mm:parameters:copper_zinc:hhh_cu_h_zn_dhh
Differences
This shows you the differences between two versions of the page.
|
mm:parameters:copper_zinc:hhh_cu_h_zn_dhh [2013/08/05 15:38] joaocoimbra |
mm:parameters:copper_zinc:hhh_cu_h_zn_dhh [2013/10/03 18:58] (current) joaocoimbra |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ====== 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 |}} | JMOL | | + | |
| Line 12: | Line 13: | ||
| | **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 | | ||
| Line 29: | Line 30: | ||
| | ND1 | NB | 14.0067 | ::: | | | ND1 | NB | 14.0067 | ::: | | ||
| | OD1 | OS | 15.9994 | ::: | | | OD1 | OS | 15.9994 | ::: | | ||
| + | |||
| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| Line 42: | Line 44: | ||
| | 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 ===== | ||
| Line 55: | Line 49: | ||
| ==== 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** | | | **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** | | ||
| Line 61: | Line 55: | ||
| | CU-NB(H46) | 2.00 | 2.17 | 2.08 | 2.07 | | | CU-NB(H46) | 2.00 | 2.17 | 2.08 | 2.07 | | ||
| | CU-NB(H61) | (3.19) | 2.20 | 2.03 | 2.03 | | | CU-NB(H61) | (3.19) | 2.20 | 2.03 | 2.03 | | ||
| - | | CU-NB(H118) | 2.03 | 2.19 | 2.04 | 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(H61) | 1.97 | 2.02 | 2.03 | 2.03 | | ||
| | ZN-NB(H69) | 2.03 | 2.07 | 2.05 | 2.04 | | | ZN-NB(H69) | 2.03 | 2.07 | 2.05 | 2.04 | | ||
| | ZN-NB(H78) | 2.07 | 1.75 | 2.06 | 2.05 | | | ZN-NB(H78) | 2.07 | 1.75 | 2.06 | 2.05 | | ||
| | ZN-OS(D81) | 1.62 | 1.84 | 1.90 | 1.92 | | | ZN-OS(D81) | 1.62 | 1.84 | 1.90 | 1.92 | | ||
| + | |||
| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| Line 81: | Line 76: | ||
| | 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 | ||
| + | ### | ||
mm/parameters/copper_zinc/hhh_cu_h_zn_dhh.1375713529.txt.gz · Last modified: 2013/08/05 15:38 by joaocoimbra
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
