0.032080
0.000000
0.000000
0.000000
0.032080
0.000000
0.000000
0.000000
0.011859
0.00000
0.00000
0.00000
Harp, J.M.
Egli, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
31.172
31.172
84.325
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 H13 Br N3 O8 P
402.093
n
5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 F N2 O8 P
340.199
1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione
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
N
86
N
N
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
C
N
93
N
C
N
94
N
BR
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
R
C
N
119
N
O
N
120
R
C
Y
121
N
N
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
N
Y
131
N
C
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
H
N
146
N
O
N
147
N
H
N
148
N
H
N
149
N
CO
N
150
N
N
N
151
N
N
N
152
N
N
N
153
N
N
N
154
N
N
N
155
N
N
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
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
O
N
175
N
P
N
176
N
O
N
177
N
O
N
178
N
O
N
179
N
C
N
180
R
C
N
181
N
O
N
182
S
C
N
183
N
O
N
184
R
C
N
185
N
O
N
186
R
C
N
187
N
N
N
188
N
C
N
189
N
O
N
190
N
N
N
191
N
C
N
192
N
O
N
193
N
C
N
194
N
C
N
195
N
H
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
O
N
209
N
C
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
N
N
216
R
C
N
217
N
O
N
218
R
C
N
219
N
F
N
220
R
C
N
221
N
O
N
222
S
C
N
223
S
C
N
224
N
C
N
225
N
O
N
226
N
P
N
227
N
O
N
228
N
O
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
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
O
N
243
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
sing
N
79
N
doub
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
sing
N
102
N
doub
N
103
N
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
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
N
135
N
sing
Y
136
N
sing
Y
137
N
sing
Y
138
N
doub
N
139
N
sing
Y
140
N
sing
N
141
N
sing
Y
142
N
doub
N
143
N
doub
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
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
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
doub
N
181
N
sing
N
182
N
sing
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
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
doub
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
doub
N
209
N
sing
N
210
N
doub
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
doub
N
220
N
sing
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
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
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
US
J.Org.Chem.
JOCEAH
0035
0022-3263
81
2261
2279
10.1021/acs.joc.5b02375
26940174
Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.
2016
10.2210/pdb5d8t/pdb
pdb_00005d8t
100
1
IMAGE PLATE
2015-07-24
MAR scanner 300 mm plate
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.91833
1.0
193718
0.145
1.09
1.200
50.000
13758
99.70
14.10
21-ID-D
APS
0.91833
SYNCHROTRON
APS BEAMLINE 21-ID-D
2621.475
RNA oligonucleotide containing (S)-C5'-Me-2'-FU
2
syn
polymer
161.116
