mm:parameters:manganese:hhdh_ho
Differences
This shows you the differences between two versions of the page.
|
mm:parameters:manganese:hhdh_ho [2013/07/26 14:13] ruineves |
mm:parameters:manganese:hhdh_ho [2013/10/03 18:55] (current) ruineves |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Manganese(II) - HDEWaWaWa ====== | + | ====== Manganese(III) - HHDH[HO] ====== |
| - | + | ### | |
| - | + | The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions. | |
| - | + | ### | |
| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | + | | **COORDINATION SPHERE** || |
| - | | {{ :mm:parameters:manganese:non-parameterized_hdewww_.png?200 |}} | {{ :mm:parameters:manganese:octahedral_highspin_d5.png?400|}} ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | + | | {{ :mm:parameters:manganese:non-parameterized_hhdhho_.png?120 |}} | \\ **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 | |
| Line 16: | Line 16: | ||
| | **TEST PROTEIN** || | | **TEST PROTEIN** || | ||
| - | | //Protein// | Citochrome //c// Oxidase | | + | | //Protein// | Manganese Superoxide Dismutase | |
| - | | //PDB Code// | 3HB3 | | + | | //PDB Code// | 1N0J | |
| - | | //Crystallographic Resolution// | 2.25 Å | | + | | //Crystallographic Resolution// | 2.20 Å | |
| - | | //Organism// | Paracoccus denitrificans | | + | | //Organism// | Homo sapiens | |
| - | | [[http://www.sciencedirect.com/science/article/pii/S0005272809001315 | [Koepke, 2009]]] || | + | | [[http://www.sciencedirect.com/science/article/pii/009286749290270M | [Borgstahl, 1992]]] || |
| Line 31: | Line 31: | ||
| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_hdewww_.png?120 |}} | | + | | MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_hhdhho_.png?120 |}} | |
| | OD1 | D1 | 15.9994 | ::: | | | OD1 | D1 | 15.9994 | ::: | | ||
| - | | OE1 | E1 | 15.9994 | ::: | | ||
| | NE2 | NI | 14.0067 | ::: | | | NE2 | NI | 14.0067 | ::: | | ||
| + | | NE2 | NJ | 14.0067 | ::: | | ||
| + | | NE2 | NK | 14.0067 | ::: | | ||
| | OW | W1 | 15.9994 | ::: | | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 15.9994 | ::: | | + | | HO | HM | 1.00794 | ::: | |
| - | | OW | W3 | 15.9994 | ::: | | + | |
| - | | HW | HM | 1.00794 | ::: | | + | |
| Line 44: | Line 43: | ||
| | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | M1-NI | 63.17 | 2.242 | [[#references | [Neves, 2013]]] | | + | | M1-NI | 106.65 | 2.1265 | [[#references | [Neves, 2013]]] | |
| - | | M1-D1 | 77.67 | 2.141 | ::: | | + | | M1-NJ | 95.00 | 2.1147 | ::: | |
| - | | M1-E1 | 68.41 | 2.147 | ::: | | + | | M1-NK | 81.69 | 2.1238 | ::: | |
| - | | M1-W1 | 31.5 | 2.3664 | ::: | | + | | M1-D1 | 129.13 | 1.9569 | ::: | |
| - | | M1-W2 | 31.4 | 2.325 | ::: | | + | | M1-W1 | 247.2 | 1.7776 | ::: | |
| - | | M1-W3 | 64.37 | 2.1601 | ::: | | + | |
| | NI-CR | 488.0 | 1.335 | | | NI-CR | 488.0 | 1.335 | | ||
| | NI-CV | 410.0 | 1.394 | | | NI-CV | 410.0 | 1.394 | | ||
| + | | NJ-CR | 488.0 | 1.335 | | ||
| + | | NJ-CV | 410.0 | 1.394 | | ||
| + | | NK-CR | 488.0 | 1.335 | | ||
| + | | NK-CV | 410.0 | 1.394 | | ||
| | D1-C | 656.0 | 1.25 | | | D1-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| | W1-HM | 553.0 | 0.9572 | | | W1-HM | 553.0 | 0.9572 | | ||
| - | | W2-HM | 553.0 | 0.9572 | | ||
| - | | W3-HM | 553.0 | 0.9572 | | ||
| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | + | | **ANGLE** | **K<sub>?</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | |
