0.020710
0.000000
0.000000
0.000000
0.020521
0.000000
0.000000
0.000000
0.008333
0.00000
0.00000
0.00000
Zhao, Q.
Han, Q.
Kissinger, C.R.
Thompson, P.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
48.286
48.730
119.999
C9 H12 Br N2 O9 P
403.077
n
5-BROMO-URIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Sr 2
87.620
STRONTIUM ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
N
22
N
BR
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
R
C
N
46
N
O
N
47
R
C
Y
48
N
N
Y
49
N
C
Y
50
N
N
Y
51
N
C
Y
52
N
C
N
53
N
N
Y
54
N
N
Y
55
N
C
Y
56
N
N
Y
57
N
C
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
R
C
N
83
N
O
N
84
R
C
N
85
N
N
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
N
N
91
N
C
N
92
N
C
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
O
N
108
N
P
N
109
N
O
N
110
N
O
N
111
N
O
N
112
N
C
N
113
R
C
N
114
N
O
N
115
S
C
N
116
N
O
N
117
R
C
N
118
N
O
N
119
R
C
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
N
129
N
N
Y
130
N
C
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
SR
N
149
N
O
N
150
N
P
N
151
N
O
N
152
N
O
N
153
N
O
N
154
N
C
N
155
R
C
N
156
N
O
N
157
S
C
N
158
N
O
N
159
R
C
N
160
N
O
N
161
R
C
N
162
N
N
N
163
N
C
N
164
N
O
N
165
N
N
N
166
N
C
N
167
N
O
N
168
N
C
N
169
N
C
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
doub
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
Y
60
N
sing
Y
61
N
sing
Y
62
N
doub
N
63
N
sing
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
doub
N
69
N
sing
N
70
N
sing
Y
71
N
sing
Y
72
N
doub
N
73
N
sing
Y
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
doub
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
64
436
443
10.1107/S0907444908002011
18391410
Structure of hepatitis C virus IRES subdomain IIa.
2008
10.2210/pdb2pn4/pdb
pdb_00002pn4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
77
1
mirrors
CCD
2006-03-04
ADSC QUANTUM 315
SAGITALLY FOCUSED Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.97949
1.0
8-BM
APS
0.97949
SYNCHROTRON
APS BEAMLINE 8-BM
7644.589
5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
HCV IRES Subdomain IIa (residue 47-70)
G47C,U48G,A70C
2
syn
polymer
6564.623
5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
HCV IRES Subdomain IIa (residue 98-117)
A99C,A116G
2
syn
polymer
87.620
STRONTIUM ION
10
syn
non-polymer
18.015
water
67
nat
water
no
no
CGGAGGAACUACUGUCUUCACGCC
CGGAGGAACUACUGUCUUCACGCC
A,C
polyribonucleotide
no
yes
GCG(5BU)GUCGUGCAGCC(5BU)CCGG
GCGUGUCGUGCAGCCUCCGG
B,D
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.48
50.48
EVAPORATION
6.2
30% MPD, 80mM SrCl2, 25mM NaCl, 50mM Cacodylate equilibrated with 60%MPD, pH 6.2, EVAPORATION, temperature 290.0K
290.0
30% MPD
1
SrCl2
1
NaCl
1
Cacodylate
1
60%MPD
2
4.510
1
19
A
47
B
116
0.876
A_C47:G116_B
1
-8.536
0.022
-0.003
-0.230
3.342
1
19
A
48
B
115
-0.400
A_G48:C115_B
2
-8.694
-0.408
0.083
-0.355
-4.359
1
19
A
49
B
114
-0.274
A_G49:C114_B
3
-11.999
-0.341
-0.181
-0.341
-6.390
1
20
A
50
B
113
1.497
A_A50:5BU113_B
4
-11.200
0.162
-0.244
-0.271
-0.094
1
19
A
51
B
112
2.239
A_G51:C112_B
5
-7.052
-0.169
-0.021
-0.190
-5.602
1
19
A
52
B
111
2.198
A_G52:C111_B
6
-5.305
-0.503
0.053
-0.084
4.719
1
19
A
58
B
110
0.929
A_C58:G110_B
7
-19.825
0.162
-0.173
-0.193
0.581
1
20
A
59
B
109
-5.942
A_U59:A109_B
8
-17.749
0.153
-0.014
-0.370
-1.709
1
19
A
60
B
108
-0.602
A_G60:C108_B
9
-13.559