COBALT HEXAMMINE(III)
4
syn
non-polymer
18.015
water
126
nat
water
no
yes
(CBV)GAA(U5M)UCG
CGAAXUCG
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
1
1.95
37.04
VAPOR DIFFUSION, SITTING DROP
5.5
40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2
298
7.111
1
19
A
1
B
8
-1.296
A_CBV1:G8_B
1
-8.572
0.123
-0.143
-0.086
-4.494
1
19
A
2
B
7
-0.597
A_G2:C7_B
2
-19.164
-0.227
0.047
-0.175
-8.964
1
20
A
3
B
6
-3.091
A_A3:U6_B
3
-11.426
0.032
-0.181
-0.089
3.342
1
20
A
6
B
3
3.453
A_U6:A3_B
4
-14.179
-0.024
0.044
-0.098
1.039
1
19
A
7
B
2
0.047
A_C7:G2_B
5
-14.459
0.252
-0.017
-0.163
-9.355
1
19
A
8
B
1
-0.813
A_G8:CBV1_B
6
-14.546
-0.177
-0.090
-0.126
2.587
36.591
A
A
1
2
20.915
B
B
8
7
3.425
12.864
0.313
-1.801
AA_CBV1G2:C7G8_BB
1
-1.757
2.857
34.285
-4.552
-0.728
2.957
36.117
A
A
2
3
11.256
B
B
7
6
3.309
6.938
-0.963
-1.560
AA_G2A3:U6C7_BB
2
0.153
-0.248
35.466
-3.464
1.574
2.911
33.484
A
A
6
7
11.729
B
B
3
2
3.257
6.714
-0.342
-1.479
AA_U6C7:G2A3_BB
3
-0.524
0.915
32.819
-3.621
0.511
2.322
34.102
A
A
7
8
26.043
B
B
2
1
3.356
14.784
0.133
-1.704
AA_C7G8:CBV1G2_BB
4
2.033
-3.582
30.751
-5.056
0.068
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_oper_list
repository
Initial release
Data collection
Data collection
Database references
Derived calculations
1
0
2016-06-29
1
1
2016-07-27
1
2
2024-03-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_oper_list.symmetry_operation
N
RCSB
Y
RCSB
2015-08-17
REL
REL
0.074
1.029
13.10
0.088
1.074
15.20
0.103
1.253
16.40
0.123
1.259
16.50
0.137
1.152
16.70
0.157
1.132
16.70
0.168
1.123
16.90
0.214
1.177
16.70
0.303
1.118
16.90
0.391
1.127
16.60
0.510
1.086
16.40
0.555
1.033
16.00
0.589
1.056
14.70
0.577
1.006
13.00
0.500
1.047
11.70
0.534
1.000
11.10
0.498
0.997
10.10
0.529
0.933
9.40
0.552
0.937
8.70
0.584
0.953
8.10
1
A
O
HOH
257
6.42
1
A
O
HOH
258
6.78
1
A
O
HOH
259
7.04
1
B
O
HOH
267
6.56
NCO
COBALT HEXAMMINE(III)
HOH
water
32630
synthetic construct
sample
1
8
NCO
101
2
NCO
NCO
101
A
NCO
102
2
NCO
NCO
102
A
NCO
101
2
NCO
NCO
101
B
NCO
102
2
NCO
NCO
102
B
HOH
201
3
HOH
HOH
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
244
3
HOH
HOH
244
A
HOH
245
3
HOH
HOH
245
A
HOH
246
3
HOH
HOH
246
A
HOH
247
3
HOH
HOH
247
A
HOH
248
3
HOH
HOH
248
A
HOH
249
3
HOH
HOH
249
A
HOH
250
3
HOH
HOH
250
A
HOH
251
3
HOH
HOH
251
A
HOH
252
3
HOH
HOH
252
A
HOH
253
3
HOH
HOH
253
A
HOH
254
3
HOH
HOH
254
A
HOH
255
3
HOH
HOH
255
A
HOH
256
3
HOH
HOH
256
A
HOH
257
3
HOH
HOH
257
A
HOH
258
3
HOH
HOH
258
A
HOH
259
3
HOH
HOH
259
A
HOH
201
3
HOH
HOH
201
B
HOH
202
3
HOH
HOH
202
B
HOH
203
3
HOH
HOH
203
B
HOH
204
3
HOH
HOH
204
B
HOH
205
3
HOH
HOH
205
B
HOH
206
3
HOH
HOH
206
B
HOH
207
3
HOH
HOH
207
B
HOH
208
3
HOH
HOH
208
B
HOH
209
3
HOH
HOH
209
B
HOH
210
3
HOH
HOH
210
B
HOH
211
3
HOH
HOH
211
B
HOH
212
3
HOH
HOH
212
B
HOH
213
3
HOH
HOH
213
B
HOH
214
3
HOH
HOH
214
B
HOH
215
3
HOH
HOH
215
B
HOH
216
3
HOH
HOH
216
B
HOH
217
3
HOH
HOH
217
B
HOH
218
3
HOH
HOH
218
B
HOH
219
3
HOH
HOH
219
B
HOH
220
3
HOH
HOH
220
B
HOH
221
3
HOH
HOH
221
B
HOH
222
3
HOH
HOH
222
B
HOH
