Мною была выбрана структура B-ДНК(1bna)
В сторону большой бороздки обращены атомы: n4, c5, c4, c6
В сторону малой бороздки обращены атомы: o2, c2
| A-форма | B-форма | Z-форма | |
|---|---|---|---|
| Тип спирали | правая | правая | левая |
| Шаг спирали | 28 | 33.61 | 43.3 |
| Число оснований на виток | 11 | 12 | 12 |
| Ширина большой бороздки | 8 | 17.27 | 18.46 |
| Ширина малой бороздки | 16.82 | 11.8 | 9.86 |
Ниже приведены торсионные углы тРНК (CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE)
Strand I
| base | alpha | beta | gamma | delta | epsilon | zeta | chi |
|---|---|---|---|---|---|---|---|
| 1 G | --- | 161.4 | 50.3 | 82.1 | -147.5 | -73.4 | -175.9 |
| 2 G | -49.3 | 177.4 | 47.2 | 80.1 | -152.5 | -77.0 | -169.4 |
| 3 A | -63.4 | -178.8 | 50.0 | 81.5 | -158.7 | -68.2 | -164.2 |
| 4 G | -65.9 | 178.8 | 53.1 | 79.4 | -144.3 | -78.5 | -168.4 |
| 5 C | -53.1 | 166.8 | 48.6 | 79.6 | -148.9 | -76.4 | -166.3 |
| 6 G | -59.7 | 170.3 | 58.2 | 80.3 | -154.1 | -66.3 | -165.1 |
| 7 G | -53.2 | 177.9 | 57.2 | 137.6 | -93.9 | -56.7 | -139.9 |
| 8 G | 27.5 | -165.3 | 66.7 | 86.7 | -143.4 | -67.4 | -179.2 |
| 9 C | -57.5 | 179.5 | 40.7 | 81.9 | -157.2 | -71.1 | -157.3 |
| 10 G | -68.7 | 178.5 | 50.6 | 83.0 | -160.9 | -58.0 | -161.4 |
| 11 G | -71.0 | 179.4 | 57.3 | 78.5 | -154.7 | -65.0 | -165.4 |
| 12 G | -65.3 | 168.5 | 65.1 | 78.7 | -159.7 | -74.8 | -170.5 |
| 13 t | -62.1 | -174.8 | 47.7 | 81.9 | -134.9 | -70.3 | -155.9 |
| 14 P | -51.0 | 166.5 | 45.1 | 86.1 | -142.6 | -72.6 | -143.0 |
| 15 C | -74.5 | 151.7 | -171.6 | 80.6 | -145.9 | -69.7 | -148.5 |
| 16 G | -47.5 | 166.9 | 43.9 | 82.4 | -148.4 | -67.9 | -164.4 |
| 17 C | -56.8 | -177.1 | 45.9 | 83.5 | -144.2 | -79.4 | -160.9 |
| 18 A | -68.3 | 161.1 | 60.2 | 83.9 | -151.1 | -79.1 | -172.5 |
| 19 G | -87.9 | 179.2 | 66.1 | 84.5 | -168.4 | -67.6 | -171.3 |
| 20 G | -62.2 | -176.0 | 53.0 | 82.5 | -145.6 | -90.3 | -166.4 |
| 21 G | -52.5 | 157.0 | 51.2 | 80.6 | -156.2 | -60.6 | -166.9 |
| 22 G | -162.0 | 164.5 | 54.0 | 84.8 | -142.8 | -67.1 | -179.0 |
| 23 U | -66.8 | 177.2 | 55.7 | 88.1 | -144.1 | -67.1 | -160.1 |
| 24 U | -74.3 | 168.5 | 60.7 | 78.3 | -153.1 | -83.2 | -162.2 |
| 25 C | -58.4 | 162.6 | 54.4 | 82.0 | -156.7 | -70.6 | -162.8 |
| 26 A | -62.4 | 174.9 | 54.2 | 72.5 | -147.3 | -62.9 | -167.6 |
| 27 G | -54.7 | 170.1 | 47.0 | 83.3 | -172.8 | 164.6 | -160.5 |
