0.028731
0.000000
0.000000
0.000000
0.021183
0.000000
0.000000
0.000000
0.004400
0.00000
0.00000
0.00000
Pikovskaya, O.
Polonskaia, A.
Patel, D.J.
Serganov, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
34.806
47.208
227.279
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 N3 O10 P2
385.161
n
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H13 N5 O5
283.241
GUANOSINE
non-polymer
C10 H16 N5 O14 P3
523.180
n
GUANOSINE-5'-TRIPHOSPHATE
non-polymer
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C4 H6 O4
118.088
SUCCINIC ACID
non-polymer
O4 S -2
96.063
SULFATE ION
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
S
P
N
74
N
O
N
75
N
O
N
76
N
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
O
N
81
N
C
N
82
R
C
N
83
N
O
N
84
R
C
N
85
N
O
N
86
R
C
N
87
N
O
N
88
R
C
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
C
N
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
O
N
111
N
P
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
C
N
116
R
C
N
117
N
O
N
118
S
C
N
119
N
O
N
120
R
C
N
121
N
O
N
122
R
C
Y
123
N
N
Y
124
N
C
Y
125
N
N
Y
126
N
C
N
127
N
C
N
128
N
O
N
129
N
N
N
130
N
C
N
131
N
N
N
132
N
N
Y
133
N
C
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
H
N
147
N
H
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
R
C
N
155
N
O
N
156
R
C
Y
157
N
N
Y
158
N
C
Y
159
N
N
Y
160
N
C
N
161
N
C
N
162
N
O
N
163
N
N
N
164
N
C
N
165
N
N
N
166
N
N
Y
167
N
C
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
H
N
181
N
P
N
182
N
O
N
183
N
O
N
184
N
O
N
185
N
O
N
186
N
P
N
187
N
O
N
188
N
O
N
189
N
O
N
190
N
P
N
191
N
O
N
192
N
O
N
193
N
O
N
194
N
C
N
195
R
C
N
196
N
O
N
197
S
C
N
198
N
O
N
199
R
C
N
200
N
O
N
201
R
C
Y
202
N
N
Y
203
N
C
Y
204
N
N
Y
205
N
C
N
206
N
C
N
207
N
O
N
208
N
N
N
209
N
C
N
210
N
N
N
211
N
N
Y
212
N
C
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
O
N
230
N
H
N
231
N
H
N
232
N
MG
N
233
N
C
N
234
N
O
N
235
N
O
N
236
N
C
N
237
N
C
N
238
N
C
N
239
N
O
N
240
N
O
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
S
N
248
N
O
N
249
N
O
N
250
N
O
N
251
N
O
N
252
N
O
N
253
N
P
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
O
N
262
R
C
N
263
N
O
N
264
R
C
N
265
N
N
N
266
N
C
N
267
N
O
N
268
N
N
N
269
N
C
N
270
N
O
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
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
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
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
N
116
N
sing
N
117
N
doub
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
Y
139
N
sing
Y
140
N
sing
Y
141
N
doub
N
142
N
sing
Y
143
N
sing
N
144
N
sing
Y
145
N
doub
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
N
172
N
sing
N
173
N
sing
Y
174
N
sing
Y
175
N
sing
Y
176
N
doub
N
177
N
sing
Y
178
N
sing
N
179
N
sing
Y
180
N
doub
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
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
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
doub
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
sing
Y
224
N
sing
Y
225
N
sing
Y
226
N
doub
N
227
N
sing
Y
228
N
sing
N
229
N
sing
Y
230
N
doub
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
doub
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
doub
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
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
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
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
doub
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
N
290
N
sing
N
291
N
doub
N
292
N
sing
N
293
N
sing
US
Nat.Chem.Biol.
1552-4450
7
748
755
10.1038/nchembio.631
21841796
Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.
