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mm:parameters:manganese:hhewawa

Table of Contents

Manganese(II) - HHEWaWa

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.

COORDINATION SPHERE

Oxidation State: Mn(II)
Spin Multiplicity: 5

Structure chosen to parameterize

TEST PROTEIN
Protein Homoprotocatechuate 2,3-Dioxygenase
PDB Code 1F1U
Crystallographic Resolution 1.50 Å
Organism Arthrobacter globiformis
[Vetting, 2004]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OE1 E1 15.9994
NE2 NI 14.0067
NE2 NJ 14.0067
OW W1 15.9994
OW W2 15.9994
HW HM 1.00794

Bond Parameters

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 Parameters

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

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
E1 1.6612 0.21
W1 1.7683 0.152
W2 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-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 Parameters

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]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Homoprotocatechuate-2,3-dioxygenase’s PDB File (1F1U.pdb)
LEAPRC file 		.pdb, leaprc

References

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

mm/parameters/manganese/hhewawa.txt · Last modified: 2013/10/03 18:58 by ruineves

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