====== Copper(II)/Zinc(II) - HHH[Cu]H[Zn]HHD ======
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The metal center of Cu, Zn Superoxide Dismutase is hereby presented, in which the zinc atom is bonded to 3 histidines, and 1 aspartate (monodentate) and the copper atom to 4 histidines. Validation for this metal centre in the protein environment is additionally provided.
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|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:copper_zinc:SOD.png?250 |}} |  \\ **Oxidation state:** Cu(II) / Zn(II) \\  **Spin multiplicity:** 1  |


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

|  **TEST PROTEIN**  ||
|  //Protein//  |  Cu, Zn Superoxide Dismutase  |
|  //PDB Code//  |  1CBJ  |
|  //Crystallographic Resolution//  |  1.65 Å  |
|  //Organism//  |  //Bos taurus//  |
|  [[http://www.ncbi.nlm.nih.gov/pubmed/10092461 | [Hough, 1999]]]  ||


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

==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  CU  |  CU  |  63.546  |  {{ :mm:parameters:copper_zinc:SOD_2.png?220 |}}  |
|  ZN  |  ZN  |  65.409  | ::: |
|  NE2  |  NB  |  14.0067  | ::: |
|  ND1  |  NB  |  14.0067  | ::: |
|  OD1  |  OS  |  15.9994  | ::: |

==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  ZN-NB  |  96.7  |  2.046  |  [[#references | [Branco, 2006]]]  |
|  ZN-OS  |  92.0  |  1.949  | ::: |
|  CU-NB  |  101.1  |  2.022  | ::: |

==== Angles Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  NB-CU-NB  |  24.6  |  147.19  |  [[#references | [Branco, 2006]]]  |
|  NB-ZN-NB  |  44.0  |  113.53  | ::: |
|  NB-ZN-OS  |  21.7  |  111.75  | ::: |

===== Validation of Parameters from MD Simulations =====

==== Bond Parameters ====

The validation considering the 1CBJ SOD structure was conducted. The two chains (A and B) were considered in the validation and the brackets denotes the decoordinated residue upon reduction. 

|  **BOND / Å**  |  **l<sub>0 crystal</sub> 1CBJ:A**  |  **l<sub>0 crystal</sub> 1CBJ:B**  |  **‹l›<sub>MD</sub> ± 0.06 A**  |  **‹l›<sub>MD</sub> ± 0.06 B**  |
|  CU-NB(H44)  |  2.07  |  2.00  |  2.03  |  2.04  | 
|  CU-NB(H46)  |  2.00  |  2.17  |  2.08  |  2.07  |
|  CU-NB(H61)  |  (3.19)  |  2.20  |  2.03  |  2.03  |
|  CU-NB(H118)  |  2.03  |  2.19  |  2.03  |  2.03  |
|  ZN-NB(H61)  |  1.97  |  2.02  |  2.03  |  2.03  | 
|  ZN-NB(H69)  |  2.03  |  2.07  |  2.05  |  2.04  |
|  ZN-NB(H78)  |  2.07  |  1.75  |  2.06  |  2.05  |
|  ZN-OS(D81)  |  1.62  |  1.84  |  1.90  |  1.92  |

==== Angle Parameters ====

|  **ANGLE**  |  **θ<sub>0 crystal</sub> 1CBJ:A**  |  **θ<sub>0 crystal</sub> 1CBJ:B**  |  **‹θ›<sub>MD</sub> ± 5 A**  |  **‹θ›<sub>MD</sub> ± 5 B**  |
|  H44-CU-H46  |  140.9  |  138.2  |  133.0  |  133.8  |
|  H44-CU-H61  |  72.5  |  86.8  |  96.6  |  97.3  |
|  H44-CU-H118  |  101.1  |  93.0  |  98.7  |  98.0  |
|  H46-CU-H61  |  92.5  |  97.6  |  101.2  |  101.5  |
|  H46-CU-H118  |  117.6  |  99.7  |  107.5  |  106.6  | 
|  H61-CU-H118  |  118.5  |  153.9  |  121.6  |  121.4  |
|  H61-ZN-H69  |  108.1  |  110.0  |  106.5  |  105.1  |
|  H61-ZN-H78  |  110.0  |  110.2  |  106.7  |  106.3  | 
|  H61-ZN-A81  |  104.6  |  103.9  |  111.4  |  112.4  | 
|  H69-ZN-H78  |  118.9  |  117.3  |  112.8  |  112.9  |
|  H69-ZN-D81  |  98.0  |  99.7  |  105.3  |  103.8  |
|  H78-ZN-D81  |  115.9  |  114.5  |  113.4  |  115.5  |


===== References =====
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Branco, J.F.B.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/jp056855l | Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase]] . //J. Phys. Chem. B//, **2006**, 110, 16754-16762
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