0.036114
-0.000000
0.000000
0.000000
0.020960
0.000000
0.000000
0.000000
0.008801
0.00000
0.00000
0.00000
Tereshko, V.
Wallace, S.
Usman, N.
Wincott, F.
Egli, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90
90
90
27.69
47.71
113.62
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 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
C7 H19 N3
145.246
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
non-polymer
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
N
C
N
84
R
C
Y
85
N
N
Y
86
N
C
Y
87
N
N
Y
88
N
C
Y
89
N
C
N
90
N
N
Y
91
N
N
Y
92
N
C
Y
93
N
N
Y
94
N
C
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
H
N
108
N
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
N
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
H
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
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
C
N
151
R
C
N
152
N
O
N
153
S
C
N
154
N
O
N
155
R
C
N
156
N
O
N
157
R
C
Y
158
N
N
Y
159
N
C
Y
160
N
N
Y
161
N
C
N
162
N
C
N
163
N
O
N
164
N
N
N
165
N
C
N
166
N
N
N
167
N
N
Y
168
N
C
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
180
N
H
N
181
N
H
N
182
N
H
N
183
N
O
N
184
N
H
N
185
N
H
N
186
N
N
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
N
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
N
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
O
N
216
N
P
N
217
N
O
N
218
N
O
N
219
N
O
N
220
N
C
N
221
R
C
N
222
N
O
N
223
S
C
N
224
N
O
N
225
R
C
N
226
N
O
N
227
R
C
N
228
N
N
N
229
N
C
N
230
N
O
N
231
N
N
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
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
Y
99
N
sing
Y
100
N
sing
Y
101
N
doub
N
102
N
sing
Y
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
Y
107
N
doub
N
108
N
sing
N
109
N
sing
Y
110
N
sing
Y
111
N
doub
N
112
N
sing
Y
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
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
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
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
Y
175
N
sing
Y
176
N
sing
Y
177
N
doub
N
178
N
sing
Y
179
N
sing
N
180
N
sing
Y
181
N
doub
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
doub
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
UK
RNA
RNARFU
2122
1355-8382
7
405
420
10.1017/S1355838201001935
11333021
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
2001
10.2210/pdb1i2x/pdb
pdb_00001i2x
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
1998-11-26
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
3471.194
DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3')
4
syn
polymer
145.246
SPERMIDINE
1
syn
non-polymer
18.015
water
79
nat
water
no
no
GCG(DA)(DT)(DA)(DT)ACGU
GCGATATACGU
A,B,D,C