-0.303
0.414
-0.209
-1.736
1
28
A
61
B
107
-0.084
A_U61:G107_B
10
-12.452
2.158
0.247
-0.622
4.244
1
19
A
62
B
105
-4.478
A_C62:G105_B
11
-11.471
-0.057
0.150
-0.225
10.000
1
18
A
63
B
104
20.506
A_U63:C104_B
12
-27.450
0.001
0.208
-1.533
3.041
1
16
A
64
B
103
20.007
A_U64:U103_B
13
-17.954
-2.423
0.767
-1.767
-6.060
1
19
A
65
B
102
3.145
A_C65:G102_B
14
-19.410
1.042
0.763
-0.400
-0.478
1
20
A
66
B
101
-3.772
A_A66:5BU101_B
15
-14.007
0.093
0.375
-0.279
5.461
1
19
A
67
B
100
-1.208
A_C67:G100_B
16
-16.536
0.123
0.290
0.009
-3.532
1
19
A
68
B
99
0.526
A_G68:C99_B
17
-23.447
0.120
0.219
-0.196
-7.671
1
19
A
69
B
98
1.055
A_C69:G98_B
18
-21.754
0.594
0.393
0.044
7.389
1
19
C
47
D
116
0.006
C_C47:G116_D
19
-12.784
0.293
-0.155
-0.246
-0.109
1
19
C
48
D
115
-1.041
C_G48:C115_D
20
-12.525
-0.463
0.049
-0.238
-5.735
1
19
C
49
D
114
2.243
C_G49:C114_D
21
-12.676
-0.358
-0.202
-0.224
-5.970
1
20
C
50
D
113
0.907
C_A50:5BU113_D
22
-12.051
0.089
-0.097
-0.266
-3.817
1
19
C
51
D
112
2.552
C_G51:C112_D
23
-10.209
-0.288
-0.111
-0.176
-7.473
1
19
C
52
D
111
0.413
C_G52:C111_D
24
-4.163
-0.472
-0.187
-0.164
5.056
1
19
C
58
D
110
-1.278
C_C58:G110_D
25
-21.765
0.210
-0.138
-0.162
-1.683
1
20
C
59
D
109
-3.746
C_U59:A109_D
26
-16.699
0.251
0.148
-0.354
-5.442
1
19
C
60
D
108
1.911
C_G60:C108_D
27
-17.409
-0.358
0.036
-0.083
-0.357
1
28
C
61
D
107
-1.610
C_U61:G107_D
28
-16.129
2.154
0.281
-0.715
2.409
1
19
C
62
D
105
-2.429
C_C62:G105_D
29
-12.270
-0.317
-0.059
-0.133
8.831
1
18
C
63
D
104
16.049
C_U63:C104_D
30
-26.809
0.101
0.052
-1.743
-2.703
1
16
C
64
D
103
12.765
C_U64:U103_D
31
-19.119
-2.238
0.700
-2.061
-5.184
1
19
C
65
D
102
2.727
C_C65:G102_D
32
-17.895
0.811
0.267
-0.325
0.396
1
20
C
66
D
101
-0.491
C_A66:5BU101_D
33
-13.913
0.280
0.462
-0.328
0.144
1
19
C
67
D
100
4.491
C_C67:G100_D
34
-18.488
-0.364
0.506
0.163
-2.111
1
19
C
68
D
99
2.970
C_G68:C99_D
35
-22.161
0.406
0.632
0.012
-4.804
1
19
C
69
D
98
3.560
C_C69:G98_D
36
-24.773
0.926
0.449
-0.096
2.668
32.561
A
A
47
48
16.597
B
B
116
115
3.213
9.183
-0.590
-1.615
AA_C47G48:C115G116_BB
1
-1.438
2.600
31.241
-4.351
0.822
3.171
33.475
A
A
48
49
8.865
B
B
115
114
3.464
5.084
0.402
-1.854
AA_G48G49:C114C115_BB
2
2.214
-3.860
33.026
-4.075
-0.325
2.862
35.051
A
A
49
50
13.854
B
B
114
113
3.256
8.270
-0.144
-1.343
AA_G49A50:5BU113C114_BB
3
0.145
-0.243
34.091
-3.408
0.259
2.945
27.109
A
A
50
51
4.480
B
B
113
112
3.089
2.098
0.796
-1.943
AA_A50G51:C1125BU113_BB
4
0.444
-0.949
27.025
-4.634
-1.595
2.998
29.621
A
A
51
52
8.621
B
B
112
111
3.337
4.391
0.548
-2.234
AA_G51G52:C111C112_BB
5
1.300
-2.552
29.273
-5.272
-0.804
2.718
38.148
A
A
58
59
22.564
B
B
110
109
3.292
14.406
-0.359
-0.967
AA_C58U59:A109G110_BB
6
-0.881
1.380
35.407
-3.221
0.443
2.674
33.722
A
A
59
60
16.515
B
B
109
108
3.103
9.456
0.535
-1.044
AA_U59G60:C108A109_BB
7
-1.543
2.695
32.370
-3.186
-1.149
3.197
45.893
A
A
60
61
5.158
B
B
108
107
3.267
4.012
0.591
-1.172
AA_G60U61:G107C108_BB
8
4.126
-5.304
45.550
-1.847
-0.403
2.094
29.767
A
A
61
62
17.630
B
B
107
105
2.720
8.894
0.306
-1.783
AA_U61C62:G105G107_BB
9
4.190
-8.305
28.131
-4.881
0.069
1.759
24.733
A
A
62
63
36.160
B
B
105
104
3.084
14.416
-0.060
-1.215
AA_C62U63:C104G105_BB
10
-4.742
11.894
19.588
-6.474
-1.057
1.696
32.941
A
A
63
64
23.408
B
B
104
103
2.898
12.626
0.248
-1.837
AA_U63U64:U103C104_BB
11
-12.094
22.423
28.028
