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mm:parameters:copper_zinc:hhh_cu_h_zn_dhh
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Copper(II)/Zinc(II) - HHH[Cu]H[Zn]HHD
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.
| COORDINATION SPHERE | |
 | Oxidation state: Cu(II) / Zn(II) Spin multiplicity: 1 |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | Cu, Zn Superoxide Dismutase |
| PDB Code | 1CBJ |
| Crystallographic Resolution | 1.65 Å |
| Organism | Bos taurus |
| [Hough, 1999] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| CU | CU | 63.546 |  |
| ZN | ZN | 65.409 | |
| NE2 | NB | 14.0067 | |
| ND1 | NB | 14.0067 | |
| OD1 | OS | 15.9994 |
Bond Parameters
| 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 |
Angles Parameters
| 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 |
Validation of Parameters from MD Simulations
Bond Parameters
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 Parameters
| 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 |
References
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
mm/parameters/copper_zinc/hhh_cu_h_zn_dhh.txt · Last modified: 2013/10/03 18:58 by joaocoimbra
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