Manganese(II) - DEE[SO2]
Crystal structures from Mandelate Racemase show that it is octameric.
The manganese(II) atom in this enzyme is bonded to the side chains of an aspartate, two glutamates and it is bidentate either to a sulfate ion or a S-altrolactate.
COORDINATION SPHERE |
|
Oxidation State: Mn(II)
Spin Multiplicity: 6 |
Structure chosen to parameterize
TEST PROTEIN |
Protein | Mandelate Racemase |
PDB Code | 2MNR |
Crystallographic Resolution | 1.90 Å |
Organism | Pseudomonas putida |
[Neidhart, 1991] |
Parameters Determined
Atom Types
ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
MN | M1 | 54.938 | |
OD2 | D1 | 15.9994 |
OE2 | E1 | 15.9994 |
OE1 | E2 | 15.9994 |
Bond Parameters
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
M1-D1 | 33.32 | 2.2509 | [Neves, 2013] |
M1-E1 | 47.15 | 2.1737 |
M1-E2 | 49.51 | 2.2008 |
M1-R1 | 41.81 | 2.1619 |
M1-R2 | 45.80 | 2.1526 |
D1-C | 656.0 | 1.25 | |
E1-C | 656.0 | 1.25 | |
E2-C | 656.0 | 1.25 | |
SO-R1 | 541.1 | 1.436 | |
SO-R2 | 541.1 | 1.436 | |
SO-O1 | 541.1 | 1.436 | |
SO-O2 | 541.1 | 1.436 | |
Angle Parameters
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
D1-M1-E1 | 45.46 | 92.3315 | [Neves, 2013] |
D1-M1-E2 | 25.03 | 123.0771 |
D1-M1-R1 | 13.27 | 96.5510 |
D1-M1-R2 | 4.321 | 121.0757 |
E1-M1-E2 | 40.08 | 86.7147 |
E1-M1-R1 | 19.90 | 160.9449 |
E1-M1-R2 | 33.00 | 93.3926 |
E2-M1-R1 | 8.95 | 102.2828 |
E2-M1-R2 | 4.405 | 115.7857 |
R1-M1-R2 | 291.6 | 67.5889 |
M1-D1-C | 16.912 | 165.3084 |
M1-E1-C | 22.912 | 145.6796 |
M1-E2-C | 15.527 | 135.3597 |
M1-R1-SO | 100.89 | 95.8499 |
M1-R2-SO | 100.89 | 95.8499 |
D1-C-CT | 70.0 | 117.0 | |
D1-C-O2 | 80.0 | 126.0 | |
E1-C-CT | 70.0 | 117.0 | |
E1-C-O2 | 80.0 | 126.0 | |
E2-C-CT | 70.0 | 117.0 | |
E2-C-O2 | 80.0 | 126.0 | |
R1-SO-O1 | 74.6 | 119.82 | |
R1-SO-O2 | 74.6 | 119.82 | |
R1-SO-R2 | 74.6 | 119.82 | |
R2-SO-O1 | 74.6 | 119.82 | |
R2-SO-O2 | 74.6 | 119.82 | |
O1-SO-O2 | 74.6 | 119.82 | |
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 | |
E1 | 1.6612 | 0.21 | |
E2 | 1.6612 | 0.21 | |
R1 | 1.6612 | 0.2100 | |
R2 | 1.6612 | 0.2100 | |
O1 | 1.6612 | 0.2100 | |
O2 | 1.6612 | 0.2100 | |
SO | 2.0000 | 0.2500 | |
Validation of Parameters from MD Simulations
Bond Parameters
BOND | l0 crystal | l0 opt | ‹l›MD ± σ(l) | ‹l›MD ± 2σ(l) |
M1-D1 | 2.03 | 2.25 | 2.41 ± 0.09 | [2.318; 2.506] |
M1-E1 | 2.15 | 2.17 | 2.28 ± 0.08 | [2.200; 2.359] |
M1-E2 | 1.95 | 2.20 | 2.27 ± 0.08 | [2.193; 2.347] |
M1-R2 | 3.54 | 2.16 | 2.18 ± 0.06 | [2.114; 2.238] |
M1-R2 | 2.20 | 2.15 | 2.17 ± 0.06 | [2.113; 2.232] |
Angle Parameters
ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
D1-M1-E1 | 87.7 | 92.3 | 89 ± 4 | [80.5; 97.0] |
D1-M1-E2 | 170.0 | 123.1 | 127 ± 5 | [117.4; 137.5] |
D1-M1-R1 | 85.6 | 96.6 | 91 ± 6 | [78.7; 103.7] |
D1-M1-R2 | 94.6 | 121.1 | 99 ± 8 | [82.2; 115.1] |
E1-M1-E2 | 88.0 | 86.7 | 87 ± 5 | [78.0; 96.9] |
E1-M1-R1 | 129.4 | 160.9 | 156 ± 4 | [147.4; 163.8] |
E1-M1-R2 | 92.1 | 93.4 | 92 ± 4 | [83.3; 100.7] |
E2-M1-R1 | 104.1 | 102.3 | 111 ± 6 | [97.8; 123.6] |
E2-M1-R2 | 94.6 | 115.8 | 133 ± 9 | [115.9; 150.5] |
R1-M1-R2 | 39.0 | 67.6 | 66 ± 1 | [63.1; 69.0] |
Downloads
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Mandelate Racemase’s PDB File (2MNR.pdb)
LEAPRC file | .pdb, leaprc |
References