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mm:parameters:iron:cc_fe_ss_fe_cc
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Table of Contents
Iron(III)/Iron(III) - CC[FE]SS[FE]CC
| Coordination Sphere | Oxidation State: Fe(III) Spin Multiplicity: 1 |
 | PATH TO IMAGE2 1) |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | [2Fe-2S] Ferrodoxin |
| PDB Code | 4FXC |
| Crystallographic Resolution | 2.50 Å |
| Organism | Spirulina platensis |
| [Fukuyama, 1995] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| FE | FE | 55.845 |  |
| SG | SX | 32.065 | |
| S | S | 32.065 |
Bond Parameters
| BOND | Kl / kcal mol-1 | l / angstrom | REFERENCE |
| FE-S | 93.4 | 2.17 | [Carvalho, 2013] |
| FE-SX | 82.6 | 2.23 | |
| CT-SX | 237.00 | 1.8100 | |
| SX-CT | 227.00 | 1.8100 |
Angle Parameters
| Angle | Ktheta / kcal mol-1 | theta / angstrom | REFERENCE |
| S-FE-S | 17.3 | 102.84 | [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 / angstrom | epsiloni / kcal mol-1 | REFERENCE |
| FE | 2.6500 | 0.0450 | [Giammona, 1984] |
| S | 2.0000 | 0.2500 | [Cornell, 1995] |
| SX | 2.0000 | 0.2500 |
Downloads
| Parameter File | .frcmod |
| Coordination Sphere Charges | .off |
| ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file | .pdb, leaprc |
References
A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. 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
1)
The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.
mm/parameters/iron/cc_fe_ss_fe_cc.1375721829.txt.gz · Last modified: 2013/08/05 17:57 by ruineves
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