1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Cross, C.W.
Rice, J.S.
Gao, X.
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
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-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
C11 H16 N2 O5
256.255
n
5'-METHYLTHYMIDINE
DNA linking
C10 H15 N2 O7 P S
338.274
n
3'-THIO-THYMIDINE-5'-PHOSPHATE
DNA 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
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
N
C
N
118
R
C
Y
119
N
N
Y
120
N
C
Y
121
N
N
Y
122
N
C
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
C
N
127
N
N
N
128
N
N
Y
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
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
C
N
163
N
C
N
164
N
C
N
165
N
H
N
166
N
H
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
180
N
O
N
181
N
P
N
182
N
O
N
183
N
O
N
184
N
O
N
185
N
C
N
186
R
C
N
187
N
O
N
188
S
C
N
189
N
O
N
190
R
C
N
191
N
O
N
192
R
C
Y
193
N
N
Y
194
N
C
Y
195
N
N
Y
196
N
C
N
197
N
C
N
198
N
O
N
199
N
N
N
200
N
C
N
201
N
N
N
202
N
N
Y
203
N
C
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
H
N
216
N
H
N
217
N
H
N
218
N
C
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
N
C
N
226
R
C
N
227
N
N
N
228
N
C
N
229
N
O
N
230
N
N
N
231
N
C
N
232
N
O
N
233
N
C
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
249
N
H
N
250
N
H
N
251
N
H
N
252
N
P
N
253
N
O
N
254
N
O
N
255
N
O
N
256
N
O
N
257
N
C
N
258
R
C
N
259
N
O
N
260
S
C
N
261
N
S
N
262
N
C
N
263
R
C
N
264
N
N
N
265
N
C
N
266
N
O
N
267
N
N
N
268
N
C
N
269
N
O
N
270
N
C
N
271
N
C
N
272
N
C
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
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
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
Y
134
N
sing
Y
135
N
sing
Y
136
N
doub
N
137
N
sing
Y
138
N
sing
N
139
N
sing
Y
140
N
doub
N
141
N
doub
N
142
N
sing
N
143
N
sing
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
doub
N
153
N
sing
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
N
175
N
doub
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
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
doub
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
Y
211
N
sing
Y
212
N
sing
Y
213
N
doub
N
214
N
sing
Y
215
N
sing
N
216
N
sing
Y
217
N
doub
N
218
N
doub
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
sing
N
248
N
sing
N
249
N
sing
N
250
N
doub
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
doub
N
255
N
sing
N
256
N
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
doub
N
292
N
sing
N
293
N
sing
N
294
N
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
36
4096
4107
10.1021/bi962382k
9100003
Solution structure of an RNA x DNA hybrid duplex containing a 3'-thioformacetal linker and an RNA A-tract.
1997
10.2210/pdb1ac3/pdb
pdb_00001ac3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
T6-3'-THIOFORMACETAL IN THE DNA STRAND
3595.477
ANTISENSE HYBRID DUPLEX
1
syn
polymer
T6-3'-THIOFORMACETAL IN THE DNA STRAND
3873.416
DNA (5'-D(*(TCP)P*TP*GP*CP*GP*C)-3')
1
syn
polymer
no
yes
(DC)(DG)(DC)(DG)(DT)(TSP)(TCP)(DT)(DG)(DC)(DG)(DC)
CGCGTTTTGCGC
A
polydeoxyribonucleotide
no
no
GCGCAAAACGCG
GCGCAAAACGCG
B