-4.880
-2.009
3.562
52.785
A
A
64
65
2.018
B
B
103
102
3.608
1.794
-0.775
-0.719
AA_U64C65:G102U103_BB
12
1.483
-1.668
52.738
-0.936
0.977
1.744
21.831
A
A
65
66
23.847
B
B
102
101
2.795
8.772
-1.114
-1.822
AA_C65A66:5BU101G102_BB
13
1.707
-4.640
19.938
-7.302
3.426
2.943
36.465
A
A
66
67
2.800
B
B
101
100
3.001
1.752
0.420
-1.320
AA_A66C67:G1005BU101_BB
14
0.662
-1.059
36.418
-2.330
-0.587
2.279
31.503
A
A
67
68
24.709
B
B
100
99
3.292
13.022
-0.287
-1.744
AA_C67G68:C99G100_BB
15
2.044
-3.879
28.676
-5.383
0.869
2.856
39.066
A
A
68
69
14.015
B
B
99
98
3.262
9.289
0.095
-1.401
AA_G68C69:G98C99_BB
16
0.740
-1.117
37.981
-3.157
-0.057
2.617
31.332
C
C
47
48
21.167
D
D
116
115
3.386
11.184
-0.659
-1.686
CC_C47G48:C115G116_DD
17
-1.933
3.659
29.253
-5.128
0.874
3.060
33.321
C
C
48
49
11.765
D
D
115
114
3.453
6.698
0.522
-1.795
CC_G48G49:C114C115_DD
18
2.044
-3.590
32.597
-4.254
-0.567
2.880
35.067
C
C
49
50
10.518
D
D
114
113
3.175
6.302
-0.360
-1.498
CC_G49A50:5BU113C114_DD
19
-1.920
3.205
34.462
-3.370
0.329
2.963
28.400
C
C
50
51
7.634
D
D
113
112
3.180
3.731
0.893
-1.953
CC_A50G51:C1125BU113_DD
20
2.304
-4.715
28.066
-4.792
-1.320
3.067
29.083
C
C
51
52
7.736
D
D
112
111
3.362
3.872
0.272
-2.114
CC_G51G52:C111C112_DD
21
1.541
-3.078
28.789
-5.048
-0.208
2.854
39.533
C
C
58
59
21.280
D
D
110
109
3.330
14.089
-0.374
-0.842
CC_C58U59:A109G110_DD
22
-2.759
4.167
36.932
-2.869
0.235
2.742
32.120
C
C
59
60
18.800
D
D
109
108
3.222
10.225
0.427
-1.089
CC_U59G60:C108A109_DD
23
1.692
-3.112
30.444
-3.687
-0.488
3.068
46.055
C
C
60
61
4.295
D
D
108
107
3.142
3.357
0.536
-1.027
CC_G60U61:G107C108_DD
24
0.419
-0.536
45.938
-1.587
-0.650
2.127
27.289
C
C
61
62
18.822
D
D
107
105
2.786
8.636
0.352
-1.660
CC_U61C62:G105G107_DD
25
6.810
-14.842
25.013
-5.210
0.587
1.823
30.364
C
C
62
63
37.388
D
D
105
104
3.149
18.138
-0.072
-1.102
CC_C62U63:C104G105_DD
26
-6.484
13.366
23.584
-5.244
-0.985
2.300
36.475
C
C
63
64
19.034
D
D
104
103
3.128
11.469
0.102
-1.449
CC_U63U64:U103C104_DD
27
-12.838
21.305
32.279
-3.720
-1.737
3.217
45.050
C
C
64
65
3.343
D
D
103
102
3.385
2.557
-1.187
-1.099
CC_U64C65:G102U103_DD
28
3.739
-4.888
44.833
-1.667
1.889
2.232
25.798
C
C
65
66
19.373
D
D
102
101
2.900
8.491
-0.614
-1.643
CC_C65A66:5BU101G102_DD
29
-0.998
2.277
24.363
-5.595
1.149
2.942
31.551
C
C
66
67
8.139
D
D
101
100
3.195
4.412
0.502
-1.661
CC_A66C67:G1005BU101_DD
30
0.230
-0.424
31.248
-3.827
-0.882
2.780
33.044
C
C
67
68
12.008
D
D
100
99
3.129
6.784
-0.136
-1.423
CC_C67G68:C99G100_DD
31
0.380
-0.673
32.357
-3.550
0.297
2.870
40.991
C
C
68
69
11.116
D
D
99
98
3.167
7.720
0.212
-1.363
CC_G68C69:G98C99_DD
32
5.447
-7.843
39.933
-2.735
0.254
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Advisory
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2008-04-01
1
1
2011-07-13
1
2
2023-08-30
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2007-04-23
REL
REL
SR
STRONTIUM ION
HOH
water
This sequence of RNA naturally exists in hepatitis C virus
sample
This sequence of RNA naturally exists in hepatitis C virus
sample
2PN3
PDB ENTRY 2PN3
PDB
experimental model
SR
1001
3
SR
SR
1001
A
SR
1002
3
SR
SR
1002
A
SR
1006
3
SR
SR
1006
A
SR
1027
3
SR
SR
1027
A
SR
1005
3
SR
SR
1005
A
SR
1003
3
SR
SR
1003
C
SR
1004
3
SR
SR
1004
C
SR
1009
3
SR
SR
1009
C
SR
1022
3
SR
SR
1022
C
SR
1008
3
SR
SR
1008
C
HOH
4
4
HOH
HOH
1028
