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mm:parameters:manganese:hhdh_ho_o

Table of Contents

Manganese(III) - HHDH[HO]O

Electronic spectroscopy studies on the resting and enzyme-substrates states of Manganese Superoxide Dismutase support the hypothesis of a side-on peroxo complex with the superoxide anion. The superoxide anion coordinates to the manganese ion between two histidines. The spin multiplicity of the coordination sphere has been reported as a quartet, due to an antiferromagnetic coupling between the superoxide and manganese species.

COORDINATION SPHERE

Oxidation State: Mn(III)
Spin Multiplicity: 4

Structure chosen to parameterize

TEST PROTEIN
Protein Manganese Superoxide Dismutase
PDB Code 1MNG
Crystallographic Resolution 1.80 Å
Organism Thermus thermophilus
[Lah, 1995]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OD1 D1 15.9994
NE2 NI 14.0067
NE2 NJ 14.0067
NE2 NK 14.0067
OW W1 15.9994
HO HM 1.00794

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-NI 82.11 2.1879 [Neves, 2013]
M1-NJ 123.46 2.0161
M1-NK 138.95 2.0175
M1-D1 111.54 2.0630
M1-R1 96.51 1.9361
M1-W1 227.9 1.7993
NI-CR 488.0 1.335
NI-CV 410.0 1.394
NJ-CR 488.0 1.335
NJ-CV 410.0 1.394
NK-CR 488.0 1.335
NK-CV 410.0 1.394
D1-C 656.0 1.25
R1-O 384.3 1.430
W1-HM 553.0 0.9572

Angle Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
NI-M1-NJ 93.41 91.0663 [Neves, 2013]
NI-M1-NK 96.11 86.5034
NI-M1-D1 118.5 82.0566
NI-M1-W1 77.66 176.5931
NI-M1-R1 83.7 84.2181
NJ-M1-NK 97.22 172.0561
NJ-M1-D1 74.40 93.5533
NJ-M1-W1 96.31 90.3808
NJ-M1-R1 95.80 86.9561
NK-M1-D1 75.579 93.5990
NK-M1-W1 92.14 92.4642
NK-M1-R1 99.09 85.2759
D1-M1-W1 83.35 94.7758
D1-M1-R1 70.04 166.2720
W1-M1-R1 61.59 98.9401
M1-NI-CR 53.671 126.4370
M1-NI-CV 53.671 126.4370
M1-NJ-CR 40.495 123.3813
M1-NJ-CV 40.495 123.3813
M1-NK-CR 31.220 112.3780
M1-NK-CV 31.220 112.3780
M1-D1-C 47.094 135.5495
M1-W1-HM 36.67 106.2284
M1-R1-O 41.32 118.4913
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
NK-CR-NA 70.0 120.0
NK-CR-H5 50.0 120.0
NK-CV-CC 70.0 120.0
CV-NK-CR 70.0 117.0
H4-CV-NK 50.0 120.0
D1-C-CT 70.0 117.0
D1-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
NJ 1.824 0.17
NK 1.824 0.17
D1 1.6612 0.21
R1 1.6612 0.2100
O 1.6612 0.2100
W1 1.7210 0.2104
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 1.80 2.06 2.09 ± 0.05 [2.038; 2.142]
M1-NI 2.15 2.19 2.20 ± 0.06 [2.141; 2.254]
M1-NJ 2.12 2.02 2.02 ± 0.05 [1.969; 2.063]
M1-NK 2.16 2.02 2.05 ± 0.05 [2.003; 2.094]
M1-W1 2.07 1.80 1.79 ± 0.04 [1.752; 1.825]
M1-R1 2.68 1.94 1.93 ± 0.06 [1.872; 1.984]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
NI-M1-NJ 92.4 91.1 92 ± 2 [86.9; 96.6]
NI-M1-NK 90.3 86.5 89 ± 2 [84.3; 93.7]
NI-M1-D1 89.1 82.1 82 ± 2 [77.6; 87.0]
NI-M1-W1 175.5 176.6 176 ± 2 [172.3; 179.7]
NI-M1-R1 97.6 84.2 86 ± 2 [80.8; 90.8]
NJ-M1-NK 130.8 172.1 170 ± 2 [165.7; 174.9]
NJ-M1-D1 110.1 93.6 93 ± 3 [87.0; 98.6]
NJ-M1-W1 90.0 90.4 87 ± 2 [82.6; 92.4]
NJ-M1-R1 66.4 87.0 85 ± 3 [80.4; 90.5]
NK-M1-D1 119.2 93.6 97 ± 3 [90.9; 102.1]
NK-M1-W1 91.0 92.5 92 ± 3 [86.9; 97.1]
NK-M1-R1 64.6 85.3 85 ± 2 [80.5; 90.2]
D1-M1-W1 86.5 94.8 96 ± 3 [90.5; 101.8]
D1-M1-R1 172.4 166.3 167 ± 3 [162.3; 172.5]
W1-M1-R1 86.8 98.9 96 ± 3 [90.1; 101.3]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Manganese Superoxide Dismutase’s PDB File (1MNG.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/hhdh_ho_o.txt · Last modified: 2013/10/03 18:56 by ruineves

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