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
34.708
1
19
A
1
B
24
-1.494
A_DC1:G24_B
1
-30.013
0.059
-0.455
0.038
13.060
1
19
A
2
B
23
1.480
A_DG2:C23_B
2
-20.635
-0.181
-0.163
-0.129
12.470
1
19
A
3
B
22
0.242
A_DC3:G22_B
3
-25.130
-0.256
-0.291
-0.064
-1.280
1
19
A
4
B
21
-2.686
A_DG4:C21_B
4
-13.479
-0.594
0.176
-0.232
6.797
1
20
A
5
B
20
-2.508
A_DT5:A20_B
5
-5.567
0.128
0.456
-0.122
24.486
1
20
A
6
B
19
0.547
A_TSP6:A19_B
6
-19.176
0.296
-0.618
-0.055
29.194
1
20
A
7
B
18
-1.958
A_TCP7:A18_B
7
-16.153
-0.121
-0.582
0.053
28.838
1
20
A
8
B
17
2.636
A_DT8:A17_B
8
-24.896
0.254
-0.910
-0.046
7.700
1
19
A
9
B
16
-0.305
A_DG9:C16_B
9
-20.205
-0.586
-0.049
-0.231
8.066
1
19
A
10
B
15
-2.261
A_DC10:G15_B
10
-24.822
0.115
0.096
-0.114
2.601
1
19
A
11
B
14
-3.728
A_DG11:C14_B
11
-19.467
-0.166
0.462
-0.157
11.488
1
19
A
12
B
13
-4.690
A_DC12:G13_B
12
-19.945
0.172
0.428
-0.166
1.791
42.778
A
A
1
2
41.580
B
B
24
23
3.610
27.824
-0.587
-1.627
AA_DC1DG2:C23G24_BB
1
-7.966
11.904
31.845
-4.908
0.038
2.873
29.893
A
A
2
3
7.160
B
B
23
22
3.085
3.669
-0.337
-1.701
AA_DG2DC3:G22C23_BB
2
-4.829
9.425
29.285
-3.997
-0.269
1.575
36.290
A
A
3
4
37.989
B
B
22
21
3.321
21.906
-0.245
-1.794
AA_DC3DG4:C21G22_BB
3
-7.803
13.533
28.055
-5.495
-0.538
2.777
31.324
A
A
4
5
9.537
B
B
21
20
3.119
5.113
-0.064
-1.784
AA_DG4DT5:A20C21_BB
4
-4.103
7.653
30.647
-4.184
-0.587
2.738
31.601
A
A
5
6
-1.003
B
B
20
19
2.734
-0.544
0.105
-1.355
AA_DT5TSP6:A19A20_BB
5
5.224
-9.635
31.172
-2.404
0.623
2.879
32.751
A
A
6
7
18.131
B
B
19
18
3.305
10.061
-0.351
-0.963
AA_TSP6TCP7:A18A19_BB
6
-1.804
3.251
31.156
-3.391
0.321
2.999
34.593
A
A
7
8
14.172
B
B
18
17
3.322
8.349
-0.379
-0.958
AA_TCP7DT8:A17A18_BB
7
0.480
-0.815
33.597
-2.875
0.710
1.578
38.317
A
A
8
9
45.781
B
B
17
16
3.653
26.869
-0.384
-1.470
AA_DT8DG9:C16A17_BB
8
-9.305
15.854
25.954
-5.501
-0.544
2.874
35.956
A
A
9
10
10.016
B
B
16
15
3.068
6.142
-0.347
-1.035
AA_DG9DC10:G15C16_BB
9
-4.125
6.727
35.212
-2.482
0.021
2.269
34.274
A
A
10
11
27.140
B
B
15
14
3.119
15.409
-0.163
-1.202
AA_DC10DG11:C14G15_BB
10
-4.195
7.389
30.425
-4.162
-0.301
2.975
34.519
A
A
11
12
-0.962
B
B
14
13
2.973
-0.570
0.080
-1.137
AA_DG11DC12:G13C14_BB
11
-2.914
4.917
34.394
-1.835
-0.546
chem_comp
ndb_struct_na_base_pair
ndb_struct_na_base_pair_step
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_keywords
entity_poly
pdbx_struct_assembly
pdbx_struct_assembly_gen
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Derived calculations
Other
Structure summary
Derived calculations
Polymer sequence
Data collection
Database references
Derived calculations
1
0
1997-06-16
1
1
2008-03-24
1
2
2011-07-13
1
3
2019-07-31
2
0
2020-07-22
2
1
2024-04-10
_chem_comp.type
_ndb_struct_na_base_pair.buckle
_ndb_struct_na_base_pair_step.tilt
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
_struct_keywords.text
_entity_poly.pdbx_seq_one_letter_code_can
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
Y
BNL
1997-02-11
REL
IONIC_STRENGTH: 0.1 M NACL, 10 MM PO4 PRESSURE: 1 SOLVENT SYSTEM: AQUEOUS THE STRUCTURE WAS DETERMINED USING PROTON-PROTON AND PROTON-PHOSPHOROUS 1D AND 2D NMR SPECTROSCOPY.