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
n
1
2.68
54.07
VAPOR DIFFUSION, SITTING DROP
6.0
spermidine, MPD. pH 6.0, VAPOR DIFFUSION, SITTING DROP at 298
298
spermidine
1
MPD
1
MPD
2
8.302
28
B
21
A
11
-2.685
B_G21:U11_A
1
1.591
-2.559
0.555
-0.524
10.228
1
19
B
22
A
10
5.634
B_C22:G10_A
2
-26.596
0.009
-0.174
0.084
-17.693
1
19
B
23
A
9
1.736
B_G23:C9_A
3
-26.512
-0.110
-0.529
-0.121
-10.364
1
B
24
A
7
11.254
B_DA24:DT7_A
4
-18.296
-0.012
0.065
0.134
7.189
1
20
B
25
A
6
-0.363
B_DT25:DA6_A
5
-10.675
0.114
-0.572
-0.376
-8.521
1
20
B
26
A
5
-1.719
B_DA26:DT5_A
6
-8.529
-0.763
-0.755
-0.597
6.270
1
20
B
27
A
4
1.330
B_DT27:DA4_A
7
-9.029
-0.377
-0.262
-0.502
8.789
1
19
B
29
A
3
-8.424
B_C29:G3_A
8
-18.341
-0.015
-0.113
-0.343
1.153
1
19
B
30
A
2
-8.308
B_G30:C2_A
9
-15.922
0.244
0.353
0.061
-2.664
28
B
31
A
1
-3.908
B_U31:G1_A
10
0.739
2.538
0.139
-0.841
9.918
1
28
C
121
D
111
4.146
C_G121:U111_D
11
-7.615
-2.139
1.008
-0.372
5.076
1
19
C
122
D
110
1.551
C_C122:G110_D
12
-16.927
-0.023
0.232
-0.347
-19.547
1
19
C
123
D
109
-4.449
C_G123:C109_D
13
-15.974
0.866
-0.331
-0.083
-17.696
1
20
C
124
D
107
14.206
C_DA124:DT107_D
14
-16.203
-0.582
-0.042
-0.129
2.402
1
20
C
125
D
106
13.491
C_DT125:DA106_D
15
-17.759
-0.708
-0.008
-0.297
6.334
1
20
C
126
D
105
-0.415
C_DA126:DT105_D
16
-18.333
-0.001
0.025
-0.002
10.987
1
20
C
127
D
104
-5.041
C_DT127:DA104_D
17
-9.669
-0.688
-0.351
0.062
17.167
1
19
C
129
D
103
2.707
C_C129:G103_D
18
-18.987
-0.240
-0.286
-0.331
-5.956
1
19
C
130
D
102
1.541
C_G130:C102_D
19
-24.246
-0.575
0.052
-0.068
-8.989
28
C
131
D
101
2.414
C_U131:G101_D
20
-5.020
2.754
0.822
-0.561
2.996
43.636
B
B
21
22
9.235
A
A
11
10
3.203
6.827
0.147
-1.137
BB_G21C22:G10U11_AA
1
4.596
-6.217
42.890
-2.156
0.224
2.575
39.720
B
B
22
23
30.252
A
A
10
9
3.838
19.705
-0.223
-1.618
BB_C22G23:C9G10_AA
2
1.614
-2.478
34.624
-4.800
0.526
2.847
24.230
B
B
23
24
13.532
A
A
9
7
3.108
5.568
-0.756
-1.178
BB_G23DA24:DT7C9_AA
3
-6.184
15.030
22.777
-4.463
-0.041
2.642
33.251
B
B
24
25
5.751
A
A
7
6
2.735
3.276
-0.210
-0.310
BB_DA24DT25:DA6DT7_AA
4
4.419
-7.756
32.806
-0.995
0.978
3.620
32.717
B
B
25
26
16.222
A
A
6
5
3.903
9.012
0.194
-0.518
BB_DT25DA26:DT5DA6_AA
5
3.156
-5.681
31.329
-2.751
0.297
2.678
34.493
B
B
26
27
9.339
A
A
5
4
2.850
5.502
0.203
-0.594
BB_DA26DT27:DA4DT5_AA
6
-4.251
7.216
33.805
-1.731
-0.906
3.221
22.215
B
B
27
29
0.222
A
A
4
3
3.239
0.086
0.877
-1.045
BB_DT27C29:G3DA4_AA
7
-0.348
0.904
22.212
-2.744
-2.405
2.555
40.128
B
B
29
30
18.296
A
A
3
2
3.293
12.347
-0.111
-1.978
BB_C29G30:C2G3_AA
8
-3.822
5.663
38.071
-4.178
-0.239
3.284
43.160
B
B
30
31
3.703
A
A
2
1
3.347
2.719
0.492
-1.427
BB_G30U31:G1C2_AA
9
3.588
-4.885
42.936
-2.211
-0.311
3.563
