The metal center of Cu, Zn Superoxide Dismutase is hereby presented, in which the zinc atom is bonded to 3 histidines, and 1 aspartate (monodentate) and the copper atom to 4 histidines. Validation for this metal centre in the protein environment is additionally provided.
TEST PROTEIN | |
Protein | Cu, Zn Superoxide Dismutase |
PDB Code | 1CBJ |
Crystallographic Resolution | 1.65 Å |
Organism | Bos taurus |
[Hough, 1999] |
BOND | Kl / kcal mol-1 Å-2 | l / Å | REFERENCE |
ZN-NB | 96.7 | 2.046 | [Branco, 2006] |
ZN-OS | 92.0 | 1.949 | |
CU-NB | 101.1 | 2.022 |
ANGLE | Kθ / kcal mol-1 rad-2 | θ / deg | REFERENCE |
NB-CU-NB | 24.6 | 147.19 | [Branco, 2006] |
NB-ZN-NB | 44.0 | 113.53 | |
NB-ZN-OS | 21.7 | 111.75 |
The validation considering the 1CBJ SOD structure was conducted. The two chains (A and B) were considered in the validation and the brackets denotes the decoordinated residue upon reduction.
BOND / Å | l0 crystal 1CBJ:A | l0 crystal 1CBJ:B | ‹l›MD ± 0.06 A | ‹l›MD ± 0.06 B |
CU-NB(H44) | 2.07 | 2.00 | 2.03 | 2.04 |
CU-NB(H46) | 2.00 | 2.17 | 2.08 | 2.07 |
CU-NB(H61) | (3.19) | 2.20 | 2.03 | 2.03 |
CU-NB(H118) | 2.03 | 2.19 | 2.03 | 2.03 |
ZN-NB(H61) | 1.97 | 2.02 | 2.03 | 2.03 |
ZN-NB(H69) | 2.03 | 2.07 | 2.05 | 2.04 |
ZN-NB(H78) | 2.07 | 1.75 | 2.06 | 2.05 |
ZN-OS(D81) | 1.62 | 1.84 | 1.90 | 1.92 |
ANGLE | θ0 crystal 1CBJ:A | θ0 crystal 1CBJ:B | ‹θ›MD ± 5 A | ‹θ›MD ± 5 B |
H44-CU-H46 | 140.9 | 138.2 | 133.0 | 133.8 |
H44-CU-H61 | 72.5 | 86.8 | 96.6 | 97.3 |
H44-CU-H118 | 101.1 | 93.0 | 98.7 | 98.0 |
H46-CU-H61 | 92.5 | 97.6 | 101.2 | 101.5 |
H46-CU-H118 | 117.6 | 99.7 | 107.5 | 106.6 |
H61-CU-H118 | 118.5 | 153.9 | 121.6 | 121.4 |
H61-ZN-H69 | 108.1 | 110.0 | 106.5 | 105.1 |
H61-ZN-H78 | 110.0 | 110.2 | 106.7 | 106.3 |
H61-ZN-A81 | 104.6 | 103.9 | 111.4 | 112.4 |
H69-ZN-H78 | 118.9 | 117.3 | 112.8 | 112.9 |
H69-ZN-D81 | 98.0 | 99.7 | 105.3 | 103.8 |
H78-ZN-D81 | 115.9 | 114.5 | 113.4 | 115.5 |
Branco, J.F.B.; Fernandes, P.A.; Ramos, M.J.. Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase . J. Phys. Chem. B, 2006, 110, 16754-16762