Практикум 3

Задание 1:

Ссылки на скачивание:
gatc-a.pdb
gatc-b.pdb
gatc-z.pdb

Задание 2:

G.png
Гуанин из A-формы (красные атомы смотрят в сторону большой бороздки, а синие в сторону малой)

В сторону большой бороздки обращены атомы: 13/N7, 13/C5, 13/C6, 13/O6, 13/N1.
В сторону малой бороздки обращены атомы: 13/N9, 13/C4, 13/N3, 13/C2, 13/N2.

Форма ДНК  Тип спирали (правая или левая)   Шаг спирали (Å)  Число оснований на виток  Ширина большой бороздки Ширина малой бороздки 
 A-форма  Правая  28,9  11  13,3 (dist /3v9d/A/A/DG`5/P, /3v9d/B/B/DC`3/P)  15,8 (dist /3v9d/B/B/DC`9/P, /3v9d/A/A/DC`10/P)
 B-форма  Правая  32,0  11  18,9 (dist /1bna/A/A/DG`4/P, /1bna/B/B/DG`16/P)  12,8 (dist /1bna/B/B/DG`22/P, /1bna/A/A/DT`8/P)
 Z-форма  Левая  20,8  6  11,0 (dist /1tne/A/A/DG`6/P, /1tne/B/B/DG`12/P)  6,5 (dist /1tne/B/B/DC`9/P, /1tne/B/B/DG`8/P)

Задание 3:

Тяжи этой РНК больше всего похожи на A-форму ДНК.

Координаты стеблей:

