====== Iron(III)/Iron(III) - CC[FE]SS[FE]CC ======
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Ferredoxin is a binuclear iron center with four cysteine residues and two sulfurs, having a redox potential of 400 mV.
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| **COORDINATION SPHERE** ||
| {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_non-parameterized.png?120|}} | \\ **Oxidation State:** Fe(III)/Fe(III) \\ **Spin Multiplicity:** 1 |
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===== 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** | **Kl** / **kcal mol-1 Å-2** | **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** | **Kθ** / **kcal mol-1 rad-2** | **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** | **Ri / Å** | **εi / kcal mol-1** | **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 =====
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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
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D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984**
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