1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Germann, M.W.
Aramini, J.M.
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 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA 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
C10 H15 N2 O8 P
322.208
n
THYMIDINE-3'-PHOSPHATE
ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE
DNA 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
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
N
N
127
N
C
N
128
N
C
N
129
N
H
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
O
N
144
N
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
O
N
151
S
C
N
152
N
O
N
153
N
C
N
154
R
C
Y
155
N
N
Y
156
N
C
Y
157
N
N
Y
158
N
C
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
C
N
163
N
N
N
164
N
N
Y
165
N
C
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
N
C
N
191
R
C
N
192
N
N
N
193
N
C
N
194
N
O
N
195
N
N
N
196
N
C
N
197
N
O
N
198
N
C
N
199
N
C
N
200
N
C
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
H
N
216
N
O
N
217
N
P
N
218
N
O
N
219
N
O
N
220
N
O
N
221
N
C
N
222
R
C
N
223
N
O
N
224
S
C
N
225
N
O
N
226
R
C
N
227
N
O
N
228
R
C
Y
229
N
N
Y
230
N
C
Y
231
N
N
Y
232
N
C
N
233
N
C
N
234
N
O
N
235
N
N
N
236
N
C
N
237
N
N
N
238
N
N
Y
239
N
C
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
H
N
253
N
H
N
254
N
P
N
255
N
O
N
256
N
O
N
257
N
O
N
258
N
O
N
259
N
C
N
260
R
C
N
261
N
O
N
262
S
C
N
263
N
O
N
264
N
C
N
265
R
C
N
266
N
N
N
267
N
C
N
268
N
O
N
269
N
N
N
270
N
C
N
271
N
O
N
272
N
C
N
273
N
C
N
274
N
C
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
288
N
H
N
289
N
H
N
290
N
O
N
291
N
P
N
292
N
O
N
293
N
O
N
294
N
O
N
295
N
C
N
296
R
C
N
297
N
O
N
298
S
C
N
299
N
O
N
300
R
C
N
301
N
O
N
302
R
C
N
303
N
N
N
304
N
C
N
305
N
O
N
306
N
N
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
C
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
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
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
doub
N
152
N
sing
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
Y
172
N
sing
Y
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
doub
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
doub
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
doub
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
doub
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
doub
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
Y
249
N
sing
Y
250
N
sing
Y
251
N
doub
N
252
N
sing
Y
253
N
sing
N
254
N
sing
Y
255
N
doub
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
doub
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
doub
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
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
doub
N
295
N
sing
N
296
N
sing
N
297
N
doub
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
doub
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
doub
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
N
333
N
sing
N
334
N
doub
N
335
N
sing
N
336
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