-39.496
B
C
31
121
-19.149
A
D
1
111
2.325
12.678
0.064
-4.422
BC_U31G121:U111G1_DA
10
-6.025
-9.099
-37.011
5.152
-0.567
3.360
40.828
C
C
121
122
4.556
D
D
111
110
3.495
3.169
-0.214
-1.120
CC_G121C122:G110U111_DD
11
4.486
-6.449
40.473
-1.972
0.826
2.263
48.942
C
C
122
123
27.822
D
D
110
109
3.508
22.283
0.064
-2.071
CC_C122G123:C109G110_DD
12
2.835
-3.539
43.768
-4.087
0.124
3.481
17.275
C
C
123
124
-6.966
D
D
109
107
3.367
-2.087
-0.166
-1.128
CC_G123DA124:DT107C109_DD
13
-0.438
1.463
17.144
-2.384
0.265
2.834
34.913
C
C
124
125
-0.611
D
D
107
106
2.834
-0.367
-0.112
-0.321
CC_DA124DT125:DA106DT107_DD
14
0.736
-1.227
34.903
-0.487
0.284
3.143
37.087
C
C
125
126
11.230
D
D
106
105
3.219
7.101
-0.440
-0.049
CC_DT125DA126:DT105DA106_DD
15
0.908
-1.435
36.413
-1.010
0.811
2.462
24.510
C
C
126
127
21.582
D
D
105
104
3.116
8.955
0.570
-1.268
CC_DA126DT127:DA104DT105_DD
16
0.599
-1.444
22.831
-5.438
-1.179
3.436
28.935
C
C
127
129
-5.519
D
D
104
103
3.223
-2.752
1.465
-1.642
CC_DT127C129:G103DA104_DD
17
1.602
-3.212
28.762
-2.665
-2.570
2.424
36.473
C
C
129
130
28.449
D
D
103
102
3.642
17.126
-0.679
-1.876
CC_C129G130:C102G103_DD
18
-3.076
5.110
32.180
-5.346
0.663
3.424
44.768
C
C
130
131
2.506
D
D
102
101
3.507
1.903
0.062
-1.095
CC_G130U131:G101C102_DD
19
-5.951
7.836
44.352
-1.622
-0.658
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-04-21
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-02-12
REL
REL
SPD
SPERMIDINE
HOH
water
SPD
200
2
SPD
SPD
200
D
HOH
205
3
HOH
HOH
205
A
HOH
208
3
HOH
HOH
208
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
219
3
HOH
HOH
219
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
224
3
HOH
HOH
224
A
HOH
227
3
HOH
HOH
227
A
HOH
231
3
HOH
HOH
231
A
HOH
239
3
HOH
HOH
239
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
246
3
HOH
HOH
246
A
HOH
252
3
HOH
HOH
252
A
HOH
253
3
HOH
HOH
253
A
HOH
257
3
HOH
HOH
257
A
HOH
258
3
HOH
HOH
258
A
HOH
260
3
HOH
HOH
260
A
HOH
281
3
HOH
HOH
281
A
HOH
201
3
HOH
HOH
201
B
HOH
207
3
HOH
HOH
207
B
HOH
209
3
HOH
HOH
209
B
HOH
211
3
HOH
HOH
211
B
HOH
216
3
HOH
HOH
216
B
HOH
218
3
HOH
HOH
218
B
HOH
229
3
HOH
HOH
229
B
HOH
237
3
HOH
HOH
237
B
HOH
240
3
HOH
HOH
240
B
HOH
243
3
HOH
HOH
243
B
HOH
248
3
HOH
HOH
248
B
HOH
249
3
HOH
HOH
249
B
HOH
259
3
HOH
HOH
259
B
HOH
265
3
HOH
HOH
265
B
HOH
279
3
HOH
HOH
279
B
HOH
202
3
HOH
HOH
202
D
HOH
203
3
HOH
HOH
203
D
HOH
204
3
HOH
HOH
204
D
HOH
206
3
HOH
HOH
206
D
HOH
217
3
HOH
HOH
217
D
HOH
228
3
HOH
HOH
228
D
HOH
234
3
HOH
HOH
234
D
HOH
235
3
HOH
HOH
235
D
HOH
238
3
HOH
HOH
238
D
HOH
244
3
HOH
HOH
244
D
HOH
245
3
HOH
HOH
245
D
HOH
247
3
HOH
HOH
247
D
HOH
263
3
HOH
HOH
263
D
HOH
264
3
HOH
HOH
264
D
HOH
266
3
HOH
HOH
266
D
HOH
268
3
HOH