2011
10.2210/pdb3skz/pdb
pdb_00003skz
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
CCD
2010-04-13
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.075
1.0
X29A
NSLS
1.075
SYNCHROTRON
NSLS BEAMLINE X29A
dG riboswitch
22018.873
RNA (68-MER)
2
syn
polymer
in vitro transcribed RNA
283.241
GUANOSINE
2
syn
non-polymer
24.305
MAGNESIUM ION
3
syn
non-polymer
96.063
SULFATE ION
8
syn
non-polymer
118.088
SUCCINIC ACID
1
syn
non-polymer
18.015
water
7
nat
water
no
yes
(GTP)GCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGU(CCC)
GGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUC
A,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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.12
41.98
VAPOR DIFFUSION, HANGING DROP
5.0
0.05 M Na-succinate, ~3.0 M ammonium sulfate, 0.5 mM spermine and 20 mM magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-12.906
1
19
A
22
A
89
1.865
A_GTP22:CCC89_A
1
-14.244
-0.892
-0.322
-0.153
11.285
1
28
A
23
A
88
3.092
A_G23:U88_A
2
-12.395
-2.679
0.710
-0.502
7.422
1
19
A
24
A
87
0.801
A_C24:G87_A
3
-21.010
0.092
0.253
-0.259
-10.232
1
19
A
25
A
86
2.334
A_C25:G86_A
4
-11.427
0.385
0.452
-0.107
-0.946
1
20
A
26
A
85
1.317
A_U26:A85_A
5
-5.862
0.280
0.411
0.159
7.242
1
20
A
27
A
84
-2.381
A_U27:A84_A
6
-16.060
0.084
-0.457
-0.055
-17.848
1
20
A
28
A
83
6.552
A_A28:U83_A
7
-15.685
-0.055
-0.224
0.257
-12.391
1
20
A
29
A
82
4.547
A_U29:A82_A
8
-17.913
-0.194
0.306
0.069
11.262
1
20
A
30
A
81
-8.769
A_A30:U81_A
9
-2.621
-0.330
0.490
0.037
-9.282
1
19
A
47
A
39
4.498
A_G47:C39_A
10
-11.199
-0.391
0.304
-0.007
4.858
1
19
A
48
A
38
3.393
A_C48:G38_A
11
-13.362
0.071
0.321
-0.042
-0.809
1
20
A
49
A
37
0.357
A_U49:A37_A
12
-4.429
-0.457
0.114
-0.181
7.074
1
20
A
50
A
36
3.522
A_A50:U36_A
13
-10.175
-0.286
0.136
-0.172
5.352
1
19
A
51
A
35
-1.945
A_C51:G35_A
14
-12.522
0.043
0.203
-0.055
-8.792
1
28
A
52
A
34
1.824
A_U52:G34_A
15
-19.179
1.975
0.299
-0.471
14.083
1
19
A
53
A
60
-3.037
A_G53:C60_A
16
-14.020
-0.020
0.421
-0.133
4.336
1
19
A
31
A
59
-2.226
A_C31:G59_A
17
-12.499
0.583
-0.183
-0.230
-15.962
1
19
A
45
A
69
-3.900
A_G45:C69_A
18
-9.672
-0.618
-0.261
-0.232
-6.626
1
19
A
46
A
68
-0.772
A_G46:C68_A
19
-10.520
-0.395
0.139
-0.171
-8.600
1
20
A
72
A
67
9.713
A_U72:A67_A
20
-10.208
-0.137
-0.261
0.122
-3.971
1
20
A
73
A
66
1.757
A_U73:A66_A
21
-7.691
-0.943
-0.494
0.034
11.079
1
20
A
74
A
65
2.983
A_U74:A65_A
22
-11.314