IDEAL GEOMETRY, NOE VIOLATIONS, COORDINATE RMSD
10
8
NOESY
DQF-COSY
7.0
298
K
7.0
288
K
1. GENERATE DISTANCE RESTRAINTS USING MARDIGRAS PROGRAM FROM T. JAMES' LAB. 2. MODEL BUILDING T. JAMES' LAB.USING QUANTA. 3. RANDOMIZE STRUCTURES BY DYNAMICS SIMULATIONS. 4. ITERATIVE CALCULATIONS. 5. FINAL RELAXATION MATRIX REFINEMENT.
SIMULATED ANNEALING, MOLECULAR DYNAMICS SIMULATIONS AND RELAXATION MATRIX REFINEMENT
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
600
Bruker
AMX-II
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
TSP
6
n
6
TSP
6
A
TCP
7
n
7
TCP
7
A
T
8
n
8
DT
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
G
11
n
11
DG
11
A
C
12
n
12
DC
12
A
G
13
n
1
G
13
B
C
14
n
2
C
14
B
G
15
n
3
G
15
B
C
16
n
4
C
16
B
A
17
n
5
A
17
B
A
18
n
6
A
18
B
A
19
n
7
A
19
B
A
20
n
8
A
20
B
C
21
n
9
C
21
B
G
22
n
10
G
22
B
C
23
n
11
C
23
B
G
24
n
12
G
24
B
author_defined_assembly
2
dimeric
A
TSP
6
3'-THIO-THYMIDINE-5'-PHOSPHATE
A
TSP
6
T
A
TCP
7
5'-METHYLTHYMIDINE
A
TCP
7
DT
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
2
B
G
15
0.075
SIDE CHAIN
3
B
C
21
0.060
SIDE CHAIN
6
B
C
21
0.069
SIDE CHAIN
7
B
C
21
0.070
SIDE CHAIN
1
5.27
0.30
108.30
113.57
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
4.24
0.30
108.30
112.54
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.41
0.30
108.30
112.71
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.98
0.30
108.30
111.28
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
3.44
0.30
108.30
111.74
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
3.44
0.30
108.30
111.74
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
4.70
0.70
108.50
113.20
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
1
4.93
0.70
108.50
113.43
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
1
5.13
0.70
108.50
113.63
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
1
4.60
0.70
108.50
113.10
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
1
5.99
0.70
108.50
114.49
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
2
5.08
0.30
108.30
113.38
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
2
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
2
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
2
3.72
0.30
108.30
112.02
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
2
3.98
0.30
108.30
112.28
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
3.03
0.30
108.30
111.33
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
2
3.95
0.30
108.30
112.25
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
2
2.85
0.30
108.30
111.15
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
2
3.82
0.30
108.30
112.12
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
2
5.23
0.70
108.50
113.73
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
2
4.45
0.70
108.50
112.95
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
2
5.11
0.70
108.50
113.61
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
2
4.75
0.70
108.50
113.25
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
2
5.93
0.70
108.50
114.43
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
3
5.38
0.30
108.30
113.68
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
3
3.11
0.30
108.30
111.41
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
3
5.16
0.30
108.30
113.46
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
3
3.34
0.30
108.30
111.64
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
3
4.01
0.30
108.30
112.31
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
3.34
0.30
108.30
111.64
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
3
3.90
0.30
108.30
112.20
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
3
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
3
3.21
0.30
108.30
111.51
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
3
5.19
0.70
108.50
113.69
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
3
5.46
0.70
108.50
113.96
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
3
4.95
0.70
108.50
113.45
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
3
4.42
0.70
108.50
112.92
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
3
6.05
0.70
108.50
114.55
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
4
5.42
0.30
108.30
113.72
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
4
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
4
4.72
0.30
108.30
113.02
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
4
3.15
0.30
108.30
111.45
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
4
4.15
0.30
108.30
112.45
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
3.58
0.30
108.30
111.88
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
4
4.39
0.30
108.30
112.69
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
4
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
4
3.60
0.30
108.30
111.90
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
4
4.82
0.70
108.50
113.32
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
4
4.98
0.70
108.50
113.48
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
4
4.96
0.70
108.50
113.46
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
4
4.67
0.70
108.50
113.17
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
4
5.74
0.70
108.50
114.24
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
5
5.45
0.30
108.30
113.75
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
5
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
5
4.96
0.30
108.30
113.26
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
5
3.28
0.30
108.30
111.58
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
5
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
3.50
0.30
108.30
111.80
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
5
3.95
0.30
108.30
112.25
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
5
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
5
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
5
4.99
0.70
108.50
113.49
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
5
4.85
0.70
