1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Chen, G.
Kennedy, S.D.
Krugh, T.R.
Turner, D.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C10 H13 N4 O7 P
332.207
n
PURINE RIBOSIDE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
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
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
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
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
H
N
108
N
H
N
109
N
H
N
110
N
H
Y
111
N
N
Y
112
N
C
Y
113
N
N
Y
114
N
C
Y
115
N
C
Y
116
N
C
Y
117
N
N
Y
118
N
C
Y
119
N
N
N
120
R
C
N
121
R
C
N
122
N
O
N
123
S
C
N
124
N
O
N
125
R
C
N
126
N
O
N
127
N
C
N
128
N
O
N
129
N
P
N
130
N
O
N
131
N
O
N
132
N
O
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
H
N
146
N
O
N
147
N
P
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
C
N
152
R
C
N
153
N
O
N
154
S
C
N
155
N
O
N
156
R
C
N
157
N
O
N
158
R
C
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
N
N
163
N
C
N
164
N
O
N
165
N
C
N
166
N
C
N
167
N
H
N
168
N
H
N
169
N
H
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
1
N
sing
N
2
N
sing
N
3
N
doub
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
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
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
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
Y
116
N
sing
Y
117
N
doub
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
Y
121
N
doub
Y
122
N
sing
Y
123
N
sing
Y
124
N
sing
N
125
N
sing
Y
126
N
doub
Y
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
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
45
6889
6903
10.1021/bi0524464
16734425
An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA
2006
10.2210/pdb2dd3/pdb
pdb_00002dd3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3256.996
5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3'
1
syn
polymer
3183.991
5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P))-3'
1
syn
polymer
no
no
GGUGAAGGCU
GGUGAAGGCU
A
polyribonucleotide
no
yes
GCCGAAGCC(P5P)
GCCGAAGCCA
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-18.368
1
19
A
1
B
19
-0.516
A_G1:C19_B
1
-13.214
-0.791
-0.446
-0.209
-19.229
1
19
A
2
B
18
0.434
A_G2:C18_B
2
-12.255
-0.234
-0.385
0.007
-8.290
1
28
A
3
B
17
5.718
A_U3:G17_B
3
-5.437
2.192
0.023
-0.249
10.403
9
11
A
4
B
16
-4.173
A_G4:A16_B
4
-2.657
6.735
-0.594
-4.139
8.467
9
11
A
6
B
14
-4.042
A_A6:G14_B
5
-12.445
-6.803
0.337
-3.850
4.001
1
19
A
7
B
13
0.670
A_G7:C13_B
6
-10.915
-0.571
-0.002
-0.114
10.670
1
19
A
8
B
12
0.021
A_G8:C12_B
7
-8.257
-0.620
0.157
-0.121
16.205
1
19
A
9
B
11
0.372
A_C9:G11_B
8
-16.152
0.792
-0.276
-0.191
2.796
33.762
A
A
1
2
15.700
B
B
19
18
3.353
9.005
0.362
-1.770
AA_G1G2:C18C19_BB
1
2.582
-4.501
32.473
-4.448
-0.222
2.972
39.265
A
A
2
3
4.989
B
B
18
17
3.087
3.348
0.460
-1.239
AA_G2U3:G17C18_BB
2
-0.250
0.372
39.127
-2.214
-0.712
3.044
51.343
A
A
3
4
-2.836
B
B
17
16
3.025
-2.456
-0.512
-0.959
AA_U3G4:A16G17_BB
3
1.978
-2.284
51.253
-0.950
0.717
6.015
30.080
A
A
4
6
8.557
B
B
16
14
6.728
4.367
0.580
-1.531
AA_G4A6:G14A16_BB
4
-8.507
16.669
28.553
-4.741
-4.605
3.476
61.033
A
A
6
7
5.841
B
B
14
13
3.581
5.924
0.440
-0.901
AA_A6G7:C13G14_BB
5
-1.631
1.608
60.753
-1.193
-0.517
2.898
30.606
A
A
7
8
6.116
B
B
13
12
3.070
3.213
-0.366
-1.720
AA_G7G8:C12C13_BB
6
-4.226
8.044
30.153
-3.843
-0.075
3.016
37.639
A
A
8
9
4.978
B
B
12
11
3.149
3.208
-0.068
-1.472
AA_G8C9:G11C12_BB
7
0.543
-0.843
37.504
-2.675
0.172
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2006-06-13
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-09
1
4
2024-05-29
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
3 sheared GA pairs closed by ua and cg WC pairs, 5'gguGGAggcu/3'pccaAAGccg
5'gguGAAggcu/3'pccgAAGccg
3 sheared GA pairs closed by ug wobble and cg WC pairs, 5'gguGGAggcu/3'pccgAAGccg
PDBJ
Y
PDBJ
2006-01-19
REL
REL
structures with the lowest energy, structures with the least restraint violations
40
18
1
closest to the average
80mM NaCl, 10mM sodium phosphate, 0.5mM Na2EDTA, 2mM total duplex concentrations, pH 5.1, pD 7.3
processing
Felix
refinement
Discover
collection
VNMR
500
Varian
INOVA
500
Bruker
AVANCE
600
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
G
8
n
8
G
8
A
C
9
n
9
C
9
A
U
10
n
10
U
10
A
G
11
n
1
G
11
B
C
12
n
2
C
12
B
C
13
n
3
C
13
B
G
14
n
4
G
14
B
A
15
n
5
A
15
B
A
16
n
6
A
16
B
G
17
n
7
G
17
B
C
18
n
8
C
18
B
C
19
n
9
C
19
B
P5P
20
n
10
P5P
20
B
author_defined_assembly
2
dimeric
B
P5P
20
PURINE RIBOSIDE-5'-MONOPHOSPHATE
B
P5P
10
A
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
A
A
5
0.055
SIDE CHAIN
1
B
A
15
0.059
SIDE CHAIN
2
A
A
5
0.070
SIDE CHAIN
2
B
G
11
0.064
SIDE CHAIN
2
B
G
14
0.050
SIDE CHAIN
2
B
A
16
0.067
SIDE CHAIN
3
B
A
15
0.066
SIDE CHAIN
4
B
G
14
0.057
SIDE CHAIN
4
B
A
15
0.059
SIDE CHAIN
5
A
A
5
0.065
SIDE CHAIN