-0.098
-0.434
-0.206
-10.558
1
19
A
75
A
64
-7.118
A_G75:C64_A
23
-18.893
-0.158
-0.512
-0.227
-1.709
1
28
A
76
A
63
-2.794
A_G76:U63_A
24
0.146
-1.200
0.100
-0.433
1.381
1
20
A
77
A
62
1.445
A_A77:U62_A
25
-12.147
-0.314
0.114
-0.130
-6.365
1
19
A
78
A
61
0.185
A_G78:C61_A
26
-12.072
-0.178
-0.334
-0.100
-2.999
1
19
B
22
B
89
0.837
B_GTP22:CCC89_B
27
-1.175
-0.350
0.003
-0.014
4.173
1
28
B
23
B
88
8.525
B_G23:U88_B
28
-19.242
-2.162
0.201
-0.152
5.792
1
19
B
24
B
87
2.515
B_C24:G87_B
29
-15.317
-0.267
-0.028
-0.099
4.630
1
19
B
25
B
86
-0.255
B_C25:G86_B
30
-8.724
0.135
0.592
0.174
1.139
1
B
26
B
85
14.343
B_U26:A85_B
31
-12.421
-0.100
0.089
0.163
5.676
1
20
B
27
B
84
13.254
B_U27:A84_B
32
-16.510
-0.764
-0.539
-0.126
-5.881
1
20
B
28
B
83
6.142
B_A28:U83_B
33
-4.272
0.112
0.385
0.107
0.513
1
20
B
29
B
82
-2.108
B_U29:A82_B
34
-13.938
-0.176
0.261
-0.086
10.120
1
20
B
30
B
81
1.230
B_A30:U81_B
35
-4.541
0.298
0.783
0.163
-5.067
1
19
B
47
B
39
4.334
B_G47:C39_B
36
-5.307
-0.363
0.361
-0.056
-7.325
1
19
B
48
B
38
6.037
B_C48:G38_B
37
-8.753
0.120
0.666
0.117
-2.476
1
20
B
49
B
37
1.183
B_U49:A37_B
38
-0.677
-0.100
0.385
-0.186
12.711
1
20
B
50
B
36
7.279
B_A50:U36_B
39
-15.991
0.267
0.414
0.156
1.790
1
19
B
51
B
35
4.555
B_C51:G35_B
40
-21.329
0.096
0.219
0.125
-6.671
1
28
B
52
B
34
4.112
B_U52:G34_B
41
-13.916
2.515
0.221
-0.535
16.452
1
19
B
53
B
60
2.108
B_G53:C60_B
42
-10.335
0.207
0.479
-0.109
5.872
1
19
B
31
B
59
-0.257
B_C31:G59_B
43
-10.533
1.179
-0.110
-0.320
-12.908
1
19
B
45
B
69
7.568
B_G45:C69_B
44
12.081
-0.707
-0.201
0.126
-24.009
1
19
B
46
B
68
8.416
B_G46:C68_B
45
-19.250
-0.718
-1.039
0.105
-7.047
1
20
B
72
B
67
7.005
B_U72:A67_B
46
-2.359
0.330
-0.307
0.002
-4.116
1
20
B
73
B
66
-1.188
B_U73:A66_B
47
-3.884
-0.553
-0.496
-0.023
7.170
1
20
B
74
B
65
-2.548
B_U74:A65_B
48
-15.318
-0.057
-0.274
-0.106
-10.332
1
19
B
75
B
64
6.296
B_G75:C64_B
49
-8.720
-1.026
-0.405
-0.147
-4.619
1
28
B
76
B
63
-1.795
B_G76:U63_B
50
-11.474
-1.792
-0.100
-0.519
1.836
1
20
B
77
B
62
1.787
B_A77:U62_B
51
0.070
0.494
0.202
-0.095
3.414
1
19
B
78
B
61
-0.324
B_G78:C61_B
52
-8.936
0.716
0.310
0.262
1.632
26.374
A
A
22
23
15.065
A
A
89
88
2.407
6.531
-0.063
-1.827
AA_GTP22G23:U88CCC89_AA
1
-12.399
28.601
22.399
-5.174
-2.081
2.891
45.663
A
A
23
24
12.705
A
A
88
87
3.247
9.791
-0.341
-1.405
AA_G23C24:G87U88_AA
2
0.416
-0.540
44.654
-2.624
0.474
2.820
36.619
A
A
24
25
16.803
A
A
