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mm:parameters:manganese:hhdhwa

Table of Contents

Manganese(III) - HHDHWa

The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions.

COORDINATION SPHERE

Oxidation State: Mn(III)
Spin Multiplicity: 5

Structure chosen to parameterize

TEST PROTEIN
Protein Manganese Superoxide Dismutase
PDB Code 1N0J
Crystallographic Resolution 2.20 Å
Organism Homo sapiens
[Borgstahl, 1992]

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
HW HM 1.00794

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-NI 59.43 2.2457 [Neves, 2013]
M1-NJ 75.35 2.1589
M1-NK 80.07 2.168
M1-D1 81.62 2.0542
M1-W1 38.02 2.2351
NI-CR 488 1.335
NI-CV 410 1.394
NJ-CR 488 1.335
NJ-CV 410 1.394
NK-CR 488 1.335
NK-CV 410 1.394
D1-C 656 1.25
W1-HM 553 0.9572

Angle Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
NI-M1-NJ 48.40 95.4086 [Neves, 2013]
NI-M1-NK 45.74 92.4322
NI-M1-D1 86.0 82.0242
NI-M1-W1 56.35 166.1284
NJ-M1-NK 37.87 139.1027
NJ-M1-D1 24.76 109.6451
NJ-M1-W1 46.58 90.8259
NK-M1-D1 23.465 111.182
NK-M1-W1 46.47 90.9222
D1-M1-W1 59.83 84.2125
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 18.57 116.025
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
HM-W1-HM 100.0 104.52

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
W1 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 1.94 2.05 2.04 ± 0.06 [1.982; 2.103]
M1-NI 2.10 2.25 2.26 ± 0.07 [2.192; 2.328]
M1-NJ 2.08 2.16 2.17 ± 0.06 [2.108; 2.234]
N1-NK 2.09 2.17 2.19 ± 0.06 [2.127; 2.246]
M1-W1 2.02 2.24 2.14 ± 0.09 [2.052; 2.232]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
NI-M1-NJ 96.8 95.4 96 ± 4 [88.7; 102.7]
NI-M1-NK 91.5 92.4 93 ± 3 [86.7; 100.2]
NI-M1-D1 82.4 82.0 82 ± 3 [77.2; 87.6]
NI-M1-W1 166.1 166.1 164 ± 3 [158.1; 169.9]
NJ-M1-NK 137.7 139.1 141 ± 4 [132.2; 149.1]
NJ-M1-D1 110.4 109.6 109 ± 5 [98.8; 119.0]
NJ-M1-W1 91.8 90.8 90 ± 4 [82.4; 97.5]
NK-M1-D1 106.4 111.2 110 ± 5 [99.9; 120.0]
NK-M1-W1 91.0 90.9 91 ± 4 [83.9; 98.4]
D1-M1-W1 83.9 84.2 82 ± 3 [76.4; 88.0]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Manganese Superoxide Dismutase’s PDB File (1N0J.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/hhdhwa.txt · Last modified: 2013/10/03 18:57 by ruineves

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