Определение формы dna8
| A-форма | B-форма | Файл dna8.pdb | |
| Тип спирали (правая или левая) | правая | правая | правая |
| Шаг спирали (Å) | 28.02 ангстрем | 33.75 ангстрем | 30.638 ангстрем |
| Число оснований на виток | 11 | 10 | 10 |
| Ширина большой бороздки | 7.98(от 8 фосфора) | 17.2(от 8 фосфора) | 19.819(от 17 фосфора) |
| Ширина малой бороздки | 16.8(от 8 фосфора) | 11.69(от 8 фосфора) | 10.856(от 345 фосфора) |
Рассмотрев таблицу, можно заметить, что dna8 является В-формой
Измерение торсионных углов
- Описание углов для gatc-a.
Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 G --- 174.8 41.7 79.0 -147.8 -75.1 -157.2 2 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 3 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 4 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 5 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 6 A -51.7 174.8 41.7 79.0 -147.8 -75.1 -157.2 7 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 8 C -51.7 174.8 41.7 79.0 -147.8 -75.0 -157.2 9 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 10 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 11 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 12 C -51.7 174.8 41.7 79.1 -147.7 -75.1 -157.2 13 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 14 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 15 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 16 C -51.7 174.8 41.7 79.1 --- --- -157.2 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -51.7 174.8 41.7 79.0 --- --- -157.2 2 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 3 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 4 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 5 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 6 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 7 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 8 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 9 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 10 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 11 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 12 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 13 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 14 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2 15 A -51.7 174.8 41.7 79.0 -147.8 -75.1 -157.2 16 G --- 174.8 41.7 79.1 -147.7 -75.1 -157.2 - Описание углов для gatc-b.
Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 G --- 136.4 31.1 143.4 -140.8 -160.5 -98.0 2 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 3 T -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9 4 C -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 5 G -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 6 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 7 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 8 C -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9 9 G -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 10 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 11 T -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 12 C -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 13 G -29.9 136.3 31.1 143.3 -140.8 -160.5 -98.0 14 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 15 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 16 C -29.9 136.4 31.1 143.4 --- --- -98.0 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -29.9 136.4 31.1 143.4 --- --- -98.0 2 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 3 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 4 G -29.9 136.3 31.1 143.3 -140.8 -160.5 -98.0 5 C -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 6 T -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 7 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 8 G -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 9 C -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9 10 T -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 11 A -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 12 G -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 13 C -29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 14 T -29.9 136.3 31.1 143.3 -140.8 -160.5 -97.9 15 A -29.9 136.3 31.2 143.3 -140.8 -160.5 -98.0 16 G --- 136.4 31.1 143.4 -140.8 -160.5 -98.0 - Описание углов для dna8.
Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 C --- --- 177.3 147.6 -153.5 -123.2 -111.8 2 G -46.4 149.7 40.4 112.4 -177.4 -105.3 -103.3 3 C -64.2 150.3 72.1 89.3 -164.7 -96.2 -137.4 4 G -53.7 171.9 55.5 141.7 -170.2 -120.3 -105.4 5 A -43.0 168.4 36.6 138.1 -176.9 -95.3 -111.5 6 A -81.0 168.0 63.2 124.0 -176.9 -93.2 -114.9 7 T -64.0 174.0 50.2 104.3 -176.0 -95.5 -123.4 8 T -45.3 171.9 31.2 125.8 173.4 -100.3 -116.3 9 C -46.4 177.2 41.0 141.2 -153.5 -102.0 -115.5 10 G -51.8 168.5 18.0 148.0 -50.7 105.4 -77.2 11 C -117.7 178.3 57.1 142.6 -172.8 -79.2 -117.1 12 G -84.1 -178.5 55.2 129.4 --- --- -94.7 Strand II base alpha beta gamma delta epsilon zeta chi 1 G -68.7 176.2 62.3 135.7 --- --- -121.4 2 C -68.1 133.1 36.5 115.9 178.2 -105.2 -120.9 3 G -89.3 171.7 66.0 146.9 -95.5 177.1 -104.2 4 C -63.2 -171.7 46.7 112.7 -163.1 -94.8 -112.7 5 T -52.3 171.2 49.0 117.8 178.4 -82.8 -123.4 6 T -94.8 -179.6 84.3 105.9 -169.3 -91.6 -134.0 7 A -85.7 -178.6 70.7 103.4 165.8 -69.0 -119.9 8 A -68.9 -163.0 59.9 136.8 174.5 -91.2 -108.5 9 G -48.0 167.7 56.8 142.6 154.7 -92.4 -96.7 10 C -76.5 162.9 73.3 100.9 -170.5 -114.9 -124.4 11 G -47.0 161.0 42.0 127.7 -178.4 -94.1 -106.4 12 C --- --- -153.9 154.0 -158.7 -112.3 -126.0
Так как наиболее различие в углах между А и В формой наблюдается для углов дельта, зета и хи, то близость этих углов в dna8 к В-форме и играет определяющую роль (т.е. остальные углы настолько похожи у А и В форм, что невозможно по ним определять форму). Сравнив углы можно опять же сделать вывод, что dna8 является В-формой ДНК.
Стопочные модели, полученные с помощью программы pdb2img
| А-форма | B-форма | dna8.pdb | |
| Вид с торца |  |
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| Вид с боку |  |
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