5
B
G
11
0.060
SIDE CHAIN
5
B
A
15
0.068
SIDE CHAIN
5
B
A
16
0.065
SIDE CHAIN
6
B
A
16
0.088
SIDE CHAIN
7
A
A
5
0.077
SIDE CHAIN
7
B
G
11
0.056
SIDE CHAIN
7
B
G
14
0.065
SIDE CHAIN
8
A
A
5
0.053
SIDE CHAIN
8
A
A
6
0.062
SIDE CHAIN
8
A
G
7
0.080
SIDE CHAIN
8
A
G
8
0.068
SIDE CHAIN
8
B
A
15
0.067
SIDE CHAIN
9
A
A
6
0.060
SIDE CHAIN
9
A
G
7
0.072
SIDE CHAIN
9
A
G
8
0.072
SIDE CHAIN
9
B
G
11
0.059
SIDE CHAIN
9
B
A
15
0.080
SIDE CHAIN
11
A
A
5
0.077
SIDE CHAIN
11
A
G
8
0.060
SIDE CHAIN
11
B
A
15
0.062
SIDE CHAIN
12
A
A
5
0.076
SIDE CHAIN
12
B
A
15
0.076
SIDE CHAIN
13
B
A
15
0.066
SIDE CHAIN
14
B
G
14
0.069
SIDE CHAIN
15
A
G
4
0.085
SIDE CHAIN
15
B
G
11
0.059
SIDE CHAIN
15
B
G
14
0.080
SIDE CHAIN
15
B
A
16
0.060
SIDE CHAIN
16
B
G
11
0.057
SIDE CHAIN
16
B
A
16
0.076
SIDE CHAIN
17
A
G
4
0.052
SIDE CHAIN
17
A
A
6
0.060
SIDE CHAIN
18
B
G
14
0.062
SIDE CHAIN
1
5.07
0.70
108.50
113.57
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
1
5.02
0.70
108.50
113.52
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
1
4.46
0.70
108.50
112.96
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
1
5.20
0.70
108.50
113.70
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
2
5.61
0.70
108.50
114.11
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
2
4.31
0.70
108.50
112.81
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
2
4.61
0.70
108.50
113.11
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
2
5.06
0.70
108.50
113.56
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
2
4.20
0.70
108.50
112.70
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
3
5.02
0.70
108.50
113.52
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
3
5.12
0.70
108.50
113.62
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
3
4.64
0.70
108.50
113.14
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
3
5.64
0.70
108.50
114.14
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
4
4.75
0.70
108.50
113.25
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
4
5.08
0.70
108.50
113.58
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
4
4.49
0.70
108.50
112.99
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
4
5.29
0.70
108.50
113.79
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
4
4.22
0.70
108.50
112.72
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
5
5.15
0.70
108.50
113.65
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
5
4.40
0.70
108.50
112.90
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
5
4.61
0.70
108.50
113.11
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
5
5.55
0.70
108.50
114.05
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
6
4.35
0.70
108.50
112.85
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
6
5.60
0.70
108.50
114.10
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
6
4.97
0.70
108.50
113.47
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
6
5.29
0.70
108.50
113.79
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
6
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N1
U
U
U
10
10
10
N
6
4.68
0.70
108.50
113.18
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
6
4.91
0.70
108.50
113.41
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
6
4.41
0.70
108.50
112.91
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
7
5.27
0.70
108.50
113.77
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
7
5.28
0.70
108.50
113.78
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
7
4.55
0.70
108.50
113.05
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
7
5.78
0.70
108.50
114.28
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
7
4.30
0.70
108.50
112.80
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
8
4.45
0.70
108.50
112.95
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
8
5.22
0.70
108.50
113.72
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
8
5.12
0.70
108.50
113.62
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
8
5.62
0.70
108.50
114.12
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
9
4.91
0.70
108.50
113.41
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
9
6.29
0.90
109.80
116.09
A
A
A
C5'
C4'
O4'
U
U
U
10
10
10
N
9
6.50
0.70
108.50
115.00
A
A
A
O4'
C1'
N1
U
U
U
10
10
10
N
9
4.74
0.70
108.50
113.24
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
9
5.55
0.70
108.50
114.05
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
10
5.24
0.70
108.50
113.74
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
10
4.95
0.70
108.50
113.45
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
10
4.54
0.70
108.50
113.04
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
10
5.23
0.70
108.50
113.73
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
10
4.28
0.70
108.50
112.78
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
11
4.34
0.70
108.50
112.84
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
11
