Manganese(II) - ED[PY2]WaWa
In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate.
Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand.
A water molecule is referred as participating in the octahedral coordination of manganese(II).
COORDINATION SPHERE |
|
Oxidation State: Mn(II)
Spin Multiplicity: 6 |
Structure chosen to parameterize
TEST PROTEIN |
Protein | Pyruvate Kinase |
PDB Code | 2G50 |
Crystallographic Resolution | 1.65 Å |
Organism | Oryctolagus cuniculus |
[Williams, 2006] |
Parameters Determined
Atom Types
ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
MN | M1 | 54.938 | |
OD2 | D1 | 15.9994 |
OE1 | E1 | 15.9994 |
OW | W1 | 15.9994 |
OW | W2 | 15.9994 |
HW | HM | 1.00794 |
Bond Parameters
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
M1-D1 | 71.90 | 2.0926 | [Neves, 2013] |
M1-E1 | 68.77 | 2.1399 |
M1-R1 | 55.39 | 2.1382 |
M1-R2 | 16.78 | 2.4332 |
M1-W1 | 24.75 | 2.3873 |
M1-W2 | 50.08 | 2.2004 |
D1-C | 656.0 | 1.25 | |
E1-C | 656.0 | 1.25 | |
W1-HM | 553.0 | 0.9572 | |
W2-HM | 553.0 | 0.9572 | |
c-R2 | 648.0 | 1.214 | |
c-R1 | 648.0 | 1.214 | |
Angle Parameters
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
D1-M1-E1 | 38.27 | 96.6209 | [Neves, 2013] |
D1-M1-R1 | 23.41 | 104.8054 |
D1-M1-R2 | 12.445 | 169.3708 |
D1-M1-W1 | 69.3 | 72.8299 |
D1-M1-W2 | 26.19 | 103.5245 |
E1-M1-R1 | 29.696 | 97.7449 |
E1-M1-R2 | 13.94 | 93.9317 |
E1-M1-W1 | 25.05 | 168.0717 |
E1-M1-W2 | 52.2 | 89.0644 |
R1-M1-R2 | 128.3 | 80.3387 |
R1-M1-W1 | 20.47 | 80.0896 |
R1-M1-W2 | 18.05 | 149.8517 |
R2-M1-W1 | 13.736 | 96.5418 |
R2-M1-W2 | 27.09 | 77.9339 |
W1-M1-W2 | 15.008 | 98.6963 |
M1-D1-C | 14.829 | 125.0463 |
M1-E1-C | 42.056 | 122.8295 |
M1-R1-c | 47.47 | 122.0775 |
M1-R2-c | 57.66 | 110.2798 |
M1-W1-HM | 12.10 | 86.3993 |
M1-W2-HM | 28.96 | 88.1336 |
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 | |
c3-c-R2 | 68.0 | 123.11 | |
R1-c-c | 66.8 | 122.34 | |
o-c-R1 | 79.1 | 127.33 | |
c-c-R2 | 66.8 | 122.34 | |
Van der Waals Parameters
ATOM TYPE | Ri / Å | εi / kcal mol-1 | REFERENCE |
M1 | 1.4544 | 0.03 | [Babu, 2006] |
D1 | 1.6612 | 0.21 | |
E1 | 1.6612 | 0.21 | |
R1 | 1.6612 | 0.2100 | |
R2 | 1.6612 | 0.2100 | |
W1 | 1.7683 | 0.152 | |
W2 | 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 | 1.97 | 2.09 | 2.16 ± 0.06 | [2.095; 2.225] |
M1-E1 | 1.96 | 2.14 | 2.22 ± 0.06 | [2.153; 2.281] |
M1-R1 | 1.98 | 2.14 | 2.13 ± 0.07 | [2.059; 2.192] |
M1-R2 | 1.95 | 2.43 | 2.4 ± 0.1 | [2.276; 2.473] |
M1-W1 | 2.29 | 2.39 | 2.4 ± 0.1 | [2.289; 2.537] |
M1-W2 | 2.26 | 2.20 | 2.18 ± 0.08 | [2.100; 2.258] |
Angle Parameters
ANGLE | θ0 crystal | θ0 QM | ‹θ›MD ± σ(θ) | ‹θ›MD ± 2σ(θ) |
D1-M1-E1 | 97.0 | 96.6 | 99 ± 5 | [89.0; 108.1] |
D1-M1-R1 | 90.8 | 104.8 | 103 ± 5 | [93.1; 112.4] |
D1-M1-R2 | 153.6 | 169.4 | 170 ± 5 | [159.4; 180.1] |
D1-M1-W1 | 78.1 | 72.8 | 75 ± 4 | [67.8; 82.2] |
D1-M1-W2 | 113.2 | 103.5 | 110 ± 5 | [99.5; 120.6] |
E1-M1-R1 | 91.7 | 97.7 | 101 ± 5 | [91.1; 110.3] |
E1-M1-R2 | 105.0 | 93.9 | 75 ± 5 | [64.3; 86.1] |
E1-M1-W1 | 163.9 | 168.1 | 168 ± 4 | [159.5; 176.5] |
E1-M1-W2 | 84.8 | 89.1 | 80 ± 4 | [71.4; 87.7] |
R1-M1-R2 | 74.4 | 80.3 | 75 ± 2 | [70.9; 79.1] |
R1-M1-W1 | 103.6 | 80.1 | 79 ± 7 | [63.7; 93.7] |
R1-M1-W2 | 156.0 | 149.9 | 146 ± 5 | [136.7; 155.4] |
R2-M1-W1 | 84.2 | 96.5 | 111 ± 7 | [97.0; 124.2] |
R2-M1-W2 | 83.5 | 77.9 | 73 ± 5 | [63.3; 82.5] |
W1-M1-W2 | 83.1 | 98.7 | 105 ± 10 | [85.6; 123.9] |
Downloads
Parameter File | .frcmod |
Coordination Sphere Charges | .off |
Pyruvate Kinase’s PDB File (2G50.pdb)
LEAPRC file | .pdb, leaprc |
References