mm:parameters:copper_zinc:hhhh_cu_dhhh_zn
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| - | ====== Copper (II) - HHHH / Zinc (II) - HHHD ====== | ||
| - | 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** | **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.)) | | ||
| - | |||
| - | |||
| - | ---- | ||
| - | |||
| - | ===== Structure chosen to parameterize ===== | ||
| - | |||
| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | Superoxide Dismutase | | ||
| - | | //PDB Code// | 1CBJ | | ||
| - | | //Crystallographic Resolution// | 1.65 Å | | ||
| - | | //Organism// | //Bos taurus// | | ||
| - | | [[http://www.ncbi.nlm.nih.gov/pubmed/10092461 | [Hough, 1999]]] || | ||
| - | |||
| - | |||
| - | ===== Parameters Determined ===== | ||
| - | |||
| - | ==== Atom Types ==== | ||
| - | |||
| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | CU | CU | 63.546 | {{ :mm:parameters:copper_zinc:SOD_2.png?220 |}} | | ||
| - | | ZN | ZN | 65.409 | ::: | | ||
| - | | NE2 | NB | 14.0067 | ::: | | ||
| - | | ND1 | NB | 14.0067 | ::: | | ||
| - | | OD1 | OS | 15.9994 | ::: | | ||
| - | ==== Bond Parameters ==== | ||
| - | |||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | ZN-NB | 96.7 | 2.046 | [[#references | [Branco, 2006]]] | | ||
| - | | ZN-OS | 92.0 | 1.949 | ::: | | ||
| - | | CU-NB | 101.1 | 2.022 | ::: | | ||
| - | |||
| - | ==== Angles Parameters ==== | ||
| - | |||
| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | NB-CU-NB | 24.6 | 147.19 | [[#references | [Branco, 2006]]] | | ||
| - | | NB-ZN-NB | 44.0 | 113.53 | ::: | | ||
| - | | 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 ===== | ||
| - | |||
| - | ==== 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. | ||
| - | |||
| - | | **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** | **θ<sub>0 crystal</sub> 1CBJ:A** | **θ<sub>0 crystal</sub> 1CBJ:B** | **‹θ›<sub>MD</sub> ± 5 A** | **‹θ›<sub>MD</sub> ± 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 | | ||
| - | ===== 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 ===== | ||
| - | 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/hhhh_cu_dhhh_zn.1375713908.txt.gz · Last modified: 2013/08/05 15:45 by joaocoimbra
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