223
3
HOH
HOH
223
B
HOH
224
3
HOH
HOH
224
B
HOH
225
3
HOH
HOH
225
B
HOH
226
3
HOH
HOH
226
B
HOH
227
3
HOH
HOH
227
B
HOH
228
3
HOH
HOH
228
B
HOH
229
3
HOH
HOH
229
B
HOH
230
3
HOH
HOH
230
B
HOH
231
3
HOH
HOH
231
B
HOH
232
3
HOH
HOH
232
B
HOH
233
3
HOH
HOH
233
B
HOH
234
3
HOH
HOH
234
B
HOH
235
3
HOH
HOH
235
B
HOH
236
3
HOH
HOH
236
B
HOH
237
3
HOH
HOH
237
B
HOH
238
3
HOH
HOH
238
B
HOH
239
3
HOH
HOH
239
B
HOH
240
3
HOH
HOH
240
B
HOH
241
3
HOH
HOH
241
B
HOH
242
3
HOH
HOH
242
B
HOH
243
3
HOH
HOH
243
B
HOH
244
3
HOH
HOH
244
B
HOH
245
3
HOH
HOH
245
B
HOH
246
3
HOH
HOH
246
B
HOH
247
3
HOH
HOH
247
B
HOH
248
3
HOH
HOH
248
B
HOH
249
3
HOH
HOH
249
B
HOH
250
3
HOH
HOH
250
B
HOH
251
3
HOH
HOH
251
B
HOH
252
3
HOH
HOH
252
B
HOH
253
3
HOH
HOH
253
B
HOH
254
3
HOH
HOH
254
B
HOH
255
3
HOH
HOH
255
B
HOH
256
3
HOH
HOH
256
B
HOH
257
3
HOH
HOH
257
B
HOH
258
3
HOH
HOH
258
B
HOH
259
3
HOH
HOH
259
B
HOH
260
3
HOH
HOH
260
B
HOH
261
3
HOH
HOH
261
B
HOH
262
3
HOH
HOH
262
B
HOH
263
3
HOH
HOH
263
B
HOH
264
3
HOH
HOH
264
B
HOH
265
3
HOH
HOH
265
B
HOH
266
3
HOH
HOH
266
B
HOH
267
3
HOH
HOH
267
B
CBV
1
n
1
CBV
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
A
4
n
4
A
4
A
U5M
5
n
5
U5M
5
A
U
6
n
6
U
6
A
C
7
n
7
C
7
A
G
8
n
8
G
8
A
CBV
1
n
1
CBV
1
B
G
2
n
2
G
2
B
A
3
n
3
A
3
B
A
4
n
4
A
4
B
U5M
5
n
5
U5M
5
B
U
6
n
6
U
6
B
C
7
n
7
C
7
B
G
8
n
8
G
8
B
author_and_software_defined_assembly
PISA
2
dimeric
2350
-1
3160
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
B
B
O
O
HOH
HOH
212
261
1.71
1
B
B
O
O
HOH
HOH
201
212
1.95
1
B
B
O
O
HOH
HOH
243
263
2.12
1
A
A
3
0.065
SIDE CHAIN
1
B
G
8
0.060
SIDE CHAIN
12.42
0.00000
0.00000
0.00000
0.00000
0.00000
-0.01000
0.975
0.956
HYDROGENS HAVE BEEN USED IF PRESENT IN
0.157
0.120
0.121
1.20
29.24
708
12988
5.200
99.6
RANDOM
1
THROUGHOUT
0.000
SAD
0.035
0.037
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.20
29.24
126
492
28
338
0
1.823
0.015
252
2.887
0.018
398
42.196
1.872
303
56.801
2.520
891
3.623
0.200
21
0.223
0.020
156
0.296
0.020
68
1.468
0.927
252
14.638
3.000
650
57.545
5.000
15
7.632
5.000
731
0.1610
0.1400
1.23
46
900
20
98.44
1.200
50.000
5D8T
13758
0.14500
1
11.3000
14.10
99.7
0.58400
1.20
1.22
1
8.10
100.0
refinement
REFMAC
5.8.0073
data collection
HKL-2000
data scaling
HKL-2000
phasing
SHELX
data extraction
PDB_EXTRACT
3.15
data reduction
HKL-2000
RNA octamer containing (S)-5' methyl, 2'-F U.
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.597
one
A
CBV
1
A
O3'
CBV
1
1_555
A
G
2
A
P
G
2
1_555
covale
1.642
both
A
A
4
A
O3'
A
4
1_555
A
U5M
5
A
P
U5M
5
1_555
covale
1.581
one
A
U5M
5
A
O3'
U5M
5
1_555
A
U
6
A
P
U
6
1_555
covale
1.600
one
B
CBV
1
B
O3'
CBV
1
1_555
B
G
2
B
P
G
2
1_555
covale
1.623
both
B
A
4
B
O3'
A
4
1_555
B
U5M
5
B
P
U5M
5
1_555
covale
1.563
one
B
U5M
5
B
O3'
U5M
5
1_555
B
U
6
B
P
U
6
1_555
hydrog
WATSON-CRICK
A
CBV
1
A
N3
CBV
1
1_555
B
G
8
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
CBV
1
A
N4
CBV
1
1_555
B
G
8
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
CBV
1
A
O2
CBV
1
1_555
B
G
8
B
N2
G