38
15448
15458
10.1021/bi9915418
10569927
Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau).
1999
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
26
5644
5654
10.1093/nar/26.24.5644
NMR solution structures of [d(GCGAAT-3'-3'-(alpha-T)-5'-5'-CGC)2] and its unmodified control
1998
10.2210/pdb1c2q/pdb
pdb_00001c2q
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
T5 IS ALPHAT ANOMERIC
2746.809
5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'
1
syn
polymer
2854.782
5'-R(GAGCACCAU)-3'
1
syn
polymer
no
yes
(DA)(DT)(DG)(DG)(T3P)(DG)(DC)(DT)(DC)
ATGGTGCTC
A
polydeoxyribonucleotide
no
no
GAGCACCAU
GAGCACCAU
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-14.855
1
20
A
1
B
18
-3.483
A_DA1:U18_B
1
-12.112
0.056
-0.338
-0.063
12.981
1
20
A
2
B
17
1.104
A_DT2:A17_B
2
-16.507
0.084
-0.340
-0.102
-0.196
1
19
A
3
B
16
0.620
A_DG3:C16_B
3
-15.757
-0.426
-0.030
-0.223
-3.473
1
19
A
4
B
15
0.089
A_DG4:C15_B
4
-11.723
-0.463
0.154
-0.224
9.001
1
20
A
5
B
14
-2.179
A_T3P5:A14_B
5
-10.114
0.055
-0.043
-0.116
4.801
1
19
A
6
B
13
0.826
A_DG6:C13_B
6
-13.429
-0.151
0.243
-0.146
4.033
1
19
A
7
B
12
0.535
A_DC7:G12_B
7
-16.100
0.405
0.054
-0.237
15.181
1
20
A
8
B
11
-1.579
A_DT8:A11_B
8
-9.147
-0.026
-0.258
0.018
19.727
1
19
A
9
B
10
0.677
A_DC9:G10_B
9
-22.747
0.289
-0.450
-0.173
2.691
29.187
A
A
1
2
1.292
B
B
18
17
2.710
0.650
0.021
-0.578
AA_DA1DT2:A17U18_BB
1
2.162
-4.295
29.102
-1.263
0.348
2.598
36.012
A
A
2
3
25.911
B
B
17
16
3.444
15.463
-0.038
-1.181
AA_DT2DG3:C16A17_BB
2
-5.524
9.256
32.161
-4.065
-0.708
3.005
32.039
A
A
3
4
9.919
B
B
16
15
3.218
5.416
-0.536
-1.285
AA_DG3DG4:C15C16_BB
3
-6.256
11.458
30.979
-3.272
-0.121
2.987
34.812
A
A
4
5
-0.343
B
B
15
14
2.987
-0.205
-0.566
-0.586
AA_DG4T3P5:A14C15_BB
4
0.187
-0.313
34.811
-0.951
0.972
2.975
34.970
A
A
5
6
9.268
B
B
14
13
3.233
5.508
0.063
-0.913
AA_T3P5DG6:C13A14_BB
5
-7.287
12.260
33.791
-2.322
-1.166
2.883
32.625
A
A
6
7
10.050
B
B
13
12
3.204
5.616
-0.356
-1.733
AA_DG6DC7:G12C13_BB
6
-1.817
3.251
32.100
-4.000
0.337
2.739
27.805
A
A
7
8
10.351
B
B
12
11
3.109
4.922
-0.402
-1.170
AA_DC7DT8:A11G12_BB
7
4.982
-10.476
26.925
-3.509
1.924
2.945
31.179
A
A
8
9
8.611
B
B
11
10
3.150
4.611
0.288
-1.107
AA_DT8DC9:G10A11_BB
8
-1.172
2.188
30.823
-2.883
-0.744
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
pdbx_validate_polymer_linkage
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Database references
Derived calculations
Data collection
1
0
1999-11-29
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
SOLUTION STRUCTURE OF A SELF-COMPLEMENTARY DNA DUPLEX CONTAINING THE SAME MODIFICATIONS (1 ALPHA-ANOMERIC THYMIDINE AND FLANKING 3'-3' AND 5'-5' PHOSPHODIESTER LINKAGES PER STRAND)
RCSB
Y
RCSB
1999-07-26
REL
REL
SYNTHETIC
sample
SYNTHETIC
sample
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES
1
2D NOESY
DQF-COSY
31P-1H CORRELATION SPECTROSCOPY
2D NOESY
6.6
AMBIENT
298
K
6.7
AMBIENT
298
K
THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED INTERACTIONS.