             Strand I                    Strand II          Helix
   1   (0.004) ....>C:.501_:[..G]G-----C[..C]:.572_:C<.... (0.005)     |
   2   (0.007) ....>C:.502_:[..G]G-*---U[..U]:.571_:C<.... (0.008)     |
   3   (0.003) ....>C:.503_:[..C]C-----G[..G]:.570_:C<.... (0.003)     |
   4   (0.003) ....>C:.504_:[..C]C-----G[..G]:.569_:C<.... (0.007)     |
   5   (0.005) ....>C:.505_:[..C]C-----G[..G]:.568_:C<.... (0.009)     |
   6   (0.005) ....>C:.506_:[..C]C-----G[..G]:.567_:C<.... (0.003)     |
   7   (0.004) ....>C:.507_:[..A]A-----U[..U]:.566_:C<.... (0.006)     |
   8   (0.004) ....>C:.549_:[..G]G-----C[..C]:.565_:C<.... (0.002)     |
   9   (0.001) ....>C:.550_:[..G]G-----C[..C]:.564_:C<.... (0.003)     |
  10   (0.007) ....>C:.551_:[..G]G-----C[..C]:.563_:C<.... (0.002)     |
  11   (0.003) ....>C:.552_:[..G]G-----C[..C]:.562_:C<.... (0.003)     |
  12   (0.005) ....>C:.553_:[..G]G-----C[..C]:.561_:C<.... (0.004)     |
  13   (0.003) ....>C:.554_:[..U]U-**--A[..A]:.558_:C<.... (0.008)     |
  14   (0.003) ....>C:.555_:[..U]U-**+-G[..G]:.518_:C<.... (0.003)     x
  15   (0.003) ....>C:.538_:[..A]A-**--C[..C]:.532_:C<.... (0.005)     |
  16   (0.005) ....>C:.539_:[..G]G-----C[..C]:.531_:C<.... (0.004)     |
  17   (0.003) ....>C:.540_:[..G]G-----C[..C]:.530_:C<.... (0.004)     |
  18   (0.005) ....>C:.541_:[..C]C-----G[..G]:.529_:C<.... (0.005)     |
  19   (0.004) ....>C:.542_:[..C]C-----G[..G]:.528_:C<.... (0.005)     |
  20   (0.006) ....>C:.543_:[..G]G-----C[..C]:.527_:C<.... (0.003)     |
  21   (0.005) ....>C:.544_:[..A]A-**--G[..G]:.526_:C<.... (0.004)     |
  22   (0.006) ....>C:.510_:[..G]G-----C[..C]:.525_:C<.... (0.004)     |
  23   (0.004) ....>C:.511_:[..U]U-----A[..A]:.524_:C<.... (0.003)     |
  24   (0.002) ....>C:.512_:[..C]C-----G[..G]:.523_:C<.... (0.011)     |
  25   (0.004) ....>C:.513_:[..U]U-*---G[..G]:.522_:C<.... (0.007)     |
  26   (0.004) ....>C:.508_:[..U]U-**--A[..A]:.546_:C<.... (0.003)     |
  27   (0.007) ....>C:.514_:[..A]A-**--A[..A]:.521_:C<.... (0.005)     |
  28   (0.018) ....>C:.515_:[..G]G-**+-C[..C]:.548_:C<.... (0.012)     x
  29   (0.004) ....>C:.519_:[..G]G-----C[..C]:.556_:C<.... (0.002)     +
  30   (0.007) ....>D:.501_:[..G]G-----C[..C]:.572_:D<.... (0.006)     |
  31   (0.007) ....>D:.502_:[..G]G-*---U[..U]:.571_:D<.... (0.003)     |
  32   (0.004) ....>D:.503_:[..C]C-----G[..G]:.570_:D<.... (0.006)     |
  33   (0.003) ....>D:.504_:[..C]C-----G[..G]:.569_:D<.... (0.006)     |
  34   (0.005) ....>D:.505_:[..C]C-----G[..G]:.568_:D<.... (0.010)     |
  35   (0.005) ....>D:.506_:[..C]C-----G[..G]:.567_:D<.... (0.004)     |
  36   (0.005) ....>D:.507_:[..A]A-----U[..U]:.566_:D<.... (0.005)     |
  37   (0.003) ....>D:.549_:[..G]G-----C[..C]:.565_:D<.... (0.005)     |
  38   (0.004) ....>D:.550_:[..G]G-----C[..C]:.564_:D<.... (0.002)     |
  39   (0.004) ....>D:.551_:[..G]G-----C[..C]:.563_:D<.... (0.002)     |
  40   (0.005) ....>D:.552_:[..G]G-----C[..C]:.562_:D<.... (0.001)     |
  41   (0.003) ....>D:.553_:[..G]G-----C[..C]:.561_:D<.... (0.004)     |
  42   (0.002) ....>D:.554_:[..U]U-**--A[..A]:.558_:D<.... (0.009)     |
  43   (0.003) ....>D:.555_:[..U]U-**+-G[..G]:.518_:D<.... (0.006)     x
  44   (0.004) ....>D:.538_:[..A]A-**--C[..C]:.532_:D<.... (0.004)     |
  45   (0.008) ....>D:.539_:[..G]G-----C[..C]:.531_:D<.... (0.008)     |
  46   (0.004) ....>D:.540_:[..G]G-----C[..C]:.530_:D<.... (0.004)     |
  47   (0.005) ....>D:.541_:[..C]C-----G[..G]:.529_:D<.... (0.006)     |
  48   (0.004) ....>D:.542_:[..C]C-----G[..G]:.528_:D<.... (0.005)     |
  49   (0.004) ....>D:.543_:[..G]G-----C[..C]:.527_:D<.... (0.006)     |
  50   (0.009) ....>D:.544_:[..A]A-**--G[..G]:.526_:D<.... (0.011)     |
  51   (0.004) ....>D:.510_:[..G]G-----C[..C]:.525_:D<.... (0.005)     |
  52   (0.003) ....>D:.511_:[..U]U-----A[..A]:.524_:D<.... (0.006)     |
  53   (0.003) ....>D:.512_:[..C]C-----G[..G]:.523_:D<.... (0.005)     |
  54   (0.004) ....>D:.513_:[..U]U-*---G[..G]:.522_:D<.... (0.010)     |
  55   (0.004) ....>D:.508_:[..U]U-**--A[..A]:.546_:D<.... (0.003)     |
  56   (0.007) ....>D:.514_:[..A]A-**--A[..A]:.521_:D<.... (0.005)     |
  57   (0.016) ....>D:.515_:[..G]G-**+-C[..C]:.548_:D<.... (0.007)     x
  58   (0.004) ....>D:.519_:[..G]G-----C[..C]:.556_:D<.... (0.003)     +

Нуклеотиды, образующие стебли:
Strand I                    Strand II
	     Chain C:
501-507	                    566-572
549-553                     561-565
538-544                     526-532
510-513                     522-525
	     Chain D:
501-507                     566-572
549-553			    561-565
538-544			    526-532
510-513			    522-525

Неканонические пары оснований:
2	[..G]G-*---U[..U]
13	[..U]U-**--A[..A]
14	[..U]U-**+-G[..G]
15	[..A]A-**--C[..C]
21	[..A]A-**--G[..G]
25	[..U]U-*---G[..G]
26	[..U]U-**--A[..A]
27	[..A]A-**--A[..A]
28	[..G]G-**+-C[..C]
31	[..G]G-*---U[..U]
42	[..U]U-**--A[..A]
43	[..U]U-**+-G[..G]
44	[..A]A-**--C[..C]
50	[..A]A-**--G[..G]
54	[..U]U-*---G[..G]
55	[..U]U-**--A[..A]
56	[..A]A-**--A[..A]
57	[..G]G-**+-C[..C]
Дополнительные водородные связи, стабилизирующие третичную структуру тРНК:
58	(0.004) ....>D:.519_:[..G]G-----C[..C]:.556_:D<.... (0.003)

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