HOH
268
D
HOH
272
3
HOH
HOH
272
D
HOH
273
3
HOH
HOH
273
D
HOH
276
3
HOH
HOH
276
D
HOH
278
3
HOH
HOH
278
D
HOH
210
3
HOH
HOH
210
C
HOH
212
3
HOH
HOH
212
C
HOH
213
3
HOH
HOH
213
C
HOH
223
3
HOH
HOH
223
C
HOH
225
3
HOH
HOH
225
C
HOH
226
3
HOH
HOH
226
C
HOH
232
3
HOH
HOH
232
C
HOH
233
3
HOH
HOH
233
C
HOH
236
3
HOH
HOH
236
C
HOH
250
3
HOH
HOH
250
C
HOH
251
3
HOH
HOH
251
C
HOH
254
3
HOH
HOH
254
C
HOH
255
3
HOH
HOH
255
C
HOH
256
3
HOH
HOH
256
C
HOH
261
3
HOH
HOH
261
C
HOH
262
3
HOH
HOH
262
C
HOH
267
3
HOH
HOH
267
C
HOH
269
3
HOH
HOH
269
C
HOH
270
3
HOH
HOH
270
C
HOH
271
3
HOH
HOH
271
C
HOH
274
3
HOH
HOH
274
C
HOH
275
3
HOH
HOH
275
C
HOH
277
3
HOH
HOH
277
C
HOH
280
3
HOH
HOH
280
C
G
1
n
1
G
1
A
C
2
n
2
C
2
A
G
3
n
3
G
3
A
A
4
n
4
DA
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
A
8
n
8
A
8
A
C
9
n
9
C
9
A
G
10
n
10
G
10
A
U
11
n
11
U
11
A
G
21
n
1
G
21
B
C
22
n
2
C
22
B
G
23
n
3
G
23
B
A
24
n
4
DA
24
B
T
25
n
5
DT
25
B
A
26
n
6
DA
26
B
T
27
n
7
DT
27
B
A
28
n
8
A
28
B
C
29
n
9
C
29
B
G
30
n
10
G
30
B
U
31
n
11
U
31
B
G
101
n
1
G
101
D
C
102
n
2
C
102
D
G
103
n
3
G
103
D
A
104
n
4
DA
104
D
T
105
n
5
DT
105
D
A
106
n
6
DA
106
D
T
107
n
7
DT
107
D
A
108
n
8
A
108
D
C
109
n
9
C
109
D
G
110
n
10
G
110
D
U
111
n
11
U
111
D
G
121
n
1
G
121
C
C
122
n
2
C
122
C
G
123
n
3
G
123
C
A
124
n
4
DA
124
C
T
125
n
5
DT
125
C
A
126
n
6
DA
126
C
T
127
n
7
DT
127
C
A
128
n
8
A
128
C
C
129
n
9
C
129
C
G
130
n
10
G
130
C
U
131
n
11
U
131
C
author_defined_assembly
2
dimeric
author_defined_assembly
2
dimeric
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
G
1
0.060
SIDE CHAIN
1
B
G
21
0.054
SIDE CHAIN
1
B
A
28
0.056
SIDE CHAIN
1
D
DT
105
0.070
SIDE CHAIN
1
C
C
129
0.066
SIDE CHAIN
1
13.15
2.00
113.00
126.15
A
A
A
C4'
C3'
O3'
U
U
U
11
11
11
N
0.2782
0.2495
2.4
10
453
6220
6220
7.3
95.7
random
1
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
2.4
10
81
1011
10
920
0
2.4
20
1I2X
6220
6220
0
0
1
95.7
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
1.0
2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
hydrog
TYPE_28_PAIR
A
G
1
A
N1
G
1
1_555
B
U
31
B
O2
U
11
1_555
hydrog
TYPE_28_PAIR
A
G
1
A
O6
G
1
1_555
B
U
31
B
N3
U
11
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
30
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
30
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
30
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
B
C
29
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
B
C
29
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
B
C
29
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
27
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
27
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
26
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