108.50
113.35
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
5
4.80
0.70
108.50
113.30
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
5
4.28
0.70
108.50
112.78
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
5
5.81
0.70
108.50
114.31
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
6
5.28
0.30
108.30
113.58
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
6
3.14
0.30
108.30
111.44
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
6
4.92
0.30
108.30
113.22
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
6
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
6
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
6
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
6
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
6
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
6
4.94
0.70
108.50
113.44
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
6
5.34
0.70
108.50
113.84
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
6
4.66
0.70
108.50
113.16
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
6
4.50
0.70
108.50
113.00
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
6
5.61
0.70
108.50
114.11
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
7
5.17
0.30
108.30
113.47
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
7
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
7
4.66
0.30
108.30
112.96
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
7
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
7
4.07
0.30
108.30
112.37
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
7
3.23
0.30
108.30
111.53
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
7
3.63
0.30
108.30
111.93
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
7
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
7
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
7
4.66
0.70
108.50
113.16
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
7
4.87
0.70
108.50
113.37
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
7
4.65
0.70
108.50
113.15
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
7
4.72
0.70
108.50
113.22
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
7
5.40
0.70
108.50
113.90
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
8
4.56
0.30
108.30
112.86
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
8
3.53
0.30
108.30
111.83
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
8
4.34
0.30
108.30
112.64
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
8
3.72
0.30
108.30
112.02
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
8
4.44
0.30
108.30
112.74
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
8
3.66
0.30
108.30
111.96
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
8
3.66
0.30
108.30
111.96
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
8
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
8
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
8
4.23
0.70
108.50
112.73
B
B
B
O4'
C1'
N9
G
G
G
13
13
13
N
8
4.81
0.70
108.50
113.31
B
B
B
O4'
C1'
N1
C
C
C
14
14
14
N
8
4.65
0.70
108.50
113.15
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
8
5.07
0.70
108.50
113.57
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
8
4.72
0.70
108.50
113.22
B
B
B
O4'
C1'
N1
C
C
C
21
21
21
N
8
5.39
0.70
108.50
113.89
B
B
B
O4'
C1'
N1
C
C
C
23
23
23
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
SOLUTION STRUCTURE OF AN RNA-DNA HYBRID DUPLEX CONTAINING A 3'-THIOFORMACETAL LINKER AND AN RNA A-TRACT, NMR, 8 STRUCTURES
1
N
N
2
N
N
covale
1.610
both
A
DT
5
A
O3'
DT
5
1_555
A
TSP
6
A
P
TSP
6
1_555
covale
1.810
none
A
TSP
6
A
S3'
TSP
6
1_555
A
TCP
7
A
CP
TCP
7
1_555
covale
1.610
both
A
TCP
7
A
O3'
TCP
7
1_555
A
DT
8
A
P
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
G
24
B
N1
G
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
G
24
B
O6
G
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
G
24
B
N2
G
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
C
23
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
C
23
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
C
23
B
N4
C
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
G
22
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
G
22
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
G
22
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
C
21
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
C
21
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
C
21
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
A
20
B
N1
A
8
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
A
20
B
N6
A
8
1_555
hydrog
WATSON-CRICK
A
TSP
6
A
N3
TSP
6
1_555
B
A
19
B
N1
A
7
1_555
hydrog
WATSON-CRICK
A
TSP
6
A
O4
TSP
6
1_555
B
A
19
B
N6
A
7
1_555
hydrog
WATSON-CRICK
A
TCP
7
A
N3
TCP
7
1_555
B
A
18
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
TCP
7
A
O4
TCP
7
1_555
B
A
18
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
A
17
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
A
17
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
C
16
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
C
16
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
C
16
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
G
15
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
G
15
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
G
15
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
C
14
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
C
14
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
C
14
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N3
DC
12
1_555
B
G
13
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
G
13
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
G
13
B
N2
G
1
1_555
DNA-RNA HYBRID
RNA, DNA, ANTISENSE OLIGONUCLEOTIDES, THIOFORMACETAL BACKBONE MODIFICATION, HYBRID DUPLEX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID
1AC3
PDB
1
1AC3
1AC3
PDB
2
1AC3
1
12
1AC3
1
12
1AC3
A
1
1
12
13
24
1AC3
13
24
1AC3
B
2
1
12
1
P 1