A
HOH
9
4
HOH
HOH
1029
A
HOH
10
4
HOH
HOH
1030
A
HOH
12
4
HOH
HOH
1031
A
HOH
18
4
HOH
HOH
1032
A
HOH
23
4
HOH
HOH
1033
A
HOH
25
4
HOH
HOH
1034
A
HOH
44
4
HOH
HOH
1035
A
HOH
46
4
HOH
HOH
1036
A
HOH
47
4
HOH
HOH
1037
A
HOH
53
4
HOH
HOH
1038
A
HOH
59
4
HOH
HOH
1039
A
HOH
63
4
HOH
HOH
1040
A
HOH
67
4
HOH
HOH
1041
A
HOH
72
4
HOH
HOH
1042
A
HOH
74
4
HOH
HOH
1043
A
HOH
75
4
HOH
HOH
1044
A
HOH
92
4
HOH
HOH
1045
A
HOH
93
4
HOH
HOH
1046
A
HOH
103
4
HOH
HOH
1047
A
HOH
153
4
HOH
HOH
1048
A
HOH
6
4
HOH
HOH
118
B
HOH
11
4
HOH
HOH
119
B
HOH
24
4
HOH
HOH
120
B
HOH
26
4
HOH
HOH
121
B
HOH
29
4
HOH
HOH
122
B
HOH
30
4
HOH
HOH
123
B
HOH
34
4
HOH
HOH
124
B
HOH
38
4
HOH
HOH
125
B
HOH
64
4
HOH
HOH
126
B
HOH
66
4
HOH
HOH
127
B
HOH
68
4
HOH
HOH
128
B
HOH
73
4
HOH
HOH
129
B
HOH
81
4
HOH
HOH
130
B
HOH
102
4
HOH
HOH
131
B
HOH
145
4
HOH
HOH
132
B
HOH
161
4
HOH
HOH
133
B
HOH
1
4
HOH
HOH
1023
C
HOH
22
4
HOH
HOH
1024
C
HOH
39
4
HOH
HOH
1025
C
HOH
45
4
HOH
HOH
1026
C
HOH
57
4
HOH
HOH
1027
C
HOH
71
4
HOH
HOH
1028
C
HOH
76
4
HOH
HOH
1029
C
HOH
77
4
HOH
HOH
1030
C
HOH
83
4
HOH
HOH
1031
C
HOH
96
4
HOH
HOH
1032
C
HOH
104
4
HOH
HOH
1033
C
HOH
136
4
HOH
HOH
1034
C
HOH
179
4
HOH
HOH
1035
C
HOH
3
4
HOH
HOH
118
D
HOH
27
4
HOH
HOH
119
D
HOH
28
4
HOH
HOH
120
D
HOH
31
4
HOH
HOH
121
D
HOH
33
4
HOH
HOH
122
D
HOH
36
4
HOH
HOH
123
D
HOH
40
4
HOH
HOH
124
D
HOH
41
4
HOH
HOH
125
D
HOH
43
4
HOH
HOH
126
D
HOH
54
4
HOH
HOH
127
D
HOH
65
4
HOH
HOH
128
D
HOH
84
4
HOH
HOH
129
D
HOH
89
4
HOH
HOH
130
D
HOH
99
4
HOH
HOH
131
D
HOH
100
4
HOH
HOH
132
D
HOH
112
4
HOH
HOH
133
D
HOH
196
4
HOH
HOH
134
D
C
47
n
1
C
47
A
G
48
n
2
G
48
A
G
49
n
3
G
49
A
A
50
n
4
A
50
A
G
51
n
5
G
51
A
G
52
n
6
G
52
A
A
53
n
7
A
53
A
A
54
n
8
A
54
A
C
55
n
9
C
55
A
U
56
n
10
U
56
A
A
57
n
11
A
57
A
C
58
n
12
C
58
A
U
59
n
13
U
59
A
G
60
n
14
G
60
A
U
61
n
15
U
61
A
C
62
n
16
C
62
A
U
63
n
17
U
63
A
U
64
n
18
U
64
A
C
65
n
19
C
65
A
A
66
n
20
A
66
A
C
67
n
21
C
67
A
G
68
n
22
G
68
A
C
69
n
23
C
69
A
C
70
n
24
C
70
A
G
98
n
1
G
98
B
C
99
n
2
C
99
B
G
100
n
3
G
100
B
5BU
101
n
4
5BU
101
B
G
102
n
5
G
102
B
U
103
n
6
U
103
B
C
104
n
7
C
104
B
G
105
n
8
G
105
B
U
106
n
9
U
106
B
G
107
n
10
G
107
B
C
108
n
11
C
108
B
A
109
n
12
A
109
B
G
110
n
13
G
110
B
C
111
n
14
C
111
B
C
112
n
15
C
112
B
5BU
113
n
16
5BU
113
B
C
114
n
17
C
114
B
C
115
n
18
C
115
B
G
116
n
19
G
116
B
G
117
n
20
G
117
B
C
47
n
1
C
47
C
G
48
n
2
G
48
C
G
49
n
3
G
49
C
A
50
n
4
A
50
C
G
51
n
5
G
51
C
G
52
n
6
G
52
C
A
53
n
7
A
53
C
A
54
n
8
A
54
C
C
55
n
9
C
55
C
U
56
n
10
U
56
C
A
57
n
11
A
57
C
C
58
n
12
C
58
C
U
59
n
13
U
59
C
G
60
n
14
G
60
C
U
61
n
15
U
61
C
C
62
n
16
C
62
C
U
63
n
17
U
63
C
U
64
n
18
U
64
C
C
65
n
19
C
65
C
A
66
n
20
A
66
C
C
67
n
21
C
67
C
G
68
n
22
G
68
C
C
69
n
23
C
69
C
C
70
n
24
C
70
C
G
98
n
1
G
98
D
C
99
n
2
C
99
D
G
100
n
3
G
100
D
5BU
101
n
4
5BU
101
D
G
102
n
5
G
102
D
U
103
n
6
U
103
D
C
104
n
7
C
104
D
G
105
n
8
G
105
D
U
106
n
9
U
106
D
G
107
n
10
G
107
D
C
108
n
11
C
108
D
A
109
n
12
A
109
D
G
110
n
13
G
110
D
C
111
n
14
C
111
D
C
112
n
15
C
112
D
5BU
113
n
16
5BU
113
D
C
114
n
17
C
114
D
C
115
n
18
C
115
D
G
116
n
19
G
116
D
G
117
n
20
G
117
D
2.8545
0.1486
0.4450
0.4417
0.2893
2.8951
0.0175
-0.2278
0.2657
-0.1410
-0.1201
-0.2420
-0.2087
0.1855
0.1026
-0.0837
-0.0447
0.0110
-0.0901
-0.0115
-0.0066
refined
-9.5438
-7.1940
14.8938
X-RAY DIFFRACTION
0.2019
-0.1002
0.0957
2.8179
