PortoBioComp

User Tools

Site Tools

Trace:

Sidebar

Home

Research Data

Software

Contact




www2.clustrmaps.com_stats_maps-no_clusters_www2.fc.up.pt-portobiocomp-database-thumb.jpg

mm:parameters:manganese:hhdhwa_example_page

This is an old revision of the document!

Table of Contents

Manganese(III) - HHDHWa

Coordination Sphere Oxidation State: Mn(III)
Spin Multiplicity: 5
IMAGE1 IMAGE2 1)

Structure chosen to parameterize

TEST PROTEIN
Protein PROTEIN NAME
PDB Code PDB CODE
Crystallographic Resolution RESOLUTION
Organism ORGANISM
[1ST AUTHOR, PUBL YEAR]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938 IMAGE
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 [Cornel, 1995]

Validation of Parameters from MD Simulations

Bond Parameters

BOND l0 crystal l0 opt <l>MD ± sigma(l) <l>MD ± 2sigma(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
ENZYME’s PDB File (PDB_CODE.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

1) The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.
mm/parameters/manganese/hhdhwa_example_page.1373527426.txt.gz · Last modified: 2013/07/11 08:23 by ruineves

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
CC Attribution-Share Alike 3.0 Unported Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki