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(III) - HHDH[HO]O ======



|  **Coordination Sphere**  |  **Oxidation State:** Mn(III)  \\  **Spin Multiplicity:** 4  |
|  IMAGE1 | IMAGE2  ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  Manganese Superoxide Dismutase  |
|  //PDB Code//  |  1MNG  |
|  //Crystallographic Resolution//  |  1.80  |
|  //Organism//  |  Thermus thermophilus  |
|  [[http://www.ncbi.nlm.nih.gov/pubmed/7849024?dopt=Abstract | [Lah, 1995]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  IMAGE  |
|  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**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-NI  |  82.11  |  2.1879  | [[#references | [Neves, 2013]]] |
|  M1-NJ  |  123.46  |  2.0161  | ::: |
|  M1-NK  |  138.95  |  2.0175  | ::: |
|  M1-D1  |  111.54  |  2.0630  | ::: |
|  M1-R1  |  96.51  |  1.9361  | ::: |
|  M1-W1  |  227.9  |  1.7993  | ::: |
|  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  |
|  R1-O  |  384.3  |  1.430  |
|  W1-HM  |  553.0  |  0.9572  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  NI-M1-NJ  |  93.41  |  91.0663  | [[#references | [Neves, 2013]]] |
|  NI-M1-NK  |  96.11  |  86.5034  | ::: |
|  NI-M1-D1  |  118.5  |  82.0566  | ::: |
|  NI-M1-W1  |  77.66  |  176.5931  | ::: |
|  NI-M1-R1  |  83.7  |  84.2181  | ::: |
|  NJ-M1-NK  |  97.22  |  172.0561  | ::: |
|  NJ-M1-D1  |  74.40  |  93.5533  | ::: |
|  NJ-M1-W1  |  96.31  |  90.3808  | ::: |
|  NJ-M1-R1  |  95.80  |  86.9561  | ::: |
|  NK-M1-D1  |  75.579  |  93.5990  | ::: |
|  NK-M1-W1  |  92.14  |  92.4642  | ::: |
|  NK-M1-R1  |  99.09  |  85.2759  | ::: |
|  D1-M1-W1  |  83.35  |  94.7758  | ::: |
|  D1-M1-R1  |  70.04  |  166.2720  | ::: |
|  W1-M1-R1  |  61.59  |  98.9401  | ::: |
|  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  |  36.67  |  106.2284  | ::: |
|  M1-R1-O  |  41.32  |  118.4913  | ::: |
|  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**  |  **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]]]  |
|  NI  |  1.824  |  0.17  |
|  NJ  |  1.824  |  0.17  |
|  NK  |  1.824  |  0.17  |
|  D1  |  1.6612  |  0.21  |
|  R1  |  1.6612  |  0.2100  |
|  O  |  1.6612  |  0.2100  |
|  W1  |  1.7210  |  0.2104  |
|  HM  |  0.6000  |  0.0157  |  [[LINK | [Cornel, 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  |  1.80  |  2.06  |  2.09 ± 0.05  |  [2.038; 2.142]  |
|  M1-NI  |  2.15  |  2.19  |  2.20 ± 0.06  |  [2.141; 2.254]  |
|  M1-NJ  |  2.12  |  2.02  |  2.02 ± 0.05  |  [1.969; 2.063]  |
|  M1-NK  |  2.16  |  2.02  |  2.05 ± 0.05  |  [2.003; 2.094]  |
|  M1-W1  |  2.07  |  1.80  |  1.79 ± 0.04  |  [1.752; 1.825]  |
|  M1-R1  |  2.68  |  1.94  |  1.93 ± 0.06  |  [1.872; 1.984]  |


==== 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)**  |
|  NI-M1-NJ  |  92.4  |  91.1  |  92 ± 2  |  [86.9; 96.6]  |
|  NI-M1-NK  |  90.3  |  86.5  |  89 ± 2  |  [84.3; 93.7]  |
|  NI-M1-D1  |  89.1  |  82.1  |  82 ± 2  |  [77.6; 87.0]  |
|  NI-M1-W1  |  175.5  |  176.6  |  176 ± 2  |  [172.3; 179.7]  |
|  NI-M1-R1  |  97.6  |  84.2  |  86 ± 2  |  [80.8; 90.8]  |
|  NJ-M1-NK  |  130.8  |  172.1  |  170 ± 2  |  [165.7; 174.9]  |
|  NJ-M1-D1  |  110.1  |  93.6  |  93 ± 3  |  [87.0; 98.6]  |
|  NJ-M1-W1  |  90.0  |  90.4  |  87 ± 2  |  [82.6; 92.4]  |
|  NJ-M1-R1  |  66.4  |  87.0  |  85 ± 3  |  [80.4; 90.5]  |
|  NK-M1-D1  |  119.2  |  93.6  |  97 ± 3  |  [90.9; 102.1]  |
|  NK-M1-W1  |  91.0  |  92.5  |  92 ± 3  |  [86.9; 97.1]  |
|  NK-M1-R1  |  64.6  |  85.3  |  85 ± 2  |  [80.5; 90.2]  |
|  D1-M1-W1  |  86.5  |  94.8  |  96 ± 3  |  [90.5; 101.8]  |
|  D1-M1-R1  |  172.4  |  166.3  |  167 ± 3  |  [162.3; 172.5]  |
|  W1-M1-R1  |  86.8  |  98.9  |  96 ± 3  |  [90.1; 101.3]  |



===== Downloads =====

|  //Parameter File//  |  {{PATH TO FRCMOD FILE| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{PATH TO CHARGE FILES| .off}}  |
|  //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file//  |  {{PATH TO PDB AND LEAPRC FILES| .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
