PortoBioComp

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

====== Manganese(II) - ED[PY2]WaWa ======
###
In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate.
Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand.
A water molecule is referred as participating in the octahedral coordination of manganese(II).
###

|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:manganese:non-parameterized_edpy2ww_.png?120 |}} |  \\ **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  Pyruvate Kinase  |
|  //PDB Code//  |  2G50  |
|  //Crystallographic Resolution//  |  1.65 Å  |
|  //Organism//  |  Oryctolagus cuniculus  |
|  [[http://pubs.acs.org/doi/abs/10.1021/bi0524262 | [Williams, 2006]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_edpy2ww_.png?120 |}}  |
|  OD2  |  D1  |  15.9994  | ::: |
|  OE1  |  E1  |  15.9994  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  OW  |  W2  |  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  |  71.90  |  2.0926  | [[#references | [Neves, 2013]]] |
|  M1-E1  |  68.77  |  2.1399  | ::: |
|  M1-R1  |  55.39  |  2.1382  | ::: |
|  M1-R2  |  16.78  |  2.4332  | ::: |
|  M1-W1  |  24.75  |  2.3873  | ::: |
|  M1-W2  |  50.08  |  2.2004  | ::: |
|  D1-C  |  656.0  |  1.25  |
|  E1-C  |  656.0  |  1.25  |
|  W1-HM  |  553.0  |  0.9572  |
|  W2-HM  |  553.0  |  0.9572  |
|  c-R2  |  648.0  |  1.214  |
|  c-R1  |  648.0  |  1.214  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  D1-M1-E1  |  38.27  |  96.6209  | [[#references | [Neves, 2013]]] |
|  D1-M1-R1  |  23.41  |  104.8054  | ::: |
|  D1-M1-R2  |  12.445  |  169.3708  | ::: |
|  D1-M1-W1  |  69.3  |  72.8299  | ::: |
|  D1-M1-W2  |  26.19  |  103.5245  | ::: |
|  E1-M1-R1  |  29.696  |  97.7449  | ::: |
|  E1-M1-R2  |  13.94  |  93.9317  | ::: |
|  E1-M1-W1  |  25.05  |  168.0717  | ::: |
|  E1-M1-W2  |  52.2  |  89.0644  | ::: |
|  R1-M1-R2  |  128.3  |  80.3387  | ::: |
|  R1-M1-W1  |  20.47  |  80.0896  | ::: |
|  R1-M1-W2  |  18.05  |  149.8517  | ::: |
|  R2-M1-W1  |  13.736  |  96.5418  | ::: |
|  R2-M1-W2  |  27.09  |  77.9339  | ::: |
|  W1-M1-W2  |  15.008  |  98.6963  | ::: |
|  M1-D1-C  |  14.829  |  125.0463  | ::: |
|  M1-E1-C  |  42.056  |  122.8295  | ::: |
|  M1-R1-c  |  47.47  |  122.0775  | ::: |
|  M1-R2-c  |  57.66  |  110.2798  | ::: |
|  M1-W1-HM  |  12.10  |  86.3993  | ::: |
|  M1-W2-HM  |  28.96  |  88.1336  | ::: |
|  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  |
|  c3-c-R2  |  68.0  |  123.11  |
|  R1-c-c  |  66.8  |  122.34  |
|  o-c-R1  |  79.1  |  127.33  |
|  c-c-R2  |  66.8  |  122.34  |


==== 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  |
|  E1  |  1.6612  |  0.21  |
|  R1  |  1.6612  |  0.2100  |
|  R2  |  1.6612  |  0.2100  |
|  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**  |  **l<sub>0 crystal</sub>**  |  **l<sub>0 opt</sub>**  |  **‹l›<sub>MD</sub> ± σ(l)**  |  **‹l›<sub>MD</sub> ± 2σ(l)**   |
|  M1-D1  |  1.97  |  2.09  |  2.16 ± 0.06  |  [2.095; 2.225]  |
|  M1-E1  |  1.96  |  2.14  |  2.22 ± 0.06  |  [2.153; 2.281]  |
|  M1-R1  |  1.98  |  2.14  |  2.13 ± 0.07  |  [2.059; 2.192]  |
|  M1-R2  |  1.95  |  2.43  |  2.4 ± 0.1  |  [2.276; 2.473]  |
|  M1-W1  |  2.29  |  2.39  |  2.4 ± 0.1  |  [2.289; 2.537]  |
|  M1-W2  |  2.26  |  2.20  |  2.18 ± 0.08  |  [2.100; 2.258]  |


==== 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-E1  |  97.0  |  96.6  |  99 ± 5  |  [89.0; 108.1]  |
|  D1-M1-R1  |  90.8  |  104.8  |  103 ± 5  |  [93.1; 112.4]  |
|  D1-M1-R2  |  153.6  |  169.4  |  170 ± 5  |  [159.4; 180.1]  |
|  D1-M1-W1  |  78.1  |  72.8  |  75 ± 4  |  [67.8; 82.2]  |
|  D1-M1-W2  |  113.2  |  103.5  |  110 ± 5  |  [99.5; 120.6]  |
|  E1-M1-R1  |  91.7  |  97.7  |  101 ± 5  |  [91.1; 110.3]  |
|  E1-M1-R2  |  105.0  |  93.9  |  75 ± 5  |  [64.3; 86.1]  |
|  E1-M1-W1  |  163.9  |  168.1  |  168 ± 4  |  [159.5; 176.5]  |
|  E1-M1-W2  |  84.8  |  89.1  |  80 ± 4  |  [71.4; 87.7]  |
|  R1-M1-R2  |  74.4  |  80.3  |  75 ± 2  |  [70.9; 79.1]  |
|  R1-M1-W1  |  103.6  |  80.1  |  79 ± 7  |  [63.7; 93.7]  |
|  R1-M1-W2  |  156.0  |  149.9  |  146 ± 5  |  [136.7; 155.4]  |
|  R2-M1-W1  |  84.2  |  96.5  |  111 ± 7  |  [97.0; 124.2]  |
|  R2-M1-W2  |  83.5  |  77.9  |  73 ± 5  |  [63.3; 82.5]  |
|  W1-M1-W2  |  83.1  |  98.7  |  105 ± 10  |  [85.6; 123.9]  |



===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:manganese:ed_py2_ww-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:ed[py2]ww_mn-ii.zip| .off}}  |
|  //Pyruvate Kinase’s PDB File (2G50.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:pyruvate_kinase.zip| .pdb, leaprc}}  |




===== References =====
###
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
###
PortoBioComp

User Tools

Site Tools

Page Tools
