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mm:parameters:manganese:ded_cl
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Table of Contents
Manganese(II) - DED[CL]
| Coordination Sphere | Oxidation State: Mn(II) Spin Multiplicity: 6 |
 |  1) |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | Chloromuconate Cycloisomerase |
| PDB Code | 2CHR |
| Crystallographic Resolution | 3.00 Å |
| Organism | Cupriavidus necator |
| [Kleywegt, 1996] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| MN | M1 | 54.938 |  |
| OD2 | D1 | 15.9994 | |
| OD2 | D2 | 15.9994 | |
| OE2 | E1 | 15.9994 |
Bond Parameters
| BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
| M1-D1 | 86.71 | 2.0770 | [Neves, 2013] |
| M1-D2 | 72.61 | 2.0834 | |
| M1-E1 | 75.79 | 2.0710 | |
| M1-R1 | 69.25 | 2.4005 | |
| D1-C | 656.0 | 1.25 | |
| D2-C | 656.0 | 1.25 | |
| E1-C | 656.0 | 1.25 |
Angle Parameters
| ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
| D1-M1-D2 | 18.812 | 124.2299 | [Neves, 2013] |
| D1-M1-E1 | 35.39 | 100.9790 | |
| D1-M1-R1 | 23.76 | 106.7074 | |
| D2-M1-E1 | 38.51 | 102.8186 | |
| D2-M1-R1 | 23.73 | 108.1030 | |
| E1-M1-R1 | 19.27 | 113.6328 | |
| M1-D1-C | 10.075 | 144.1664 | |
| M1-D2-C | 45.967 | 141.6861 | |
| M1-E1-C | 20.462 | 135.2443 | |
| D1-C-CT | 70.0 | 117.0 | |
| D1-C-O2 | 80.0 | 126.0 | |
| D2-C-CT | 70.0 | 117.0 | |
| D2-C-O2 | 80.0 | 126.0 | |
| E1-C-CT | 70.0 | 117.0 | |
| E1-C-O2 | 80.0 | 126.0 |
Van der Waals Parameters
| ATOM TYPE | Ri / Å | εi / kcal mol-1 | REFERENCE |
| M1 | 1.4544 | 0.03 | [Babu, 2006] |
| D1 | 1.6612 | 0.21 | |
| D2 | 1.6612 | 0.21 | |
| E1 | 1.6612 | 0.21 | |
| R1 | 1.948 | 0.265 |
Validation of Parameters from MD Simulations
Bond Parameters
| BOND | l0 crystal | l0 opt | ‹l›MD ± σ(l) | ‹l›MD ± 2σ(l) |
| M1-D1 | 3.08 | 2.08 | 2.10 ± 0.06 | [2.042; 2.161] |
| M1-D2 | 2.10 | 2.08 | 2.08 ± 0.07 | [2.016; 2.148] |
| M1-E1 | 2.05 | 2.07 | 2.07 ± 0.06 | [2.011; 2.137] |
| M1-R1 | 2.95 | 2.40 | 2.38 ± 0.07 | [2.316; 2.451] |
Angle Parameters
| ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
| D1-M1-D2 | 173.5 | 124.2 | 138 ± 5 | [127.1; 148.5] |
| D1-M1-E1 | 80.0 | 101.0 | 107 ± 5 | [96.8; 116.8] |
| D1-M1-R1 | 87.2 | 106.7 | 80 ± 7 | [66.5; 93.4] |
| D2-M1-E1 | 99.4 | 102.8 | 105 ± 5 | [95.9; 114.8] |
| D2-M1-R1 | 87.1 | 108.1 | 79 ± 6 | [65.8; 91.4] |
| E1-M1-R1 | 112.9 | 113.6 | 85 ± 7 | [71.7; 98.4] |
Downloads
| Parameter File | .frcmod |
| Coordination Sphere Charges | .off |
| Integrase’s PDB File (2CHR.pdb) LEAPRC file | .pdb, leaprc |
References
Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins . J. Chem. Theory Comput., 2013, 9 (6), 2718–2732
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/manganese/ded_cl.1374841651.txt.gz · Last modified: 2013/07/26 13:27 by ruineves
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