| 28 G | -61.8 | -156.8 | 33.7 | 130.8 | 75.0 | -155.7 | -76.3 |
Strand II
| base | alpha | beta | gamma | delta | epsilon | zeta | chi |
|---|---|---|---|---|---|---|---|
| 1 C | -69.7 | -172.5 | 50.8 | 81.5 | -148.6 | -61.3 | -163.9 |
| 2 C | -55.9 | 162.1 | 55.3 | 80.6 | -162.4 | -72.0 | -156.6 |
| 3 U | -65.5 | 173.6 | 47.5 | 81.1 | -144.8 | -76.7 | -154.1 |
| 4 U | -58.6 | 172.2 | 51.5 | 83.5 | -154.6 | -81.4 | -161.2 |
| 5 G | -57.3 | 175.0 | 48.9 | 80.4 | -148.5 | -67.3 | -164.2 |
| 6 C | -57.4 | 178.2 | 42.3 | 80.0 | -156.0 | -75.6 | -156.5 |
| 7 C | -62.1 | 175.9 | 49.3 | 80.5 | -153.9 | -73.8 | -159.8 |
| 8 P | -58.7 | 171.5 | 49.9 | 87.6 | -158.2 | -81.1 | -156.3 |
| 9 G | -56.5 | 172.8 | 43.9 | 80.0 | -151.3 | -67.0 | -165.8 |
| 10 C | -64.8 | -175.9 | 47.4 | 82.1 | -156.4 | -71.5 | -155.6 |
| 11 C | -57.6 | 174.9 | 47.2 | 82.4 | -151.2 | -70.8 | -163.6 |
| 12 C | -87.7 | -170.6 | 41.9 | 83.6 | -151.5 | -77.5 | -164.8 |
| 13 A | -59.8 | -129.1 | 54.3 | 150.1 | -89.9 | 178.6 | -72.1 |
| 14 G | 150.3 | 123.2 | 36.5 | 140.1 | -133.1 | -131.5 | -107.7 |
| 15 C | -78.2 | -172.2 | 52.8 | 83.3 | -135.3 | -115.1 | -158.4 |
| 16 C | -79.5 | -167.8 | 53.5 | 84.2 | -166.7 | -60.7 | -158.8 |
| 17 G | -58.8 | 179.9 | 43.4 | 82.6 | -169.0 | -62.7 | -165.9 |
| 18 U | -51.0 | 178.7 | 37.5 | 80.3 | -159.4 | -69.9 | -160.3 |
| 19 C | -52.1 | 167.8 | 41.9 | 79.4 | -145.9 | -73.4 | -158.5 |
| 20 C | -56.2 | 164.5 | 48.7 | 80.0 | -141.9 | -81.8 | -156.7 |
| 21 A | -67.4 | 167.2 | 57.1 | 85.5 | -131.4 | -77.6 | -166.5 |
| 22 U | -60.2 | 162.2 | 52.9 | 83.0 | -151.2 | -66.7 | -162.3 |
| 23 A | -64.7 | 171.0 | 52.4 | 82.3 | -145.0 | -71.0 | -157.6 |
| 24 A | -59.1 | 163.3 | 60.0 | 82.4 | -152.4 | -74.4 | -155.8 |
| 25 G | 80.0 | -165.0 | -176.7 | 83.7 | -156.7 | -75.5 | -156.2 |
| 26 u | -75.1 | -156.7 | 58.6 | 89.0 | -119.1 | -128.1 | -159.6 |
| 27 C | -48.6 | 146.1 | 30.1 | 140.4 | -131.7 | 84.2 | -135.4 |
| 28 C | 154.4 | 166.3 | 59.5 | 85.2 | -130.0 | -75.4 | -178.3 |
Тяжи структуры данной тРНК похожи на А-ДНК, судя по значениям торсионных углов
Фрагмент файла 1c0a_old.out с информацией о структуре водородных связей между основаниями данной тРНК:
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.016) ....>B:.601_:[..G]G-----C[..C]:.672_:B<.... (0.004) |
2 (0.010) ....>B:.602_:[..G]G-----C[..C]:.671_:B<.... (0.007) |
3 (0.006) ....>B:.603_:[..A]A-----U[..U]:.670_:B<.... (0.008) |
