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mm:parameters:manganese:hhe_d2

Table of Contents

Manganese(II) - HHE[D2]

During the crystallographic refinements of Pneumococcal Surface Antigen Adhesin A the metal ion was modeled as zinc, with attempts to model manganese(II) failed. The metal atom is expected to be tetrahedral bonded to two histidines, a glutamate and an aspartate, with angles ranging from 93o to 131o.

COORDINATION SPHERE

Oxidation State: Mn(II)
Spin Multiplicity: 6

Structure chosen to parameterize

TEST PROTEIN
Protein Pneumococcal Surface Antigen Adhesin A
PDB Code 1PSZ
Crystallographic Resolution 2.00 Å
Organism Streptococcus pneumoniae
[Lawrence, 1998]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938
OE1 E1 15.9994
NE2 NI 14.0067
NE2 NJ 14.0067

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-NI 70.46 2.1984 [Neves, 2013]
M1-NJ 74.91 2.1938
M1-D1 19.70 2.3425
M1-D2 44.64 2.1299
M1-E1 88.82 2.0723
NI-CR 488.0 1.335
NI-CV 410.0 1.394
NJ-CR 488.0 1.335
NJ-CV 410.0 1.394
D1-C 656.0 1.25
D2-C 656.0 1.25
E1-C 656.0 1.25
D1-C D2 80.0

Angle Parameters

ANGLE Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
NI-M1-NJ 34.37 107.8506 [Neves, 2013]
NI-M1-D1 18.529 105.7841
NI-M1-D2 17.70 103.3854
NI-M1-E1 30.53 99.0461
NJ-M1-D1 56.3 86.6415
NJ-M1-D2 26.03 138.8515
NJ-M1-E1 41.44 94.4727
D1-M1-D2 269.0 59.1658
D1-M1-E1 15.58 153.5286
D2-M1-E1 32.59 106.4565
M1-NI-CR 38.80 124.8643
M1-NI-CV 38.80 124.8643
M1-NJ-CR 44.269 126.5684
M1-NJ-CV 44.269 126.5684
M1-D1-C 52.84 89.6886
M1-D2-C 52.84 89.6886
M1-E1-C 22.930 129.8278
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
D1-C-CT 70.0 117.0
D1-C-O2 80.0 126.0
D2-C-CT 70.0 117.0
D2-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
NJ 1.824 0.17
D1 1.6612 0.21
D2 1.6612 0.21
E1 1.6612 0.21

Validation of Parameters from MD Simulations

Bond Parameters

BOND l0 crystal l0 opt ‹l›MD ± σ(l) ‹l›MD ± 2σ(l)
M1-NI 2.00 2.20 2.12 ± 0.07 [2.059; 2.190]
M1-NJ 2.01 2.19 2.17 ± 0.06 [2.105; 2.229]
M1-D1 2.03 2.34 2.24 ± 0.08 [2.160; 2.317]
M1-D2 2.84 2.13 2.19 ± 0.06 [2.128; 2.255]
M1-E1 2.05 2.07 2.09 ± 0.06 [2.028; 2.148]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
NI-M1-NJ 106.9 107.9 105 ± 5 [95.1; 114.6]
NI-M1-D1 109.9 105.8 102 ± 6 [90.7; 113.6]
NI-M1-D2 101.1 103.4 92 ± 5 [81.6; 103.0]
NI-M1-E1 122.5 99.0 95 ± 5 [85.2; 105.3]
NJ-M1-D1 82.8 86.6 85 ± 3 [78.8; 90.3]
NJ-M1-D2 131.3 138.9 142 ± 3 [135.5; 147.8]
NJ-M1-E1 103.8 94.5 98 ± 4 [89.8; 106.4]
D1-M1-D2 50.1 59.2 59 ± 1 [56.0; 61.8]
D1-M1-E1 121.3 153.5 160 ± 6 [148.6; 172.0]
D2-M1-E1 93.1 106.5 114 ± 5 [104.3; 122.8]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
Pneumococcal Surface Antigen Adhesin A’s PDB File (1PSZ.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/hhe_d2.txt · Last modified: 2013/10/03 18:57 by ruineves

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