-0.0331
2.0653
-0.1730
-0.1624
-0.1329
-0.2827
0.0546
0.2617
0.2838
-0.1908
0.1184
-0.0229
-0.0504
-0.0022
-0.1024
0.0186
-0.0170
refined
-29.1709
-27.0239
15.1391
X-RAY DIFFRACTION
A
47
A
1
A
70
A
24
X-RAY DIFFRACTION
1
B
98
B
1
B
117
B
20
X-RAY DIFFRACTION
1
C
47
C
1
C
70
C
24
X-RAY DIFFRACTION
2
D
98
D
1
D
117
D
20
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
4600
-144.5
7570
4600
-144.5
7570
A
C
55
A
O2
C
9
1_555
A
SR
1001
E
SR
SR
1_555
A
HOH
1046
O
O
HOH
1_555
67.0
A
C
55
A
O2
C
9
1_555
A
SR
1001
E
SR
SR
1_555
B
HOH
126
P
O
HOH
1_555
86.8
A
HOH
1046
O
O
HOH
1_555
A
SR
1001
E
SR
SR
1_555
B
HOH
126
P
O
HOH
1_555
137.5
A
G
60
A
O6
G
14
1_555
A
SR
1002
F
SR
SR
1_555
A
HOH
1038
O
O
HOH
1_555
70.3
A
HOH
1032
O
O
HOH
1_555
A
SR
1005
I
SR
SR
1_555
A
HOH
1045
O
O
HOH
1_555
88.9
C
G
60
C
O6
G
14
1_555
C
SR
1003
J
SR
SR
1_555
C
HOH
1032
Q
O
HOH
1_555
69.5
B
5BU
101
5-BROMO-URIDINE-5'-MONOPHOSPHATE
B
5BU
4
U
B
5BU
113
5-BROMO-URIDINE-5'-MONOPHOSPHATE
B
5BU
16
U
D
5BU
101
5-BROMO-URIDINE-5'-MONOPHOSPHATE
D
5BU
4
U
D
5BU
113
5-BROMO-URIDINE-5'-MONOPHOSPHATE
D
5BU
16
U
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
C
C
O
O
HOH
HOH
1023
1024
1.96
1
-8.03
1.00
102.60
94.57
A
A
A
C4'
C3'
C2'
G
G
G
52
52
52
N
1
4.35
0.70
108.50
112.85
A
A
A
O4'
C1'
N1
C
C
C
55
55
55
N
1
7.93
1.20
119.70
127.63
A
A
A
C3'
O3'
P
C
C
U
55
55
56
Y
1
3.28
0.50
110.60
113.88
A
A
A
C2
N3
C4
A
A
A
57
57
57
N
1
4.47
0.70
108.50
112.97
A
A
A
O4'
C1'
N1
U
U
U
59
59
59
N
1
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N1
U
U
U
63
63
63
N
1
4.46
0.70
108.50
112.96
A
A
A
O4'
C1'
N1
C
C
C
67
67
67
N
1
-8.02
0.70
109.70
101.68
B
B
B
C1'
O4'
C4'
G
G
G
105
105
105
N
1
7.45
0.70
108.50
115.95
B
B
B
O4'
C1'
N9
G
G
G
105
105
105
N
1
7.34
1.20
119.70
127.04
B
B
B
C3'
O3'
P
C
C
5BU
112
112
113
Y
1
4.34
0.70
108.50
112.84
C
C
C
O4'
C1'
N1
U
U
U
56
56
56
N
1
-3.07
0.50
129.30
126.23
C
C
C
N1
C2
N3
A
A
A
57
57
57
N
1
4.57
0.70
108.50
113.07
D
D
D
O4'
C1'
N1
C
C
C
99
99
99
N
1
5.99
0.90
109.80
115.79
D
D
D
C5'
C4'
O4'
G
G
G
100
100
100
N
1
-4.39
0.70
109.70
105.31
D
D
D
C1'
O4'
C4'
G
G
G
105
105
105
N
1
4.86
0.70
108.50
113.36
D
D
D
O4'
C1'
N9
A
A
A
109
109
109
N
1
-3.12
0.50
129.30
126.18
D
D
D
N1
C2
N3
A
A
A
109
109
109
N
1
8.64
1.20
119.70
128.34
D
D
D
C3'
O3'
P
C
C
5BU
112
112
113
Y
51.272
-2.24
0.00
0.00
-0.38
0.00
2.62
0.909
0.872
spare matrix least squares procedure
0.32037
0.26141
0.26515
0.26405
2.32
59.98
598
12210
11590
4.9
94.92
16.579
0.220
RANDOM
LIKELY RESIDUAL
1
Isotropic
THROUGHOUT
0
MOLECULAR REPLACEMENT
0.445
0.314
0.80
0.80
1.40
PDB ENTRY 2PN3
MAXIMUM LIKELIHOOD
MASK
0.38
0.39
5
0.32
0.335
2.32
59.98
67
1937
10
1860
0
0.010
0.021
2072
1.835
3.000
3224
0.078
0.200
436
0.008
0.020
904
0.165
0.200
732
0.279
0.200
1250
0.162
0.200
94
0.222
0.200
7
0.164
0.200
46
0.317
0.200
10
1.409
3.000
2562
1.940
4.500
3224
0.43
0.301
2.380
36
752
1247
20
86.03
59.9
2.32
59.98
2PN4
12751
12228
0
0.108
1
17.5
5.5
95.9
0.714
2.32
2.43
2.4
1247
1
6.9
100
refinement
REFMAC
5.2.0019
data collection
ADSC
Quantum
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHASER
Crystal Structure of Hepatitis C Virus IRES Subdomain IIa
1
N
N
2
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
The biological assembly is generated by applying the operation X, Y, Z to chains A, B or by applying the operation X, Y, Z to chains C, D.
