Rubredoxin is a mononuclear iron tetrahedral metal center coordinated with four cysteines that are not directly connected in the backbone of the protein.
TEST PROTEIN | |
Protein | Rubredoxin |
PDB Code | 1IRO |
Crystallographic Resolution | 1.10 Å |
Organism | Clostridium pasteurianum |
[Dauter, 1996] |
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
FE-SF | 80.75 | 2.3170 | [Carvalho, 2013] |
CT-SF | 237.00 | 1.8100 |
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
SF-FE-SF | 33.15 | 109.8650 | [Carvalho, 2013] |
CT-SF-FE | 27.60 | 100.9150 | |
SF-CT-H1 | 50.00 | 109.5000 | |
CT-CT-SF | 50.00 | 108.6000 |
ATOM TYPE | Ri / Å | εi / kcal mol-1 | REFERENCE |
FE | 2.6500 | 0.0450 | [Giammona, 1984] |
SF | 2.0000 | 0.2500 | [Cornell, 1995] |
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Rubredoxin’s PDB File (1IRO.pdb)\ LEAPRC file | .pdb, leaprc |
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