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.
TEST PROTEIN | |
Protein | Mandelate Racemase |
PDB Code | 2MNR |
Crystallographic Resolution | 1.90 Å |
Organism | Pseudomonas putida |
[Neidhart, 1991] |
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 | 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 |
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 |
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 | 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] |
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Mandelate Racemase’s PDB File (2MNR.pdb) LEAPRC file | .pdb, leaprc |
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