covale
1.603
both
B
G
100
B
O3'
G
3
1_555
B
5BU
101
B
P
5BU
4
1_555
covale
1.614
both
B
5BU
101
B
O3'
5BU
4
1_555
B
G
102
B
P
G
5
1_555
covale
1.601
both
B
C
112
B
O3'
C
15
1_555
B
5BU
113
B
P
5BU
16
1_555
covale
1.602
both
B
5BU
113
B
O3'
5BU
16
1_555
B
C
114
B
P
C
17
1_555
covale
1.592
both
D
G
100
D
O3'
G
3
1_555
D
5BU
101
D
P
5BU
4
1_555
covale
1.618
both
D
5BU
101
D
O3'
5BU
4
1_555
D
G
102
D
P
G
5
1_555
covale
1.596
both
D
C
112
D
O3'
C
15
1_555
D
5BU
113
D
P
5BU
16
1_555
covale
1.591
both
D
5BU
113
D
O3'
5BU
16
1_555
D
C
114
D
P
C
17
1_555
metalc
2.213
A
A
54
A
OP1
A
8
1_555
A
SR
1027
H
SR
SR
1_555
metalc
2.561
A
C
55
A
O2
C
9
1_555
A
SR
1001
E
SR
SR
1_555
metalc
2.759
A
G
60
A
O6
G
14
1_555
A
SR
1002
F
SR
SR
1_555
metalc
2.322
A
SR
1001
E
SR
SR
1_555
A
HOH
1046
O
O
HOH
1_555
metalc
2.523
A
SR
1001
E
SR
SR
1_555
B
HOH
126
P
O
HOH
1_555
metalc
2.701
A
SR
1002
F
SR
SR
1_555
A
HOH
1038
O
O
HOH
1_555
metalc
2.634
A
SR
1005
I
SR
SR
1_555
A
HOH
1032
O
O
HOH
1_555
metalc
2.541
A
SR
1005
I
SR
SR
1_555
A
HOH
1045
O
O
HOH
1_555
metalc
2.275
C
A
54
C
OP1
A
8
1_555
C
SR
1022
M
SR
SR
1_555
metalc
2.554
C
C
55
C
O2
C
9
1_555
C
SR
1004
K
SR
SR
1_555
metalc
2.733
C
G
60
C
O6
G
14
1_555
C
SR
1003
J
SR
SR
1_555
metalc
2.714
C
SR
1003
J
SR
SR
1_555
C
HOH
1032
Q
O
HOH
1_555
metalc
2.672
C
SR
1008
N
SR
SR
1_555
C
HOH
1034
Q
O
HOH
1_555
metalc
2.691
C
SR
1009
L
SR
SR
1_555
C
HOH
1033
Q
O
HOH
1_555
hydrog
WATSON-CRICK
A
C
47
A
N3
C
1
1_555
B
G
116
B
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
47
A
N4
C
1
1_555
B
G
116
B
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
47
A
O2
C
1
1_555
B
G
116
B
N2
G
19
1_555
hydrog
WATSON-CRICK
A
G
48
A
N1
G
2
1_555
B
C
115
B
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
48
A
N2
G
2
1_555
B
C
115
B
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
48
A
O6
G
2
1_555
B
C
115
B
N4
C
18
1_555
hydrog
WATSON-CRICK
A
G
49
A
N1
G
3
1_555
B
C
114
B
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
49
A
N2
G
3
1_555
B
C
114
B
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
49
A
O6
G
3
1_555
B
C
114
B
N4
C
17
1_555
hydrog
WATSON-CRICK
A
A
50
A
N1
A
4
1_555
B
5BU
113
B
N3
5BU
16
1_555
hydrog
WATSON-CRICK
A
A
50
A
N6
A
4
1_555
B
5BU
113
B
O4
5BU
16
1_555
hydrog
WATSON-CRICK
A
G
51
A
N1
G
5
1_555
B
C
112
B
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
51
A
N2
G
5
1_555
B
C
112
B
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
51
A
O6
G
5
1_555
B
C
112
B
N4
C
15
1_555
hydrog
WATSON-CRICK
A
G
52
A
N1
G
6
1_555
B
C
111
B
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
52
A
N2
G
6
1_555
B
C
111
B
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
52
A
O6
G
6
1_555
B
C
111
B
N4
C
14
1_555
hydrog
WATSON-CRICK
A
C
58
A
N3
C
12
1_555
B
G
110
B
N1
G
13
1_555
hydrog
WATSON-CRICK
A
C
58
A
N4
C
12
1_555
B
G
110
B
O6
G
13
1_555
hydrog
WATSON-CRICK
A
C
58
A
O2
C
12
1_555
B
G
110
B
N2
G
13
1_555
hydrog
WATSON-CRICK
A
U
59
A
N3
U
13
1_555
B
A
109
B
N1
A
12
1_555
hydrog
WATSON-CRICK
A
U
59
A
O4
U
13
1_555
B
A
109
B
N6
