mm:parameters:iron:cc_fe_ss_fe_cc
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mm:parameters:iron:cc_fe_ss_fe_cc [2013/08/05 17:57] ruineves |
mm:parameters:iron:cc_fe_ss_fe_cc [2013/10/03 19:00] (current) ruineves |
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| ====== Iron(III)/Iron(III) - CC[FE]SS[FE]CC ====== | ====== 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 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 1 | | + | |
| - | | {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_non-parameterized.png?200|}} | PATH TO IMAGE2 ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | + | |
| Line 16: | Line 17: | ||
| | **TEST PROTEIN** || | | **TEST PROTEIN** || | ||
| - | | //Protein// | [2Fe-2S] Ferrodoxin | | + | | //Protein// | [2Fe-2S] Ferredoxin | |
| | //PDB Code// | 4FXC | | | //PDB Code// | 4FXC | | ||
| | //Crystallographic Resolution// | 2.50 Å | | | //Crystallographic Resolution// | 2.50 Å | | ||
| Line 31: | Line 32: | ||
| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_parameterized.png?200|}} | | + | | FE | FE | 55.845 | {{ :mm:parameters:iron:ccc[fe]ss[fe]ccc_parameterized.png?120|}} | |
| | SG | SX | 32.065 | ::: | | | SG | SX | 32.065 | ::: | | ||
| | S | S | 32.065 | ::: | | | S | S | 32.065 | ::: | | ||
| Line 38: | Line 39: | ||
| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | + | | **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-S | 93.4 | 2.17 | [[#references | [Carvalho, 2013]]] | | ||
| | FE-SX | 82.6 | 2.23 | ::: | | | FE-SX | 82.6 | 2.23 | ::: | | ||
| Line 47: | Line 48: | ||
| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | + | | **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]]] | | | S-FE-S | 17.3 | 102.84 | [[#references | [Carvalho, 2013]]] | | ||
| | SX-FE-S | 17.3 | 102.84 | ::: | | | SX-FE-S | 17.3 | 102.84 | ::: | | ||
| Line 63: | Line 64: | ||
| ==== Van der Waals Parameters ==== | ==== Van der Waals Parameters ==== | ||
| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | + | | **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]]] | | | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | ||
| | S | 2.0000 | 0.2500 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | | | S | 2.0000 | 0.2500 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | | ||
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| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | + | | //Parameter File// | {{mm:parameters:iron:cc_fe_ss_fe_cc-frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | + | | //Coordination Sphere Charges// | {{mm:parameters:iron:cc_fe_ss_fe_cc_fe-iii-fe-iii.zip| .off}} | |
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} | | + | | //Ferredoxin’s PDB File (4FXC.pdb)\ LEAPRC file// | {{ferredoxin.zip| .pdb, leaprc}} | |
| Line 80: | Line 81: | ||
| ===== References ===== | ===== 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 | 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** | D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | ||
| + | ### | ||
mm/parameters/iron/cc_fe_ss_fe_cc.1375721829.txt.gz · Last modified: 2013/08/05 17:57 by ruineves
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