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mm:parameters:manganese:ed_py2_wawa

Table of Contents

Manganese(II) - ED[PY2]WaWa

In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate. Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand. A water molecule is referred as participating in the octahedral coordination of manganese(II).

COORDINATION SPHERE

Oxidation State: Mn(II)
Spin Multiplicity: 6

Structure chosen to parameterize

TEST PROTEIN
Protein Pyruvate Kinase
PDB Code 2G50
Crystallographic Resolution 1.65 Å
Organism Oryctolagus cuniculus
[Williams, 2006]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OD2 D1 15.9994
OE1 E1 15.9994
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-D1 71.90 2.0926 [Neves, 2013]
M1-E1 68.77 2.1399
M1-R1 55.39 2.1382
M1-R2 16.78 2.4332
M1-W1 24.75 2.3873
M1-W2 50.08 2.2004
D1-C 656.0 1.25
E1-C 656.0 1.25
W1-HM 553.0 0.9572
W2-HM 553.0 0.9572
c-R2 648.0 1.214
c-R1 648.0 1.214

Angle Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
D1-M1-E1 38.27 96.6209 [Neves, 2013]
D1-M1-R1 23.41 104.8054
D1-M1-R2 12.445 169.3708
D1-M1-W1 69.3 72.8299
D1-M1-W2 26.19 103.5245
E1-M1-R1 29.696 97.7449
E1-M1-R2 13.94 93.9317
E1-M1-W1 25.05 168.0717
E1-M1-W2 52.2 89.0644
R1-M1-R2 128.3 80.3387
R1-M1-W1 20.47 80.0896
R1-M1-W2 18.05 149.8517
R2-M1-W1 13.736 96.5418
R2-M1-W2 27.09 77.9339
W1-M1-W2 15.008 98.6963
M1-D1-C 14.829 125.0463
M1-E1-C 42.056 122.8295
M1-R1-c 47.47 122.0775
M1-R2-c 57.66 110.2798
M1-W1-HM 12.10 86.3993
M1-W2-HM 28.96 88.1336
HM-W1-HM 100.0 104.52
HM-W2-HM 100.0 104.52
HM-W3-HM 100.0 104.52
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
c3-c-R2 68.0 123.11
R1-c-c 66.8 122.34
o-c-R1 79.1 127.33
c-c-R2 66.8 122.34

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
R1 1.6612 0.2100
R2 1.6612 0.2100
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-D1 1.97 2.09 2.16 ± 0.06 [2.095; 2.225]
M1-E1 1.96 2.14 2.22 ± 0.06 [2.153; 2.281]
M1-R1 1.98 2.14 2.13 ± 0.07 [2.059; 2.192]
M1-R2 1.95 2.43 2.4 ± 0.1 [2.276; 2.473]
M1-W1 2.29 2.39 2.4 ± 0.1 [2.289; 2.537]
M1-W2 2.26 2.20 2.18 ± 0.08 [2.100; 2.258]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
D1-M1-E1 97.0 96.6 99 ± 5 [89.0; 108.1]
D1-M1-R1 90.8 104.8 103 ± 5 [93.1; 112.4]
D1-M1-R2 153.6 169.4 170 ± 5 [159.4; 180.1]
D1-M1-W1 78.1 72.8 75 ± 4 [67.8; 82.2]
D1-M1-W2 113.2 103.5 110 ± 5 [99.5; 120.6]
E1-M1-R1 91.7 97.7 101 ± 5 [91.1; 110.3]
E1-M1-R2 105.0 93.9 75 ± 5 [64.3; 86.1]
E1-M1-W1 163.9 168.1 168 ± 4 [159.5; 176.5]
E1-M1-W2 84.8 89.1 80 ± 4 [71.4; 87.7]
R1-M1-R2 74.4 80.3 75 ± 2 [70.9; 79.1]
R1-M1-W1 103.6 80.1 79 ± 7 [63.7; 93.7]
R1-M1-W2 156.0 149.9 146 ± 5 [136.7; 155.4]
R2-M1-W1 84.2 96.5 111 ± 7 [97.0; 124.2]
R2-M1-W2 83.5 77.9 73 ± 5 [63.3; 82.5]
W1-M1-W2 83.1 98.7 105 ± 10 [85.6; 123.9]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Pyruvate Kinase’s PDB File (2G50.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/ed_py2_wawa.txt · Last modified: 2013/10/03 18:55 by ruineves

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