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mm:parameters:manganese:ddwawawawa

Table of Contents

Manganese (II) - DDWaWaWa

The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules.

COORDINATION SPHERE

Oxidation state: Mn(II)
Spin multiplicity: 6

Structure chosen to parameterize

TEST PROTEIN
Protein Integrase
PDB Code 1A5V
Crystallographic Resolution 1.90 Å
Organism Rous Sarcoma Virus
[Lubkowski, 1998]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OD1 D1 15.9994
OD2 D2 15.9994
OW W1 15.9994
OW W2 15.9994
OW W3 15.9994
OW W4 15.9994
HW HM 1.00794

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-D1 86.69 2.0912 [Neves, 2013]
M1-D2 73.44 2.1278
M1-W1 41.1 2.2458
M1-W2 58.63 2.1786
M1-W3 34.55 2.3171
M1-W4 25.05 2.3835
D1-C 656 1.25
D2-C 656 1.25
W1-HM 553 0.9572
W2-HM 553 0.9572
W3-HM 553 0.9572
W4-HM 553 0.9572

Angles Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
D1-M1-D2 38.782 108.3864 [Neves, 2013]
D1-M1-W1 52.48 86.0095
D1-M1-W2 40.523 93.9632
D1-M1-W3 14.18 90.4522
D1-M1-W4 22.791 173.2496
D2-M1-W1 26.46 97.5246
D2-M1-W2 55.17 91.2115
D2-M1-W3 14.57 157.0825
D2-M1-W4 49.51 85.9497
W1-M1-W2 22.81 165.2888
W1-M1-W3 21.4 75.017
W1-M1-W4 30.33 100.0581
W2-M1-W3 16.61 92.3995
W2-M1-W4 21.06 84.0447
W3-M1-W4 16.8 84.2736
M1-D1-C 52.071 128.7239
M1-D2-C 46.53 125.6353
M1-W1-HM 24.91 107.2734
M1-W2-HM 24.17 105.0104
M1-W3-HM 7.36 101.1843
M1-W4-HM 7.764 101.9263
HM-W1-HM 100 104.52
HM-W2-HM 100 104.52
HM-W3-HM 100 104.52
HM-W4-HM 100 104.52
D1-C-CT 70 117
D1-C-O2 80 126
D2-C-CT 70 117
D2-C-O2 80 126

Van der Waals Parameters

ATOM TYPE Ri / Å εi / kcal mol-1 REFERENCE
M1 1.4544 0.03 [Babu, 2006]
HM 0.6 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 2.22 2.09 2.25 ± 0.06 [2.13; 2.37]
M1-D2 2.23 2.13 2.18 ± 0.07 [2.04; 2.31]
M1-W1 2.10 2.25 2.23 ± 0.09 [2.05; 2.40]
M1-W2 2.18 2.18 2.16 ± 0.08 [2.01; 2.31]
M1-W3 2.17 2.32 2.3 ± 0.1 [2.1; 2.5]
M1-W4 2.51 2.38 2.4 ± 0.1 [2.1; 2.6]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
D1-M1-D2 90.6 108.4 105 ± 5 [95; 116]
D1-M1-W1 87.3 86.0 85 ± 4 [76; 94]
D1-M1-W2 94.2 94.0 104 ± 6 [92; 117]
D1-M1-W3 84.5 90.5 99 ± 7 [85; 114]
D1-M1-W4 171.9 173.2 171 ± 4 [162; 179]
D2-M1-W1 89.9 97.5 96 ± 7 [83; 109]
D2-M1-W2 90.2 91.2 88 ± 5 [79; 98]
D2-M1-W3 179.0 157.1 149 ± 7 [136; 163]
D2-M1-W4 97.4 85.9 80 ± 5 [71; 89]
W1-M1-W2 178.6 165.3 164 ± 5 [153; 175]
W1-M1-W3 90.9 75.0 70 ± 7 [56; 84]
W1-M1-W4 94.2 100.1 94 ± 6 [83; 106]
W2-M1-W3 89.1 92.4 101 ± 10 [82; 120]
W2-M1-W4 84.4 84.0 75 ± 9 [57; 93]
W3-M1-W4 87.5 84.3 76 ± 7 [62; 89]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Integrase’s PDB File (1A5V.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/ddwawawawa.txt · Last modified: 2013/10/03 18:46 by ruineves

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