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mm:parameters:copper_zinc:hhh_cu_h_zn_dhh [2013/08/05 14:29] ruineves |
mm:parameters:copper_zinc:hhh_cu_h_zn_dhh [2013/10/03 18:58] (current) joaocoimbra |
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- | ===== Copper(II)/Zinc(II) - HHH[Cu]H[Zn]HHD ===== | + | ====== 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. | ||
+ | ### | ||
- | The metal center of 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** || |
- | + | | {{ :mm:parameters:copper_zinc:SOD.png?250 |}} | \\ **Oxidation state:** Cu(II) / Zn(II) \\ **Spin multiplicity:** 1 | | |
- | | **Coordination Sphere** | **Oxidation state:** Cu(II) / Zn(II) \\ **Spin multiplicity:** 1 | | + | |
- | | {{ :mm:parameters:copper_zinc:SOD.png?300 |}} | {{ :mm:parameters:copper_zinc:image.png?400|}} ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | + | |
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| **TEST PROTEIN** || | | **TEST PROTEIN** || | ||
- | | //Protein// | Superoxide Dismutase | | + | | //Protein// | Cu, Zn Superoxide Dismutase | |
| //PDB Code// | 1CBJ | | | //PDB Code// | 1CBJ | | ||
| //Crystallographic Resolution// | 1.65 Å | | | //Crystallographic Resolution// | 1.65 Å | | ||
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| ND1 | NB | 14.0067 | ::: | | | ND1 | NB | 14.0067 | ::: | | ||
| OD1 | OS | 15.9994 | ::: | | | OD1 | OS | 15.9994 | ::: | | ||
+ | |||
==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
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| NB-ZN-NB | 44.0 | 113.53 | ::: | | | NB-ZN-NB | 44.0 | 113.53 | ::: | | ||
| NB-ZN-OS | 21.7 | 111.75 | ::: | | | NB-ZN-OS | 21.7 | 111.75 | ::: | | ||
- | |||
- | ==== Van der Waals Parameters ==== | ||
- | |||
- | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | ||
- | | ZN | | | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | | ||
- | | CU | | | [[http://www.ncbi.nlm.nih.gov/pubmed/7716168 | [Ryde, 1995]]] | | ||
- | | OS | 1.6612 | 0.2100 | | | ||
- | | NB | 1.8240 | 0.1700 | ::: | | ||
===== Validation of Parameters from MD Simulations ===== | ===== Validation of Parameters from MD Simulations ===== | ||
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==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
- | The validation considering two SOD structures was conducted: 1 for the fully reduced enzyme - 1Q0E (resolution of 1.15 Å); and for the structure used in the parameterization - 1CBJ. The two chains were considered in the validation (A, and B), and the brackets denotes the decoordinated residue upon reduction. | + | 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** | **l<sub>0 crystal</sub> 1CBJ:A** | **l<sub>0 crystal</sub> 1CBJ:B** | **‹l›<sub>MD</sub> ± 0.06 A** | **‹l›<sub>MD</sub> ± 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 | | ||
- | | **BOND / Å** | **l<sub>0 crystal</sub> 1CBJ:A** | **l<sub>0 crystal</sub> 1CBJ:B** | **l<sub>0 crystal</sub> 1Q0E:A** | **l<sub>0 crystal</sub> 1Q0E:B** | **‹l›<sub>MD</sub> ± 0.06 A** | **‹l›<sub>MD</sub> ± 0.06 B** | | ||
- | | CU-NB(H44) | 2.07 | 2.00 | 2.02 | 2.05 | 2.03 | 2.04 | | ||
- | | CU-NB(H46) | 2.00 | 2.17 | 1.96 | 2.01 | 2.08 | 2.07 | | ||
- | | CU-NB(H61) | (3.19) | 2.20 | (3.39) | (3.32) | 2.03 | 2.03 | | ||
- | | CU-NB(H118) | 2.03 | 2.19 | 2.08 | 2.04 | 2.03 | 2.03 | | ||
- | | ZN-NB(H61) | 1.97 | 2.02 | 2.05 | 2.05 | 2.03 | 2.03 | | ||
- | | ZN-NB(H69) | 2.03 | 2.07 | 2.05 | 2.05 | 2.05 | 2.04 | | ||
- | | ZN-NB(H78) | 2.07 | 1.75 | 2.06 | 2.06 | 2.06 | 2.05 | | ||
- | | ZN-OS(D81) | 1.62 | 1.84 | 1.99 | 2.00 | 1.90 | 1.92 | | ||
==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
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| H69-ZN-D81 | 98.0 | 99.7 | 105.3 | 103.8 | | | H69-ZN-D81 | 98.0 | 99.7 | 105.3 | 103.8 | | ||
| H78-ZN-D81 | 115.9 | 114.5 | 113.4 | 115.5 | | | H78-ZN-D81 | 115.9 | 114.5 | 113.4 | 115.5 | | ||
- | ===== Downloads ===== | + | |
- | | //Parameter File// | {{:mm:parameters:copper_zinc:hdc_zn-II.frcmod.zip| .frcmod}} | | + | |
- | | //Coordination Sphere Charges// | {{:mm:parameters:copper_zinc:lib_files_1.zip| .lib}} | | + | |
- | | //LEAPRC file// | {{:mm:parameters:copper_zinc:leaprc.zip| leaprc}} | | + | |
===== References ===== | ===== References ===== | ||
+ | ### | ||
Branco, J.F.B.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/jp056855l | Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase]] . //J. Phys. Chem. B//, **2006**, 110, 16754-16762 | Branco, J.F.B.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/jp056855l | Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase]] . //J. Phys. Chem. B//, **2006**, 110, 16754-16762 | ||
+ | ### |