4 (0.011) ....>B:.604_:[..G]G-*---U[..U]:.669_:B<.... (0.006) |
5 (0.008) ....>B:.605_:[..C]C-----G[..G]:.668_:B<.... (0.006) |
6 (0.012) ....>B:.606_:[..G]G-----C[..C]:.667_:B<.... (0.006) |
7 (0.011) ....>B:.607_:[..G]G-----C[..C]:.666_:B<.... (0.006) |
8 (0.007) ....>B:.649_:[..G]G-*---P[PSU]:.665_:B<.... (0.044) |
9 (0.003) ....>B:.650_:[..C]C-----G[..G]:.664_:B<.... (0.010) |
10 (0.006) ....>B:.651_:[..G]G-----C[..C]:.663_:B<.... (0.002) |
11 (0.009) ....>B:.652_:[..G]G-----C[..C]:.662_:B<.... (0.003) |
12 (0.009) ....>B:.653_:[..G]G-----C[..C]:.661_:B<.... (0.007) |
13 (0.003) ....>B:.654_:[5MU]t-**--A[..A]:.658_:B<.... (0.006) |
14 (0.045) ....>B:.655_:[PSU]P-**+-G[..G]:.618_:B<.... (0.004) x
15 (0.004) ....>B:.638_:[..C]C-**--C[..C]:.632_:B<.... (0.005) |
16 (0.005) ....>B:.639_:[..G]G-----C[..C]:.631_:B<.... (0.008) |
17 (0.004) ....>B:.640_:[..C]C-----G[..G]:.630_:B<.... (0.009) |
18 (0.005) ....>B:.641_:[..A]A-----U[..U]:.629_:B<.... (0.008) |
19 (0.007) ....>B:.642_:[..G]G-----C[..C]:.628_:B<.... (0.004) |
20 (0.006) ....>B:.643_:[..G]G-----C[..C]:.627_:B<.... (0.008) |
21 (0.005) ....>B:.644_:[..G]G-**--A[..A]:.626_:B<.... (0.004) |
22 (0.004) ....>B:.610_:[..G]G-*---U[..U]:.625_:B<.... (0.008) |
23 (0.011) ....>B:.611_:[..U]U-----A[..A]:.624_:B<.... (0.003) |
24 (0.007) ....>B:.612_:[..U]U-----A[..A]:.623_:B<.... (0.013) |
25 (0.006) ....>B:.613_:[..C]C-----G[..G]:.622_:B<.... (0.007) |
26 (0.006) ....>B:.614_:[..A]A-**--u[4SU]:.608_:B<.... (0.006) |
27 (0.007) ....>B:.615_:[..G]G-**+-C[..C]:.648_:B<.... (0.006) x
28 (0.010) ....>B:.619_:[..G]G-----C[..C]:.656_:B<.... (0.004) +
Note: This structure contains 9[6] non-Watson-Crick base-pairs.
| Стебли | Позиции в приведённом фрагменте | Координаты |
|---|---|---|
| Акцепторный стебель | 1-7 | 601-607 |
| D-стебель | 8-12 | 649-653 |
| T-стебель | 16-21 | 639-644 |
| Антикодоновый стебель | 22-25 | 610-613 |
Остальные 6 пар стабилизируют третичную структуру
Неканонические пары:
[..G]G-*---U[..U] [..G]G-*---P[PSU] [5MU]t-**--A[..A] [PSU]P-**+-G[..G] [..C]C-**--C[..C] [..G]G-**--A[..A] [..G]G-*---U[..U] [..A]A-**--u[4SU] [..G]G-**+-C[..C]
Последние 2 пары([..A]A-**--u[4SU] и [..G]G-**+-C[..C]) не являются каноническими, так как водородные связи между этими основаниями не соответствуют стандартным Уотсон-Криковским связям:
![[..A]A-**--u[4SU]](AU.jpg)
![[..G]G-**+-C[..C]](GC.jpg)