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====== Copper (II) - HHHH / Zinc (II) - HHHD ======

The metal center of 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.

|  **Coordination Sphere**  |  **Oxidation state:** Cu(II) / Zn(II) \\  **Spin multiplicity:** 1 / 1  |
|  {{ :mm:parameters:copper_zinc:image.png?200 |}} | {{ :mm:parameters:copper_zinc:image.png?400|}} ((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//  |  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:image.png?120 |}}  |
|  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  | ::: |

==== Van der Waals Parameters ====

|  **ATOM TYPE**  |  **R<sub>i</sub> / Å**  |  **ε<sub>i</sub> / kcal mol<sup>-1</sup>**  |  **REFERENCE**  |
|  ZN  |    |    |  [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]]  |
|  CU  |    |    |  [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]]  |
|  OS  |  1.6612  |  0.2100  |    |
|  NB  |  1.8240  |  0.1700  | ::: |

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

==== Bond Parameters ====

|  **BOND**  |  **l<sub>0 crystal</sub> 1CBJ chain A**  |  **l<sub>0 crystal</sub> 1CBJ chain B**  |  **l<sub>0 crystal</sub> 1Q0E chain A**  |  **l<sub>0 crystal</sub> 1Q0E chain B**  |  **‹l›<sub>MD</sub> ± 0.06(l) chain A**  |  **‹l›<sub>MD</sub> ± 0.06(l) chain B**  |
|  CU-NB(H44)  |  2.07  |  2.00  |  2.02  |  2.05  |  2.03  |  2.04  | 
|  CU-NB(H46)  |  2.00  |  2.17  |  1.96  |  2.01  |  2.08  |  2.07  |
|  CU-NB(H61)  |  (3.19)  |  2.20  |  (3.39)  |  (3.32)  |  2.03  |  2.03  |
|  CU-NB(H118)  |  2.03  |  2.19  |  2.08  |  2.04  |  2.03  |  2.03  |
|  ZN-NB(H61)  |  1.97  |  2.02  |  2.05  |  2.05  |  2.03  |  2.03  | 
|  ZN-NB(H69)  |  2.03  |  2.07  |  2.05  |  2.05  |  2.05  |  2.04  |
|  ZN-NB(H78)  |  2.07  |  1.75  |  2.06  |  2.06  |  2.06  |  2.05  |
|  ZN-OS(D81)  |  1.62  |  1.84  |  1.99  |  2.00  |  1.90  |  1.92  |
==== Angle Parameters ====

|  **ANGLE**  |  **θ<sub>0 crystal</sub>**  |  **‹θ›<sub>MD</sub> ± σ(θ)**  |  **‹θ›<sub>MD</sub> ± σ(θ)**  |
|  NF-ZF-SF  |  118  |  119 ± 5  |  114 ± 6  |
|  OF-ZF-NF  |  120  |  101 ± 6  |  102 ± 7  |
|  OF-ZF-OG  |  56  |  64 ± 1  |  63 ± 1  |
|  OF-ZF-SF  |  104  |  124 ± 6  |  124 ± 6  | 
|  OG-ZF-NF  |  90  |  81 ± 4  |  80 ± 5  |
|  SF-ZF-OG  |  80  |  84 ± 6  |  83 ± 6  | 

===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:copper_zinc:hdc_zn-II.frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:copper_zinc:lib_files_1.zip| .lib}}  |
|  //LEAPRC file//  |  {{:mm:parameters:copper_zinc:leaprc.zip| leaprc}}  |
===== References =====
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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