PortoBioComp

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

====== Iron(III)/Iron(III) - CC[FE]SS[FE]CC ======
###
Ferredoxin is a binuclear iron center with four cysteine residues and two sulfurs, having a redox potential of 400 mV.
###

|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_non-parameterized.png?120|}}  |  \\ **Oxidation State:** Fe(III)/Fe(III)  \\  **Spin Multiplicity:** 1  |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  [2Fe-2S] Ferredoxin  |
|  //PDB Code//  |  4FXC  |
|  //Crystallographic Resolution//  |  2.50 Å  |
|  //Organism//  |  Spirulina platensis  |
|  [[http://jb.oxfordjournals.org/content/117/5/1017.long | [Fukuyama, 1995]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  FE  |  FE  |  55.845  |  {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_parameterized.png?120|}}  |
|  SG  |  SX  |  32.065  | ::: |
|  S  |  S  |  32.065  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  FE-S  |  93.4  |  2.17  | [[#references | [Carvalho, 2013]]] |
|  FE-SX  |  82.6  |  2.23  | ::: |
|  CT-SX  |  237.00  |  1.8100  |
|  SX-CT  |  227.00  |  1.8100  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  S-FE-S  |  17.3  |  102.84  | [[#references | [Carvalho, 2013]]] |
|  SX-FE-S  |  17.3  |  102.84  | ::: |
|  FE-S-FE  |  18.0  |  77.200  | ::: |
|  SX-FE-SX  |  65.5  |  108.44  | ::: |
|  FE-SX-CT  |  65.5  |  108.44  | ::: |
|  HS-SX-FE  |  65.5  |  108.44  | ::: |
|  SX-CT-H1  |  50.00  |  109.5000  |
|  SX-FE-SX  |  33.15  |  109.8650  | ::: |
|  CT-CT-SX  |  50.00  |  108.6000  |
|  CT-SX-CT  |  62.00  |  98.9000  |
|  CT-CT-SX  |  50.00  |  114.7000  |


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

|  **ATOM TYPE**  |  **R<sub>i</sub> / Å**  |  **ε<sub>i</sub> / kcal mol<sup>-1</sup>**  |  **REFERENCE**  |
|  FE  |  2.6500  |  0.0450  |  [[#references | [Giammona, 1984]]]  |
|  S  |  2.0000  |  0.2500  |  [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]]  |
|  SX  |  2.0000  |  0.2500  | ::: |



===== Downloads =====

|  //Parameter File//  |  {{mm:parameters:iron:cc_fe_ss_fe_cc-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{mm:parameters:iron:cc_fe_ss_fe_cc_fe-iii-fe-iii.zip| .off}}  |
|  //Ferredoxin’s PDB File (4FXC.pdb)\ LEAPRC file//  |  {{ferredoxin.zip| .pdb, leaprc}}  |




===== References =====
###
A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. [[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23287/abstract;jsessionid=415EECAA000727C4BCBA82544438C428.d03t02 | Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins]]. //J. Comput. Chem.//, **2013**, 34, 1540-1548
###
###
D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984**
###
PortoBioComp

User Tools

Site Tools

Page Tools
