Manganese(III) - HHDHWa
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 |
HW | HM | 1.00794 |
Bond Parameters
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
M1-NI | 59.43 | 2.2457 | [Neves, 2013] |
M1-NJ | 75.35 | 2.1589 |
M1-NK | 80.07 | 2.168 |
M1-D1 | 81.62 | 2.0542 |
M1-W1 | 38.02 | 2.2351 |
NI-CR | 488 | 1.335 | |
NI-CV | 410 | 1.394 | |
NJ-CR | 488 | 1.335 | |
NJ-CV | 410 | 1.394 | |
NK-CR | 488 | 1.335 | |
NK-CV | 410 | 1.394 | |
D1-C | 656 | 1.25 | |
W1-HM | 553 | 0.9572 | |
Angle Parameters
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
NI-M1-NJ | 48.40 | 95.4086 | [Neves, 2013] |
NI-M1-NK | 45.74 | 92.4322 |
NI-M1-D1 | 86.0 | 82.0242 |
NI-M1-W1 | 56.35 | 166.1284 |
NJ-M1-NK | 37.87 | 139.1027 |
NJ-M1-D1 | 24.76 | 109.6451 |
NJ-M1-W1 | 46.58 | 90.8259 |
NK-M1-D1 | 23.465 | 111.182 |
NK-M1-W1 | 46.47 | 90.9222 |
D1-M1-W1 | 59.83 | 84.2125 |
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 | |
HM-W1-HM | 100.0 | 104.52 | |
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 | 2.05 | 2.04 ± 0.06 | [1.982; 2.103] |
M1-NI | 2.10 | 2.25 | 2.26 ± 0.07 | [2.192; 2.328] |
M1-NJ | 2.08 | 2.16 | 2.17 ± 0.06 | [2.108; 2.234] |
N1-NK | 2.09 | 2.17 | 2.19 ± 0.06 | [2.127; 2.246] |
M1-W1 | 2.02 | 2.24 | 2.14 ± 0.09 | [2.052; 2.232] |
Angle Parameters
ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
NI-M1-NJ | 96.8 | 95.4 | 96 ± 4 | [88.7; 102.7] |
NI-M1-NK | 91.5 | 92.4 | 93 ± 3 | [86.7; 100.2] |
NI-M1-D1 | 82.4 | 82.0 | 82 ± 3 | [77.2; 87.6] |
NI-M1-W1 | 166.1 | 166.1 | 164 ± 3 | [158.1; 169.9] |
NJ-M1-NK | 137.7 | 139.1 | 141 ± 4 | [132.2; 149.1] |
NJ-M1-D1 | 110.4 | 109.6 | 109 ± 5 | [98.8; 119.0] |
NJ-M1-W1 | 91.8 | 90.8 | 90 ± 4 | [82.4; 97.5] |
NK-M1-D1 | 106.4 | 111.2 | 110 ± 5 | [99.9; 120.0] |
NK-M1-W1 | 91.0 | 90.9 | 91 ± 4 | [83.9; 98.4] |
D1-M1-W1 | 83.9 | 84.2 | 82 ± 3 | [76.4; 88.0] |
Downloads
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)
LEAPRC file | .pdb, leaprc |
References