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mm:parameters:manganese:denwawawa

Table of Contents

Manganese(II) - DENWaWaWa

D-Glutarate Dehydratase is analogous to mandelate racemase and enolase. The manganese coordination sphere has a manganese(II) atom bonded to a glutamate, an aspartate and an asparagine from the same subunit.

COORDINATION SPHERE

Oxidation State: Mn(II)
Spin Multiplicity: 6

Structure chosen to parameterize

TEST PROTEIN
Protein D-Glucarate Dehydratase
PDB Code 3NXL
Crystallographic Resolution 1.89 Å
Organism Burkholderia sp. 383
[Fedorov, 2010]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OD2 D1 15.9994
OE2 E1 15.9994
OD1 NW 15.9994
OW W1 15.9994
OW W2 15.9994
OW W3 15.9994
HW HM 1.00794

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-NW 35.45 2.2737 [Neves, 2013]
M1-D1 67.93 2.1478
M1-E1 92.09 2.0644
M1-W1 50.25 2.2190
M1-W2 33.63 2.3313
M1-W3 41.73 2.2662
NW-C 570.0 1.229
D1-C 656.0 1.25
E1-C 656.0 1.25
W1-HM 553.0 0.9572
W2-HM 553.0 0.9572
W3-HM 553.0 0.9572

Angle Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
NW-M1-D1 50.31 168.8916 [Neves, 2013]
NW-M1-E1 36.14 92.7969
NW-M1-W1 38.04 100.6537
NW-M1-W2 30.57 95.9566
NW-M1-W3 33.91 78.7883
D1-M1-E1 35.463 100.5525
D1-M1-W1 64.49 85.2832
D1-M1-W2 48.3 73.9644
D1-M1-W3 32.46 94.4909
E1-M1-W1 27.16 94.9567
E1-M1-W2 16.85 166.1705
E1-M1-W3 44.90 89.8914
W1-M1-W2 13.16 97.1854
W1-M1-W3 26.160 175.1204
W2-M1-W3 23.22 78.0892
M1-NW-C 10.785 144.0557
M1-D1-C 47.557 125.7501
M1-E1-C 36.476 122.3574
M1-W1-HM 24.67 106.0283
M1-W2-HM 9.470 89.9559
M1-W3-HM 23.78 97.5290
HM-W1-HM 100.0 104.52
HM-W2-HM 100.0 104.52
HM-W3-HM 100.0 104.52
NW-C-CT 80.0 120.40
NW-C-N 80.0 122.90
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

Van der Waals Parameters

ATOM TYPE Ri / Å εi / kcal mol-1 REFERENCE
M1 1.4544 0.03 [Babu, 2006]
NW 1.6612 0.21
D1 1.6612 0.21
E1 1.6612 0.21
W1 1.7683 0.152
W2 1.7683 0.152
W3 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 2.28 2.15 2.16 ± 0.06 [2.095; 2.224]
M1-E1 2.45 2.06 2.13 ± 0.06 [2.066; 2.186]
M1-NW 2.40 2.27 2.29 ± 0.09 [2.195; 2.383]
M1-W1 2.26 2.22 2.21 ± 0.08 [2.127; 2.290]
M1-W2 2.51 2.33 2.3 ± 0.1 [2.222; 2.416]
M1-W3 2.47 2.27 2.25 ± 0.09 [2.165; 2.341]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
D1-M1-E1 100.8 100.6 98 ± 4 [89.3; 106.1]
D1-M1-NW 154.1 168.9 165 ± 3 [158.6; 172.1]
D1-M1-W1 84.5 85.3 85 ± 4 [78.1; 92.1]
D1-M1-W2 93.4 73.9 70 ± 4 [61.8; 77.6]
D1-M1-W3 80.9 94.5 91 ± 4 [82.4; 100.0]
E1-M1-NW 66.7 88.4 94 ± 4 [85.9; 102.0]
E1-M1-W1 113.1 94.9 96 ± 5 [86.4; 104.6]
E1-M1-W2 160.1 166.2 157 ± 5 [148.0; 166.1]
E1-M1-W3 95.6 89.9 88 ± 5 [78.7; 97.4]
NW-M1-W1 95.7 100.7 101 ± 4 [92.7; 109.3]
NW-M1-W2 86.6 95.9 97 ± 4 [88.2; 105.4]
NW-M1-W3 98.7 78.8 82 ± 4 [73.2; 90.6]
W1-M1-W2 107.8 97.2 101 ± 5 [91.3; 111.6]
W1-M1-W3 149.8 175.1 172 ± 4 [164.7; 179.6]
W2-M1-W3 69.2 78.1 74 ± 6 [62.6; 85.8]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
D-Glutarate Dehydratase’s PDB File (3NXL.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/denwawawa.txt · Last modified: 2013/10/03 18:53 by ruineves

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