Manganese(III) - HHDH[HO]
The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions.
COORDINATION SPHERE |
|
Oxidation State: Mn(III)
Spin Multiplicity: 5 |
Structure chosen to parameterize
TEST PROTEIN |
Protein | Manganese Superoxide Dismutase |
PDB Code | 1N0J |
Crystallographic Resolution | 2.20 Å |
Organism | Homo sapiens |
[Borgstahl, 1992] |
Parameters Determined
Atom Types
ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
MN | M1 | 54.938 | |
OD1 | D1 | 15.9994 |
NE2 | NI | 14.0067 |
NE2 | NJ | 14.0067 |
NE2 | NK | 14.0067 |
OW | W1 | 15.9994 |
HO | HM | 1.00794 |
Bond Parameters
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
M1-NI | 106.65 | 2.1265 | [Neves, 2013] |
M1-NJ | 95.00 | 2.1147 |
M1-NK | 81.69 | 2.1238 |
M1-D1 | 129.13 | 1.9569 |
M1-W1 | 247.2 | 1.7776 |
NI-CR | 488.0 | 1.335 | |
NI-CV | 410.0 | 1.394 | |
NJ-CR | 488.0 | 1.335 | |
NJ-CV | 410.0 | 1.394 | |
NK-CR | 488.0 | 1.335 | |
NK-CV | 410.0 | 1.394 | |
D1-C | 656.0 | 1.25 | |
W1-HM | 553.0 | 0.9572 | |
Angle Parameters
ANGLE | K? / kcal mol-1 rad-2 | θ / deg | REFERENCE |
NI-M1-NJ | 88.01 | 91.6707 | [Neves, 2013] |
NI-M1-NK | 86.76 | 88.725 |
NI-M1-D1 | 131.4 | 82.9759 |
NI-M1-W1 | 75.8 | 176.7937 |
NJ-M1-NK | 30.68 | 136.3174 |
NJ-M1-D1 | 23.09 | 110.6038 |
NJ-M1-W1 | 89.71 | 91.1769 |
NK-M1-D1 | 20.64 | 112.8695 |
NK-M1-W1 | 89.03 | 90.3375 |
D1-M1-W1 | 100.0 | 94.5712 |
M1-NI-CR | 53.671 | 126.4370 |
M1-NI-CV | 53.671 | 126.4370 |
M1-NJ-CR | 40.495 | 123.3813 |
M1-NJ-CV | 40.495 | 123.3813 |
M1-NK-CR | 31.220 | 112.3780 |
M1-NK-CV | 31.220 | 112.3780 |
M1-D1-C | 47.094 | 135.5495 |
M1-W1-HM | 18.57 | 116.025 |
NI-CR-NA | 70.0 | 120.0 | |
NI-CR-H5 | 50.0 | 120.0 | |
NI-CV-CC | 70.0 | 120.0 | |
CV-NI-CR | 70.0 | 117.0 | |
H4-CV-NI | 50.0 | 120.0 | |
NJ-CR-NA | 70.0 | 120.0 | |
NJ-CR-H5 | 50.0 | 120.0 | |
NJ-CV-CC | 70.0 | 120.0 | |
CV-NJ-CR | 70.0 | 117.0 | |
H4-CV-NJ | 50.0 | 120.0 | |
NK-CR-NA | 70.0 | 120.0 | |
NK-CR-H5 | 50.0 | 120.0 | |
NK-CV-CC | 70.0 | 120.0 | |
CV-NK-CR | 70.0 | 117.0 | |
H4-CV-NK | 50.0 | 120.0 | |
D1-C-CT | 70.0 | 117.0 | |
D1-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] |
NI | 1.824 | 0.17 | |
NJ | 1.824 | 0.17 | |
NK | 1.824 | 0.17 | |
D1 | 1.6612 | 0.21 | |
W1 | 1.7683 | 0.152 | |
HM | 0.6000 | 0.0157 | [Cornell, 1995] |
Validation of Parameters from MD Simulations
Bond Parameters
BOND | l0 crystal | l0 opt | ‹l›MD ± σ(l) | ‹l›MD ± 2σ(l) |
M1-D1 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] |
M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] |
M1-NJ | 2.08 | 2.12 | 2.11 ± 0.06 | [2.053; 2.163] |
N1-NK | 2.09 | 2.12 | 2.14 ± 0.06 | [2.080; 2.197] |
M1-W1 | 2.02 | 1.78 | 1.76 ± 0.04 | [1.722; 1.792] |
Angle Parameters
ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
NI-M1-NJ | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] |
NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] |
NI-M1-D1 | 82.4 | 83.0 | 83 ± 2 | [79.0; 87.6] |
NI-M1-W1 | 166.1 | 176.8 | 174 ± 2 | [169.9; 179.1] |
NJ-M1-NK | 137.7 | 136.4 | 138 ± 5 | [128.8; 146.9] |
NJ-M1-D1 | 110.4 | 110.4 | 111 ± 5 | [100.1; 121.9] |
NJ-M1-W1 | 91.8 | 91.1 | 91 ± 3 | [85.8; 96.4] |
NK-M1-D1 | 106.4 | 112.9 | 111 ± 6 | [99.6; 122.2] |
NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] |
D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] |
Downloads
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)
LEAPRC file | .pdb, leaprc |
References