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
7
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
B
U
6
B
N3
U
6
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
B
U
6
B
O4
U
6
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
B
A
3
B
N1
A
3
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
B
A
3
B
N6
A
3
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
B
CBV
1
B
N3
CBV
1
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
B
CBV
1
B
O2
CBV
1
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
B
CBV
1
B
N4
CBV
1
1_555
RNA
RNA, modified base
5D8T
PDB
1
1
5D8T
1
8
5D8T
1
8
5D8T
A
1
1
8
1
8
5D8T
1
8
5D8T
B
1
1
8
binding site for residue NCO A 101
A
NCO
101
Software
10
binding site for residue NCO A 102
A
NCO
102
Software
10
binding site for residue NCO B 101
B
NCO
101
Software
12
binding site for residue NCO B 102
B
NCO
102
Software
6
binding site for Di-nucleotide CBV B 1 and G B 2
B
CBV
1
Software
21
binding site for Di-nucleotide A B 4 and U5M B 5
B
A
4
Software
25
A
A
3
A
A
3
10
1_555
A
U5M
5
A
U5M
5
10
1_555
A
U
6
A
U
6
10
1_555
A
HOH
220
G
HOH
10
1_555
A
HOH
223
G
HOH
10
1_555
A
HOH
230
G
HOH
10
1_555
A
HOH
236
G
HOH
10
1_555
A
HOH
237
G
HOH
10
1_555
B
HOH
222
H
HOH
10
1_555
B
HOH
244
H
HOH
10
4_545
A
CBV
1
A
CBV
1
10
6_535
A
G
2
A
G
2
10
6_535
A
A
4
A
A
4
10
1_555
A
U5M
5
A
U5M
5
10
1_555
A
HOH
240
G
HOH
10
1_555
A
HOH
256
G
HOH
10
6_535
B
HOH
245
H
HOH
10
6_535
B
HOH
248
H
HOH
10
4_545
B
HOH
252
H
HOH
10
6_535
B
HOH
261
H
HOH
10
4_545
A
CBV
1
A
CBV
1
12
1_555
A
G
2
A
G
2
12
1_555
A
HOH
215
G
HOH
12
1_555
A
HOH
238
G
HOH
12
1_555
A
HOH
246
G
HOH
12
3_444
B
G
2
B
G
2
12
1_555
B
A
3
B
A
3
12
1_555
B
HOH
225
H
HOH
12
1_555
B
HOH
229
H
HOH
12
1_555
B
HOH
230
H
HOH
12
1_555
B
HOH
241
H
HOH
12
1_555
B
HOH
247
H
HOH
12
1_555
A
C
7
A
C
7
6
3_444
A
G
8
A
G
8
6
3_444
A
HOH
224
G
HOH
6
3_444
A
HOH
255
G
HOH
6
3_444
B
A
4
B
A
4
6
1_555
B
HOH
215
H
HOH
6
1_555
A
A
4
A
A
4
21
6_435
A
C
7
A
C
7
21
1_555
A
G
8
A
G
8
21
1_555
A
HOH
242
G
HOH
21
6_435
B
A
3
B
A
3
21
1_555
B
G
8
B
G
8
21
4_545
B
NCO
101
E
NCO
21
1_555
B
HOH
203
H
HOH
21
1_555
B
HOH
204
H
HOH
21
1_555
B
HOH
217
H
HOH
21
1_555
B
HOH
218
H
HOH
21
1_555
B
HOH
219
H
HOH
21
1_555
B
HOH
221
H
HOH
21
1_555
B
HOH
222
H
HOH
21
1_555
B
HOH
232
H
HOH
21
1_555
B
HOH
234
H
HOH
21
1_555
B
HOH
236
H
HOH
21
1_555
B
HOH
241
H
HOH
21
1_555
B
HOH
244
H
HOH
21
4_545
B
HOH
245
H
HOH
21
1_555
B
HOH
249
H
HOH
21
1_555
A
A
4
A
A
4
25
1_555
A
U5M
5
A
U5M
5
25
1_555
A
U
6
A
U
6
25
6_445
A
U
6
A
U
6
25
1_555
A
HOH
211
G
HOH
25
6_545
A
HOH
227
G
HOH
25
6_445
A
HOH
237
G
HOH
25
1_555
A
HOH
251
G
HOH
25
6_545
A
HOH
255
G
HOH
25
3_444
B
A
3
B
A
3
25
1_555
B
U
6
B
U
6
25
1_555
B
NCO
102
F
NCO
25
1_555
B
HOH
206
H
HOH
25
1_555
B
HOH
207
H
HOH
25
1_555
B
HOH
208
H
HOH
25
1_555
B
HOH
214
H
HOH
25
1_555
B
HOH
216
H
HOH
25
1_555
B
HOH
224
H
HOH
25
1_555
B
HOH
225
H
HOH
25
1_555
B
HOH
226
H
HOH
25
1_555
B
HOH
227
H
HOH
25
1_555
B
HOH
230
H
HOH
25
1_555
B
HOH
237
H
HOH
25
1_555
B
HOH
240
H
HOH
25
1_555
B
HOH
243
H
HOH
25
1_555
96
P 43 21 2