Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same. Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions.
TEST PROTEIN | |
Protein | Homoprotocatechuate 2,3-Dioxygenase |
PDB Code | 1F1U |
Crystallographic Resolution | 1.50 Å |
Organism | Arthrobacter globiformis |
[Vetting, 2004] |
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
M1-NI | 81.53 | 2.1862 | [Neves, 2013] |
M1-NJ | 78.93 | 2.1763 | |
M1-E1 | 90.87 | 2.0648 | |
M1-W1 | 43.45 | 2.2506 | |
M1-W2 | 45.59 | 2.2237 | |
NI-CR | 488.0 | 1.335 | |
NI-CV | 410.0 | 1.394 | |
NJ-CR | 488.0 | 1.335 | |
NJ-CV | 410.0 | 1.394 | |
E1-C | 656.0 | 1.25 | |
W1-HM | 553.0 | 0.9572 | |
W2-HM | 553.0 | 0.9572 |
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
NI-M1-NJ | 35.670 | 106.2009 | [Neves, 2013] |
NI-M1-E1 | 66.76 | 90.0029 | |
NI-M1-W1 | 27.91 | 89.1764 | |
NI-M1-W2 | 27.25 | 152.3584 | |
NJ-M1-E1 | 58.53 | 100.4401 | |
NJ-M1-W1 | 8.378 | 121.3184 | |
NJ-M1-W2 | 30.649 | 101.1859 | |
E1-M1-W1 | 8.825 | 136.6245 | |
E1-M1-W2 | 64.45 | 88.6732 | |
W1-M1-W2 | 41.88 | 73.2308 | |
M1-NI-CR | 46.273 | 126.3998 | |
M1-NI-CV | 46.273 | 126.3998 | |
M1-NJ-CR | 31.467 | 118.1041 | |
M1-NJ-CV | 31.467 | 118.1041 | |
M1-E1-C | 49.84 | 127.7223 | |
M1-W1-HM | 7.881 | 110.4316 | |
M1-W2-HM | 26.41 | 109.0419 | |
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 | |
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 | |
HM-W1-HM | 100.0 | 104.52 | |
HM-W2-HM | 100.0 | 104.52 |
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 | |
E1 | 1.6612 | 0.21 | |
W1 | 1.7683 | 0.152 | |
W2 | 1.7683 | 0.152 | |
HM | 0.6000 | 0.0157 | [Cornell, 1995] |
BOND | l0 crystal | l0 opt | ‹l›MD ± σ(l) | ‹l›MD ± 2σ(l) |
M1-NI | 2.21 | 2.19 | 2.15 ± 0.06 | [2.086; 2.205] |
M1-NJ | 2.03 | 2.18 | 2.15 ± 0.06 | [2.086; 2.212] |
M1-E1 | 2.11 | 2.06 | 2.08 ± 0.06 | [2.017; 2.133] |
M1-W1 | 2.38 | 2.25 | 2.18 ± 0.08 | [2.098; 2.266] |
M1-W2 | 2.18 | 2.22 | 2.17 ± 0.08 | [2.095; 2.255] |
ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
NI-M1-NJ | 95.6 | 106.2 | 110 ± 4 | [102.1; 117.0] |
NI-M1-E1 | 86.7 | 90.0 | 94 ± 3 | [86.9; 100.5] |
NI-M1-W1 | 91.4 | 89.2 | 80 ± 4 | [71.5; 89.3] |
NI-M1-W2 | 151.4 | 152.4 | 152 ± 4 | [143.9; 159.7] |
NJ-M1-E1 | 97.3 | 100.4 | 102 ± 4 | [93.6; 110.1] |
NJ-M1-W1 | 93.4 | 121.3 | 122 ± 7 | [108.5; 135.2] |
NJ-M1-W2 | 109.2 | 101.2 | 97 ± 4 | [88.6; 104.7] |
E1-M1-W1 | 169.3 | 136.6 | 135 ± 7 | [121.3; 148.7] |
E1-M1-W2 | 103.5 | 88.7 | 89 ± 4 | [82.0; 96.6] |
W1-M1-W2 | 73.6 | 73.2 | 78 ± 4 | [69.5; 86.8] |
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Homoprotocatechuate-2,3-dioxygenase’s PDB File (1F1U.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