|  D1-M1-W3  |  12.63  |  104.2522  | ::: |
|  D2-M1-E1  |  52.68  |  94.9867  | ::: |
|  D2-M1-W1  |  51.096  |  88.2121  | ::: |
|  D2-M1-W2  |  70.4  |  68.8061  | ::: |
|  D2-M1-W3  |  15.15  |  83.2134  | ::: |
|  E1-M1-W1  |  28.47  |  108.9767  | ::: |
|  E1-M1-W2  |  27.038  |  151.2138  | ::: |
|  E1-M1-W3  |  78.1  |  70.7310  | ::: |
|  W1-M1-W2  |  22.205  |  95.5613  | ::: |
|  W1-M1-W3  |  11.62  |  171.1984  | ::: |
|  W2-M1-W3  |  24.74  |  84.5113  | ::: |
|  M1-D1-C  |  42.921  |  132.3478  | ::: |
|  M1-D2-C  |  38.71  |  134.0663  | ::: |
|  M1-E1-C  |  14.90  |  132.1818  | ::: |
|  M1-W1-HM  |  19.45  |  110.5423  | ::: |
|  M1-W2-HM  |  13.29  |  96.8796  | ::: |
|  M1-W3-HM  |  14.52  |  88.2507  | ::: |
|  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  |
|  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**  |  **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]]]  |
|  D1  |  1.6612  |  0.21  |
|  D2  |  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**  |  **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-D2  |  2.16  |  2.14  |  2.26 ± 0.06  |  [2.194; 2.324]  |
|  M1-E1  |  2.00  |  2.12  |  2.14 ± 0.07  |  [2.076; 2.212]  |
|  M1-W1  |  2.03  |  2.27  |  2.28 ± 0.09  |  [2.184; 2.370]  |
|  M1-W2  |  1.94  |  2.39  |  2.4 ± 0.1  |  [2.295; 2.536]  |
|  M1-W3  |  1.97  |  2.35  |  2.3 ± 0.1  |  [2.225; 2.443]  |


==== Angle Parameters ====

|  **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-E1  |  89.4  |  98.7  |  98 ± 4  |  [90.0; 106.0]  |
|  D1-M1-W1  |  93.4  |  84.6  |  87 ± 4  |  [78.7; 95.2]  |
|  D1-M1-W2  |  94.1  |  100.3  |  103 ± 5  |  [93.4; 112.2]  |
|  D1-M1-W3  |  89.6  |  104.3  |  106 ± 6  |  [94.1; 118.1]  |
|  D2-M1-E1  |  94.2  |  95.0  |  93 ± 4  |  [85.3; 100.0]  |
|  D2-M1-W1  |  88.8  |  88.2  |  88 ± 4  |  [80.4; 96.5]  |
|  D2-M1-W2  |  81.9  |  68.8  |  68 ± 3  |  [61.3; 74.6]  |
|  D2-M1-W3  |  86.6  |  83.2  |  78 ± 5  |  [67.5; 88.9]  |
|  E1-M1-W1  |  102.9  |  109.0  |  112 ± 5  |  [102.6; 121.9]  |
|  E1-M1-W2  |  169.8  |  151.2  |  146 ± 4  |  [138.1; 153.5]  |
|  E1-M1-W3  |  102.8  |  70.7  |  69 ± 3  |  [62.4; 75.8]  |
|  W1-M1-W2  |  86.5  |  94.6  |  95 ± 5  |  [85.4; 104.9]  |
|  W1-M1-W3  |  154.2  |  171.2  |  165 ± 5  |  [155.6; 175.3]  |
|  W2-M1-W3  |  67.7  |  84.5  |  80 ± 5  |  [70.5; 89.0]  |



===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:manganese:dedwww-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:dedwww_mn-ii.zip| .off}}  |
|  //Muconate Cycloisomerase’s PDB File (3CT2.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:muconate_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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