| - | | NI-M1-D1 | 55.1 | 90.0153 | [[#references | [Neves, 2013]]] | | + | | NI-M1-NJ | 88.01 | 91.6707 | [[#references | [Neves, 2013]]] | |
| - | | NI-M1-E1 | 41.458 | 159.9206 | ::: | | + | | NI-M1-NK | 86.76 | 88.725 | ::: | |
| - | | NI-M1-W1 | 24.19 | 94.3889 | ::: | | + | | NI-M1-D1 | 131.4 | 82.9759 | ::: | |
| - | | NI-M1-W2 | 31.3 | 89.0778 | ::: | | + | | NI-M1-W1 | 75.8 | 176.7937 | ::: | |
| - | | NI-M1-W3 | 34.86 | 98.8181 | ::: | | + | | NJ-M1-NK | 30.68 | 136.3174 | ::: | |
| - | | D1-M1-E1 | 50.26 | 103.9094 | ::: | | + | | NJ-M1-D1 | 23.09 | 110.6038 | ::: | |
| - | | D1-M1-W1 | 42.6 | 73.0866 | ::: | | + | | NJ-M1-W1 | 89.71 | 91.1769 | ::: | |
| - | | D1-M1-W2 | 12.075 | 162.4957 | ::: | | + | | NK-M1-D1 | 20.64 | 112.8695 | ::: | |
| - | | D1-M1-W3 | 56.22 | 90.7127 | ::: | | + | | NK-M1-W1 | 89.03 | 90.3375 | ::: | |
| - | | E1-M1-W1 | 37.25 | 76.4231 | ::: | | + | | D1-M1-W1 | 100.0 | 94.5712 | ::: | |
| - | | E1-M1-W2 | 54.4 | 73.2795 | ::: | | + | | M1-NI-CR | 53.671 | 126.4370 | ::: | |
| - | | E1-M1-W3 | 37.25 | 95.45 | ::: | | + | | M1-NI-CV | 53.671 | 126.4370 | ::: | |
| - | | W1-M1-W2 | 12.36 | 89.5541 | ::: | | + | | M1-NJ-CR | 40.495 | 123.3813 | ::: | |
| - | | W1-M1-W3 | 32.47 | 159.1053 | ::: | | + | | M1-NJ-CV | 40.495 | 123.3813 | ::: | |
| - | | W2-M1-W3 | 11.975 | 106.6994 | ::: | | + | | M1-NK-CR | 31.220 | 112.3780 | ::: | |
| - | | M1-NI-CR | 34.139 | 123.4259 | ::: | | + | | M1-NK-CV | 31.220 | 112.3780 | ::: | |
| - | | M1-NI-CV | 34.139 | 123.4259 | ::: | | + | | M1-D1-C | 47.094 | 135.5495 | ::: | |
| - | | M1-D1-C | 46.237 | 123.2712 | ::: | | + | | M1-W1-HM | 18.57 | 116.025 | ::: | |
| - | | M1-E1-C | 44.53 | 121.9953 | ::: | | + | |
| - | | M1-W1-HM | 8.322 | 99.514 | ::: | | + | |
| - | | M1-W2-HM | 9.174 | 99.3627 | ::: | | + | |
| - | | M1-W3-HM | 33.538 | 97.246 | ::: | | + | |
| | NI-CR-NA | 70.0 | 120.0 | | | NI-CR-NA | 70.0 | 120.0 | | ||
| | NI-CR-H5 | 50.0 | 120.0 | | | NI-CR-H5 | 50.0 | 120.0 | | ||
| Line 89: | Line 84: | ||
| | CV-NI-CR | 70.0 | 117.0 | | | CV-NI-CR | 70.0 | 117.0 | | ||
| | H4-CV-NI | 50.0 | 120.0 | | | H4-CV-NI | 50.0 | 120.0 | | ||
| - | | HM-W1-HM | 100.0 | 104.52 | | + | | NJ-CR-NA | 70.0 | 120.0 | |
| - | | HM-W2-HM | 100.0 | 104.52 | | + | | NJ-CR-H5 | 50.0 | 120.0 | |
| - | | HM-W3-HM | 100.0 | 104.52 | | + | | NJ-CV-CC | 70.0 | 120.0 | |
| + | | CV-NJ-CR | 70.0 | 117.0 | | ||
| + | | H4-CV-NJ | 50.0 | 120.0 | | ||
| + | | NK-CR-NA | 70.0 | 120.0 | | ||
| + | | NK-CR-H5 | 50.0 | 120.0 | | ||
| + | | NK-CV-CC | 70.0 | 120.0 | | ||
| + | | CV-NK-CR | 70.0 | 117.0 | | ||
| + | | H4-CV-NK | 50.0 | 120.0 | | ||
| | D1-C-CT | 70.0 | 117.0 | | | D1-C-CT | 70.0 | 117.0 | | ||
| | D1-C-O2 | 80.0 | 126.0 | | | D1-C-O2 | 80.0 | 126.0 | | ||
| - | | E1-C-CT | 70.0 | 117.0 | | ||
| - | | E1-C-O2 | 80.0 | 126.0 | | ||
| Line 103: | Line 103: | ||
| | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | ||
| | NI | 1.824 | 0.17 | | | NI | 1.824 | 0.17 | | ||
| + | | NJ | 1.824 | 0.17 | | ||
| + | | NK | 1.824 | 0.17 | | ||
| | D1 | 1.6612 | 0.21 | | | D1 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| | W1 | 1.7683 | 0.152 | | | W1 | 1.7683 | 0.152 | | ||
| - | | W2 | 1.7683 | 0.152 | | + | | HM | 0.6000 | 0.0157 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
| - | | W3 | 1.7683 | 0.152 | | + | |
| - | | HM | 0.6000 | 0.0157 | [[LINK | [Cornel, 1995]]] | | + | |
| Line 118: | Line 117: | ||
| | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **‹l›<sub>MD</sub> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | | ||
| - | | M1-NI | 1.98 | 2.24 | 2.17 ± 0.06 | [2.111; 2.238] | | + | | M1-D1 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] | |
| - | | M1-D1 | 2.17 | 2.14 | 2.18 ± 0.06 | [2.117; 2.245] | | + | | M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] | |
| - | | M1-E1 | 2.19 | 2.15 | 2.18 ± 0.07 | [2.112; 2.245] | | + | | M1-NJ | 2.08 | 2.12 | 2.11 ± 0.06 | [2.053; 2.163] | |
| - | | M1-W1 | 2.20 | 2.37 | 2.3 ± 0.1 | [2.189; 2.383] | | + | | N1-NK | 2.09 | 2.12 | 2.14 ± 0.06 | [2.080; 2.197] | |
| - | | M1-W2 | 2.14 | 2.33 | 2.3 ± 0.1 | [2.170; 2.371] | | + | | M1-W1 | 2.02 | 1.78 | 1.76 ± 0.04 | [1.722; 1.792] | |
| - | | M1-W3 | 2.11 | 2.16 | 2.14 ± 0.07 | [2.070; 2.215] | | + | |
| Line 129: | Line 127: | ||
| | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | | | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | | ||
| - | | NI-M1-D1 | 74.7 | 90.0 | 84 ± 4 | [76.5; 90.8] | | + | | NI-M1-NJ | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] | |
| - | | NI-M1-E1 | 171.1 | 159.9 | 159 ± 3 | [151.8; 165.4] | | + | | NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] | |
| - | | NI-M1-W1 | 87.0 | 94.4 | 88 ± 4 | [81.0; 95.7] | | + | | NI-M1-D1 | 82.4 | 83.0 | 83 ± 2 | [79.0; 87.6] | |
| - | | NI-M1-W2 | 99.9 | 89.1 | 82 ± 4 | [73.3; 90.8] | | + | | NI-M1-W1 | 166.1 | 176.8 | 174 ± 2 | [169.9; 179.1] | |
| - | | NI-M1-W3 | 98.0 | 98.8 | 96 ± 5 | [86.6; 105.4] | | + | | NJ-M1-NK | 137.7 | 136.4 | 138 ± 5 | [128.8; 146.9] | |
| - | | D1-M1-E1 | 113.6 | 103.9 | 100 ± 4 | [92.0; 107.2] | | + | | NJ-M1-D1 | 110.4 | 110.4 | 111 ± 5 | [100.1; 121.9] | |
| - | | D1-M1-W1 | 72.3 | 73.1 | 76 ± 4 | [68.2; 83.2] | | + | | NJ-M1-W1 | 91.8 | 91.1 | 91 ± 3 | [85.8; 96.4] | |
| - | | D1-M1-W2 | 166.7 | 162.5 | 135 ± 6 | [123.2; 146.7] | | + | | NK-M1-D1 | 106.4 | 112.9 | 111 ± 6 | [99.6; 122.2] | |
| - | | D1-M1-W3 | 86.4 | 90.7 | 84 ± 4 | [76.2; 91.5] | | + | | NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] | |
| - | | E1-M1-W1 | 86.4 | 76.4 | 73 ± 4 | [64.6; 81.0] | | + | | D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] | |
| - | | E1-M1-W2 | 71.3 | 73.3 | 81 ± 4 | [73.5; 89.0] | | + | |
| - | | E1-M1-W3 | 79.7 | 95.5 | 105 ± 5 | [95.1; 114.4] | | + | |
| - | | W1-M1-W2 | 120.1 | 89.6 | 62 ± 6 | [50.6; 72.9] | | + | |
| - | | W1-M1-W3 | 156.1 | 159.1 | 158 ± 4 | [149.5; 166.0] | | + | |
| - | | W2-M1-W3 | 82.2 | 106.7 | 139 ± 6 | [127.5; 151.4] | | + | |
| Line 149: | Line 143: | ||
| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:manganese:hhdh_oh-frcmod.zip| .frcmod}} | | + | | //Parameter File// | {{:mm:parameters:manganese:hhdh_ho-frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[oh]_mn-iii.zip| .off}} | | + | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:hhdh[ho]_mn-iii.zip| .off}} | |
| | //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase-oh.zip| .pdb, leaprc}} | | | //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:mn_superoxide_dismutase-oh.zip| .pdb, leaprc}} | | ||
| - | |||
| ===== References ===== | ===== References ===== | ||
| + | ### | ||
| Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | ||
| + | ### | ||
mm/parameters/manganese/hhdh_ho.1374844396.txt.gz · Last modified: 2013/07/26 14:13 by ruineves
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