4.53
0.70
108.50
113.03
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
11
4.48
0.70
108.50
112.98
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
11
4.83
0.70
108.50
113.33
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
11
5.26
0.70
108.50
113.76
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
11
7.37
1.20
119.70
127.07
B
B
B
C3'
O3'
P
A
A
A
15
15
16
Y
12
5.58
0.70
108.50
114.08
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
12
4.78
0.70
108.50
113.28
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
12
5.00
0.70
108.50
113.50
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
12
4.22
0.70
108.50
112.72
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
13
4.76
0.70
108.50
113.26
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
13
5.78
0.70
108.50
114.28
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
13
4.94
0.70
108.50
113.44
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
13
4.60
0.70
108.50
113.10
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
13
5.29
0.70
108.50
113.79
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
14
5.79
0.70
108.50
114.29
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
14
5.22
0.70
108.50
113.72
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
14
4.79
0.70
108.50
113.29
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
14
5.18
0.70
108.50
113.68
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
14
4.22
0.70
108.50
112.72
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
15
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
15
5.10
0.70
108.50
113.60
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
15
4.44
0.70
108.50
112.94
A
A
A
O4'
C1'
N9
G
G
G
4
4
4
N
15
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
15
4.35
0.70
108.50
112.85
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
15
4.97
0.70
108.50
113.47
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
15
4.30
0.70
108.50
112.80
B
B
B
O4'
C1'
N9
A
A
A
16
16
16
N
16
5.60
0.70
108.50
114.10
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
16
5.16
0.70
108.50
113.66
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
16
4.55
0.70
108.50
113.05
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
16
5.86
0.70
108.50
114.36
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
16
4.22
0.70
108.50
112.72
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
17
5.05
0.70
108.50
113.55
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
17
5.08
0.70
108.50
113.58
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
17
4.69
0.70
108.50
113.19
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
17
5.72
0.70
108.50
114.22
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
17
5.28
0.70
108.50
113.78
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
18
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
18
5.03
0.70
108.50
113.53
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
18
4.41
0.70
108.50
112.91
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
18
5.25
0.70
108.50
113.75
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
18
4.23
0.70
108.50
112.73
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack
1
N
N
2
N
N
covale
1.616
both
B
C
19
B
O3'
C
9
1_555
B
P5P
20
B
P
P5P
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
19
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
19
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
19
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
18
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
18
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
18
B
N4
C
8
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
N3
U
3
1_555
B
G
17
B
O6
G
7
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
O2
U
3
1_555
B
G
17
B
N1
G
7
1_555
hydrog
TYPE_11_PAIR
A
G
4
A
N2
G
4
1_555
B
A
16
B
N7
A
6
1_555
hydrog
TYPE_11_PAIR
A
G
4
A
N3
G
4
1_555
B
A
16
B
N6
A
6
1_555
hydrog
TYPE_11_PAIR
A
A
6
A
N6
A
6
1_555
B
G
14
B
N3
G
4
1_555
hydrog
TYPE_11_PAIR
A
A
6
A
N7
A
6
1_555
B
G
14
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
13
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
13
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
13
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
B
C
12
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
B
C
12
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
B
C
12
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
G
11
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
G
11
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
G
11
B
N2
G
1
1_555
RNA
rapid conformation exchange, alternating sheared AA pair, sequence specific A-minor motif, Kink-turn motif, thermodynamics, RNA secondary structure prediction, RNA
2DD3
PDB
1
2DD3
2DD3
PDB
2
2DD3
1
10
2DD3
1
10
2DD3
A
1
1
10
11
20
2DD3
11
20
2DD3
B
2
1
10
1
P 1