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mm:parameters:manganese:hdewawawa

Table of Contents

Manganese(II) - HDEWaWaWa

In Citochrome c Oxidase the manganese ion has a nonredox role. Manganese(II) is bonded to residues from different subunits: a glutamate, an aspartate and histidine ligands and possibly one to three water molecules. The glutamate ligand is also coordinated to a copper atom and the histidine is hydrogen bonded to a heme a3 propionate.

COORDINATION SPHERE

Oxidation State: Mn(II)
Spin Multiplicity: 6

Structure chosen to parameterize

TEST PROTEIN
Protein Citochrome c Oxidase
PDB Code 3HB3
Crystallographic Resolution 2.25 Å
Organism Paracoccus denitrificans
[Koepke, 2009]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OD1 D1 15.9994
OE1 E1 15.9994
NE2 NI 14.0067
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-NI 63.17 2.242 [Neves, 2013]
M1-D1 77.67 2.141
M1-E1 68.41 2.147
M1-W1 31.5 2.3664
M1-W2 31.4 2.325
M1-W3 64.37 2.1601
NI-CR 488.0 1.335
NI-CV 410.0 1.394
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
NI-M1-D1 55.1 90.0153 [Neves, 2013]
NI-M1-E1 41.458 159.9206
NI-M1-W1 24.19 94.3889
NI-M1-W2 31.3 89.0778
NI-M1-W3 34.86 98.8181
D1-M1-E1 50.26 103.9094
D1-M1-W1 42.6 73.0866
D1-M1-W2 12.075 162.4957
D1-M1-W3 56.22 90.7127
E1-M1-W1 37.25 76.4231
E1-M1-W2 54.4 73.2795
E1-M1-W3 37.25 95.45
W1-M1-W2 12.36 89.5541
W1-M1-W3 32.47 159.1053
W2-M1-W3 11.975 106.6994
M1-NI-CR 34.139 123.4259
M1-NI-CV 34.139 123.4259
M1-D1-C 46.237 123.2712
M1-E1-C 44.53 121.9953
M1-W1-HM 8.322 99.514
M1-W2-HM 9.174 99.3627
M1-W3-HM 33.538 97.246
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
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

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
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-NI 1.98 2.24 2.17 ± 0.06 [2.111; 2.238]
M1-D1 2.17 2.14 2.18 ± 0.06 [2.117; 2.245]
M1-E1 2.19 2.15 2.18 ± 0.07 [2.112; 2.245]
M1-W1 2.20 2.37 2.3 ± 0.1 [2.189; 2.383]
M1-W2 2.14 2.33 2.3 ± 0.1 [2.170; 2.371]
M1-W3 2.11 2.16 2.14 ± 0.07 [2.070; 2.215]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
NI-M1-D1 74.7 90.0 84 ± 4 [76.5; 90.8]
NI-M1-E1 171.1 159.9 159 ± 3 [151.8; 165.4]
NI-M1-W1 87.0 94.4 88 ± 4 [81.0; 95.7]
NI-M1-W2 99.9 89.1 82 ± 4 [73.3; 90.8]
NI-M1-W3 98.0 98.8 96 ± 5 [86.6; 105.4]
D1-M1-E1 113.6 103.9 100 ± 4 [92.0; 107.2]
D1-M1-W1 72.3 73.1 76 ± 4 [68.2; 83.2]
D1-M1-W2 166.7 162.5 135 ± 6 [123.2; 146.7]
D1-M1-W3 86.4 90.7 84 ± 4 [76.2; 91.5]
E1-M1-W1 86.4 76.4 73 ± 4 [64.6; 81.0]
E1-M1-W2 71.3 73.3 81 ± 4 [73.5; 89.0]
E1-M1-W3 79.7 95.5 105 ± 5 [95.1; 114.4]
W1-M1-W2 120.1 89.6 62 ± 6 [50.6; 72.9]
W1-M1-W3 156.1 159.1 158 ± 4 [149.5; 166.0]
W2-M1-W3 82.2 106.7 139 ± 6 [127.5; 151.4]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Citochrome c Oxidase’s PDB File (3HB3.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/hdewawawa.txt · Last modified: 2013/10/03 18:54 by ruineves

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