SIMULATED ANNEALING/MOLECULAR DYNAMICS
1
minimized average structure
0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O
0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH 6.7, 90% H2O/10% D2O
BRUKER
collection
UXNMR
2.1
BORGIAS & JAMES, 1989
iterative matrix relaxation
MARDIGRAS
3.2
BORGIAS & JAMES, 1988
data analysis
CORMA
5.2
UCSF
data analysis
Sparky
3.33
PEARLMAN ET AL., 1995
refinement
Amber
4.1
WIDMER & WUTHRICH, 1987
data analysis
SPHINX/LINSHA
LAVERY & SKLENAR, 1996
data analysis
Curves
5.1
PEARLMAN ET AL., 1995
structure solution
Amber
4.1
600
Bruker
AMX
A
1
n
1
DA
1
A
T
2
n
2
DT
2
A
G
3
n
3
DG
3
A
G
4
n
4
DG
4
A
X
5
n
5
T3P
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
G
10
n
1
G
10
B
A
11
n
2
A
11
B
G
12
n
3
G
12
B
C
13
n
4
C
13
B
A
14
n
5
A
14
B
C
15
n
6
C
15
B
C
16
n
7
C
16
B
A
17
n
8
A
17
B
U
18
n
9
U
18
B
author_defined_assembly
2
dimeric
A
T3P
5
THYMIDINE-3'-PHOSPHATE
A
T3P
5
DT
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
C1'
T3P
5
WRONG HAND
1
A
DG
6
0.070
SIDE CHAIN
1
B
A
11
0.057
SIDE CHAIN
1
B
A
14
0.097
SIDE CHAIN
1
B
A
17
0.079
SIDE CHAIN
1
3.70
0.60
106.00
109.70
A
A
A
O4'
C4'
C3'
DA
DA
DA
1
1
1
N
1
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
3.66
0.60
106.00
109.66
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
4.18
0.30
108.30
112.48
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
53.17
1.90
104.00
157.17
A
A
A
O3'
P
O5'
DG
T3P
T3P
4
5
5
Y
1
5.30
0.60
106.00
111.30
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
N
1
8.25
1.20
102.50
110.75
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
1
3.65
0.30
108.30
111.95
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
4.21
0.60
106.00
110.21
A
A
A
O4'
C4'
C3'
DC
DC
DC
7
7
7
N
1
7.14
1.10
109.80
116.94
A
A
A
C5'
C4'
O4'
DC
DC
DC
7
7
7
N
1
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-3.82
0.60
122.90
119.08
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
4.40
0.30
108.30
112.70
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
5.90
0.70
108.50
114.40
B
B
B
O4'
C1'
N9
G
G
G
10
10
10
N
1
4.30
0.70
108.50
112.80
B
B
B
O4'
C1'
N9
A
A
A
11
11
11
N
1
-3.80
0.60
118.60
114.80
B
B
B
N1
C6
N6
A
A
A
11
11
11
N
1
6.64
0.70
108.50
115.14
B
B
B
O4'
C1'
N9
G
G
G
12
12
12
N
1
6.25
0.70
108.50
114.75
B
B
B
O4'
C1'
N1
C
C
C
13
13
13
N
1
6.41
0.70
108.50
114.91
B
B
B
O4'
C1'
N1
C
C
C
15
15
15
N
1
6.89
0.70
108.50
115.39
B
B
B
O4'
C1'
N1
C
C
C
16
16
16
N
1
4.79
0.70
108.50
113.29
B
B
B
O4'
C1'
N1
U
U
U
18
18
18
N
minimized average
SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS
1
N
N
2
N
N
covale
1.614
both
A
DG
4
A
O3'
DG
4
1_555
A
T3P
5
A
P
T3P
5
1_555
covale
1.608
one
A
T3P
5
A
O5'
T3P
5
1_555
A
DG
6
A
P
DG
6
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
U
18
B
N3
U
9
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
U
18
B
O4
U
9
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
A
17
B
N1
A
8
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
A
17
B
N6
A
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
C
16
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
C
16
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
C
16
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
C
15
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
C
15
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
C
15
B
N4
C
6
1_555
hydrog
WATSON-CRICK
A
T3P
5
A
N3
T3P
5
1_555
B
A
14
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
T3P
5
A
O4
T3P
5
1_555
B
A
14
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
C
13
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
C
13
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
C
13
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
G
12
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
G
12
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
G
12
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
A
11
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
A
11
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
G
10
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
G
10
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
G
10
B
N2
G
1
1_555
DNA-RNA HYBRID
DNA/RNA HYBRID, ALPHAT-ANOMERIC THYMIDINE, 3'-3'/5'-5' PHOSPHODIESTER LINKAGES, DNA-RNA HYBRID
1C2Q
PDB
1
1C2Q
1C2Q
PDB
2
1C2Q
1
9
1C2Q
1
9
1C2Q
A
1
1
9
10
18
1C2Q
10
18
1C2Q
B
2
1
9
1
P 1