A
12
1_555
hydrog
WATSON-CRICK
A
G
60
A
N1
G
14
1_555
B
C
108
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
60
A
N2
G
14
1_555
B
C
108
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
60
A
O6
G
14
1_555
B
C
108
B
N4
C
11
1_555
hydrog
TYPE_28_PAIR
A
U
61
A
N3
U
15
1_555
B
G
107
B
O6
G
10
1_555
hydrog
TYPE_28_PAIR
A
U
61
A
O2
U
15
1_555
B
G
107
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
62
A
N3
C
16
1_555
B
G
105
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
C
62
A
N4
C
16
1_555
B
G
105
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
C
62
A
O2
C
16
1_555
B
G
105
B
N2
G
8
1_555
hydrog
TYPE_18_PAIR
A
U
63
A
N3
U
17
1_555
B
C
104
B
N3
C
7
1_555
hydrog
TYPE_18_PAIR
A
U
63
A
O4
U
17
1_555
B
C
104
B
N4
C
7
1_555
hydrog
TYPE_16_PAIR
A
U
64
A
N3
U
18
1_555
B
U
103
B
O2
U
6
1_555
hydrog
TYPE_16_PAIR
A
U
64
A
O4
U
18
1_555
B
U
103
B
N3
U
6
1_555
hydrog
WATSON-CRICK
A
C
65
A
N3
C
19
1_555
B
G
102
B
N1
G
5
1_555
hydrog
WATSON-CRICK
A
C
65
A
N4
C
19
1_555
B
G
102
B
O6
G
5
1_555
hydrog
WATSON-CRICK
A
C
65
A
O2
C
19
1_555
B
G
102
B
N2
G
5
1_555
hydrog
WATSON-CRICK
A
A
66
A
N1
A
20
1_555
B
5BU
101
B
N3
5BU
4
1_555
hydrog
WATSON-CRICK
A
A
66
A
N6
A
20
1_555
B
5BU
101
B
O4
5BU
4
1_555
hydrog
WATSON-CRICK
A
C
67
A
N3
C
21
1_555
B
G
100
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
67
A
N4
C
21
1_555
B
G
100
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
67
A
O2
C
21
1_555
B
G
100
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
G
68
A
N1
G
22
1_555
B
C
99
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
68
A
N2
G
22
1_555
B
C
99
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
68
A
O6
G
22
1_555
B
C
99
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
69
A
N3
C
23
1_555
B
G
98
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
69
A
N4
C
23
1_555
B
G
98
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
69
A
O2
C
23
1_555
B
G
98
B
N2
G
1
1_555
hydrog
WATSON-CRICK
C
C
47
C
N3
C
1
1_555
D
G
116
D
N1
G
19
1_555
hydrog
WATSON-CRICK
C
C
47
C
N4
C
1
1_555
D
G
116
D
O6
G
19
1_555
hydrog
WATSON-CRICK
C
C
47
C
O2
C
1
1_555
D
G
116
D
N2
G
19
1_555
hydrog
WATSON-CRICK
C
G
48
C
N1
G
2
1_555
D
C
115
D
N3
C
18
1_555
hydrog
WATSON-CRICK
C
G
48
C
N2
G
2
1_555
D
C
115
D
O2
C
18
1_555
hydrog
WATSON-CRICK
C
G
48
C
O6
G
2
1_555
D
C
115
D
N4
C
18
1_555
hydrog
WATSON-CRICK
C
G
49
C
N1
G
3
1_555
D
C
114
D
N3
C
17
1_555
hydrog
WATSON-CRICK
C
G
49
C
N2
G
3
1_555
D
C
114
D
O2
C
17
1_555
hydrog
WATSON-CRICK
C
G
49
C
O6
G
3
1_555
D
C
114
D
N4
C
17
1_555
hydrog
WATSON-CRICK
C
A
50
C
N1
A
4
1_555
D
5BU
113
D
N3
5BU
16
1_555
hydrog
WATSON-CRICK
C
A
50
C
N6
A
4
1_555
D
5BU
113
D
O4
5BU
16
1_555
hydrog
WATSON-CRICK
C
G
51
C
N1
G
5
1_555
D
C
112
D
N3
C
15
1_555
hydrog
WATSON-CRICK
C
G
51
C
N2
G
5
1_555
D
C
112
D
O2
C
15
1_555
hydrog
WATSON-CRICK
C
G
51
C
O6
G
5
1_555
D
C
112
D
N4
C
15
1_555
hydrog
WATSON-CRICK
C
G
52
C
N1
G
6
1_555
D
C
111
D
N3
C
14
1_555
hydrog
WATSON-CRICK
C
G
52
C
N2
G
6
1_555
D
C
111
D
O2
C
14
1_555
hydrog
WATSON-CRICK
C