26
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
25
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
25
B
O4
DT
5
1_555
hydrog
DT-DA PAIR
A
DT
7
A
N3
DT
7
1_555
B
DA
24
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
G
23
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
G
23
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
G
23
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
B
C
22
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
B
C
22
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
B
C
22
B
N4
C
2
1_555
hydrog
TYPE_28_PAIR
A
U
11
A
N3
U
11
1_555
B
G
21
B
O6
G
1
1_555
hydrog
TYPE_28_PAIR
A
U
11
A
O2
U
11
1_555
B
G
21
B
N1
G
1
1_555
hydrog
TYPE_28_PAIR
D
G
101
C
N1
G
1
1_555
C
U
131
D
O2
U
11
1_555
hydrog
TYPE_28_PAIR
D
G
101
C
O6
G
1
1_555
C
U
131
D
N3
U
11
1_555
hydrog
WATSON-CRICK
D
C
102
C
N3
C
2
1_555
C
G
130
D
N1
G
10
1_555
hydrog
WATSON-CRICK
D
C
102
C
N4
C
2
1_555
C
G
130
D
O6
G
10
1_555
hydrog
WATSON-CRICK
D
C
102
C
O2
C
2
1_555
C
G
130
D
N2
G
10
1_555
hydrog
WATSON-CRICK
D
G
103
C
N1
G
3
1_555
C
C
129
D
N3
C
9
1_555
hydrog
WATSON-CRICK
D
G
103
C
N2
G
3
1_555
C
C
129
D
O2
C
9
1_555
hydrog
WATSON-CRICK
D
G
103
C
O6
G
3
1_555
C
C
129
D
N4
C
9
1_555
hydrog
WATSON-CRICK
D
DA
104
C
N1
DA
4
1_555
C
DT
127
D
N3
DT
7
1_555
hydrog
WATSON-CRICK
D
DA
104
C
N6
DA
4
1_555
C
DT
127
D
O4
DT
7
1_555
hydrog
WATSON-CRICK
D
DT
105
C
N3
DT
5
1_555
C
DA
126
D
N1
DA
6
1_555
hydrog
WATSON-CRICK
D
DT
105
C
O4
DT
5
1_555
C
DA
126
D
N6
DA
6
1_555
hydrog
WATSON-CRICK
D
DA
106
C
N1
DA
6
1_555
C
DT
125
D
N3
DT
5
1_555
hydrog
WATSON-CRICK
D
DA
106
C
N6
DA
6
1_555
C
DT
125
D
O4
DT
5
1_555
hydrog
WATSON-CRICK
D
DT
107
C
N3
DT
7
1_555
C
DA
124
D
N1
DA
4
1_555
hydrog
WATSON-CRICK
D
DT
107
C
O4
DT
7
1_555
C
DA
124
D
N6
DA
4
1_555
hydrog
WATSON-CRICK
D
C
109
C
N3
C
9
1_555
C
G
123
D
N1
G
3
1_555
hydrog
WATSON-CRICK
D
C
109
C
N4
C
9
1_555
C
G
123
D
O6
G
3
1_555
hydrog
WATSON-CRICK
D
C
109
C
O2
C
9
1_555
C
G
123
D
N2
G
3
1_555
hydrog
WATSON-CRICK
D
G
110
C
N1
G
10
1_555
C
C
122
D
N3
C
2
1_555
hydrog
WATSON-CRICK
D
G
110
C
N2
G
10
1_555
C
C
122
D
O2
C
2
1_555
hydrog
WATSON-CRICK
D
G
110
C
O6
G
10
1_555
C
C
122
D
N4
C
2
1_555
hydrog
TYPE_28_PAIR
D
U
111
C
N3
U
11
1_555
C
G
121
D
O6
G
1
1_555
hydrog
TYPE_28_PAIR
D
U
111
C
O2
U
11
1_555
C
G
121
D
N1
G
1
1_555
DNA-RNA HYBRID
'adenine bulge, A-type NA, DNA/RNA hybrid', DNA-RNA HYBRID
1I2X
PDB
1
1I2X
1
11
1I2X
1
11
1I2X
A
1
1
11
21
31
1I2X
21
31
1I2X
B
1
1
11
101
111
1I2X
101
111
1I2X
D
1
1
11
121
131
1I2X
121
131
1I2X
C
1
1
11
BINDING SITE FOR RESIDUE SPD D 200
D
SPD
200
Software
3
A
A
8
A
A
8
3
3_545
D
C
102
C
C
2
3
1_555
D
G
103
C
G
3
3
1_555
19
orthorhombic
P 21 21 21