G
52
C
O6
G
6
1_555
D
C
111
D
N4
C
14
1_555
hydrog
WATSON-CRICK
C
C
58
C
N3
C
12
1_555
D
G
110
D
N1
G
13
1_555
hydrog
WATSON-CRICK
C
C
58
C
N4
C
12
1_555
D
G
110
D
O6
G
13
1_555
hydrog
WATSON-CRICK
C
C
58
C
O2
C
12
1_555
D
G
110
D
N2
G
13
1_555
hydrog
WATSON-CRICK
C
U
59
C
N3
U
13
1_555
D
A
109
D
N1
A
12
1_555
hydrog
WATSON-CRICK
C
U
59
C
O4
U
13
1_555
D
A
109
D
N6
A
12
1_555
hydrog
WATSON-CRICK
C
G
60
C
N1
G
14
1_555
D
C
108
D
N3
C
11
1_555
hydrog
WATSON-CRICK
C
G
60
C
N2
G
14
1_555
D
C
108
D
O2
C
11
1_555
hydrog
WATSON-CRICK
C
G
60
C
O6
G
14
1_555
D
C
108
D
N4
C
11
1_555
hydrog
TYPE_28_PAIR
C
U
61
C
N3
U
15
1_555
D
G
107
D
O6
G
10
1_555
hydrog
TYPE_28_PAIR
C
U
61
C
O2
U
15
1_555
D
G
107
D
N1
G
10
1_555
hydrog
WATSON-CRICK
C
C
62
C
N3
C
16
1_555
D
G
105
D
N1
G
8
1_555
hydrog
WATSON-CRICK
C
C
62
C
N4
C
16
1_555
D
G
105
D
O6
G
8
1_555
hydrog
WATSON-CRICK
C
C
62
C
O2
C
16
1_555
D
G
105
D
N2
G
8
1_555
hydrog
TYPE_18_PAIR
C
U
63
C
N3
U
17
1_555
D
C
104
D
N3
C
7
1_555
hydrog
TYPE_18_PAIR
C
U
63
C
O4
U
17
1_555
D
C
104
D
N4
C
7
1_555
hydrog
TYPE_16_PAIR
C
U
64
C
N3
U
18
1_555
D
U
103
D
O2
U
6
1_555
hydrog
TYPE_16_PAIR
C
U
64
C
O4
U
18
1_555
D
U
103
D
N3
U
6
1_555
hydrog
WATSON-CRICK
C
C
65
C
N3
C
19
1_555
D
G
102
D
N1
G
5
1_555
hydrog
WATSON-CRICK
C
C
65
C
N4
C
19
1_555
D
G
102
D
O6
G
5
1_555
hydrog
WATSON-CRICK
C
C
65
C
O2
C
19
1_555
D
G
102
D
N2
G
5
1_555
hydrog
WATSON-CRICK
C
A
66
C
N1
A
20
1_555
D
5BU
101
D
N3
5BU
4
1_555
hydrog
WATSON-CRICK
C
A
66
C
N6
A
20
1_555
D
5BU
101
D
O4
5BU
4
1_555
hydrog
WATSON-CRICK
C
C
67
C
N3
C
21
1_555
D
G
100
D
N1
G
3
1_555
hydrog
WATSON-CRICK
C
C
67
C
N4
C
21
1_555
D
G
100
D
O6
G
3
1_555
hydrog
WATSON-CRICK
C
C
67
C
O2
C
21
1_555
D
G
100
D
N2
G
3
1_555
hydrog
WATSON-CRICK
C
G
68
C
N1
G
22
1_555
D
C
99
D
N3
C
2
1_555
hydrog
WATSON-CRICK
C
G
68
C
N2
G
22
1_555
D
C
99
D
O2
C
2
1_555
hydrog
WATSON-CRICK
C
G
68
C
O6
G
22
1_555
D
C
99
D
N4
C
2
1_555
hydrog
WATSON-CRICK
C
C
69
C
N3
C
23
1_555
D
G
98
D
N1
G
1
1_555
hydrog
WATSON-CRICK
C
C
69
C
N4
C
23
1_555
D
G
98
D
O6
G
1
1_555
hydrog
WATSON-CRICK
C
C
69
C
O2
C
23
1_555
D
G
98
D
N2
G
1
1_555
RNA
HCV, IRES, subdoamin IIa, RNA, Strontium, Hepatitis
2PN4
PDB
1
2PN4
CGGAGGAACUACUGUCUUCACGCC
2PN4
PDB
2
2PN4
GCGUGUCGUGCAGCCUCCGG
47
70
2PN4
47
70
2PN4
A
1
1
24
47
70
2PN4
47
70
2PN4
C
1
1
24
98
117
2PN4
98
117
2PN4
B
2
1
20
98
117
2PN4
98
117
2PN4
D
2
1
20
BINDING SITE FOR RESIDUE SR A 1001
A
SR
1001
Software
2
BINDING SITE FOR RESIDUE SR A 1002
A
SR
1002
Software
1
BINDING SITE FOR RESIDUE SR C 1003
C
SR
1003
Software
1
BINDING SITE FOR RESIDUE SR C 1022
C
SR
1022
Software
1
BINDING SITE FOR RESIDUE SR A 1027
A
SR
1027
Software
1
BINDING SITE FOR RESIDUE SR A 1005
A
SR
1005
Software
2
BINDING SITE FOR RESIDUE SR C 1008
C
SR
1008
Software
2
A
HOH
1046
O
HOH
2
1_555
B
HOH
126
P
HOH
2
1_555
A
HOH
1038
O
HOH
1
1_555
C
HOH
1032
Q
HOH
1
1_555
A
HOH
1035
O
HOH
1
1_555
A
HOH
1036
O
HOH
1
1_555
A
HOH
1032
O
HOH
2
1_555
A
HOH
1045
O
HOH
2
1_555
C
HOH
1028
Q
HOH
2
1_555
C
HOH
1034
Q
HOH
2
1_555
19
P 21 21 21