87
86
3.453
10.420
-0.054
-1.811
AA_C24C25:G86G87_AA
3
-0.821
1.324
35.145
-4.286
-0.025
2.335
25.073
A
A
25
26
13.517
A
A
86
85
2.839
5.814
-0.428
-1.956
AA_C25U26:A85G86_AA
4
-1.203
2.797
24.370
-5.885
0.701
2.884
32.865
A
A
26
27
2.061
A
A
85
84
2.938
1.161
0.230
-1.502
AA_U26U27:A84A85_AA
5
5.377
-9.547
32.414
-2.833
0.418
2.412
39.138
A
A
27
28
31.820
A
A
84
83
3.650
20.333
0.408
-1.411
AA_U27A28:U83A84_AA
6
-2.140
3.350
33.554
-4.559
-0.868
2.734
33.256
A
A
28
29
16.065
A
A
83
82
3.146
9.083
-0.225
-1.139
AA_A28U29:A82U83_AA
7
-0.726
1.284
32.017
-3.382
0.282
1.957
25.615
A
A
29
30
21.305
A
A
82
81
2.641
9.227
0.071
-1.430
AA_U29A30:U81A82_AA
8
2.255
-5.207
23.816
-5.132
0.306
2.863
32.945
A
A
47
48
2.626
A
A
39
38
2.954
1.489
-0.708
-1.430
AA_G47C48:G38C39_AA
9
1.122
-1.980
32.894
-2.746
1.419
2.521
31.516
A
A
48
49
21.250
A
A
38
37
3.181
11.296
0.216
-1.320
AA_C48U49:A37G38_AA
10
0.914
-1.720
29.457
-4.332
-0.244
2.764
33.699
A
A
49
50
10.396
A
A
37
36
3.022
5.995
-0.141
-1.250
AA_U49A50:U36A37_AA
11
-1.437
2.492
33.146
-3.027
0.034
2.846
34.768
A
A
50
51
10.105
A
A
36
35
3.144
6.004
0.046
-1.443
AA_A50C51:G35U36_AA
12
-2.616
4.403
34.164
-3.262
-0.446
3.181
45.836
A
A
51
52
11.258
A
A
35
34
3.457
8.698
0.718
-1.554
AA_C51U52:G34G35_AA
13
5.851
-7.573
44.684
-2.772
-0.399
2.377
48.120
A
A
52
53
5.219
A
A
34
60
2.744
4.248
2.900
-2.081
AA_U52G53:C60G34_AA
14
-3.164
3.887
47.845
-2.814
-3.751
3.045
59.662
A
A
53
31
9.588
A
A
60
59
3.081
9.501
-2.191
-0.782
AA_G53C31:G59C60_AA
15
-3.429
3.460
58.878
-1.235
2.040
2.414
31.839
A
A
45
46
12.116
A
A
69
68
2.957
6.594
0.153
-2.280
AA_G45G46:C68C69_AA
16
-2.574
4.729
31.063
-5.158
-0.669
3.082
27.540
A
A
46
72
3.833
A
A
68
67
3.379
1.820
-0.951
-2.621
AA_G46U72:A67C68_AA
17
2.992
-6.302
27.321
-5.947
2.723
2.720
30.102
A
A
72
73
17.738
A
A
67
66
2.916
9.010
-1.093
-0.771
AA_U72U73:A66A67_AA
18
-6.234
12.274
28.080
-3.129
0.966
3.057
36.564
A
A
73
74
2.006
A
A
66
65
3.112
1.258
0.421
-1.212
AA_U73U74:A65A66_AA
19
-1.059
1.689
36.528
-2.096
-0.809
2.564
31.192
A
A
74
75
28.143
A
A
65
64
3.888
14.571
-0.658
-1.957
AA_U74G75:C64A65_AA
20
-0.203
0.392
27.654
-6.549
1.183
2.620
32.013
A
A
75
76
7.634
A
A
64
63
2.996
4.177
0.243
-2.057
AA_G75G76:U63C64_AA
21
-5.743
10.496
31.236
-4.385
-1.342
3.138
28.303
A
A
76
77
4.403
A
A
63
62
3.264
2.147
0.204
-1.623
AA_G76A77:U62U63_AA
22
3.029
-6.211
28.064
-3.807
0.272
2.239
32.346
A
A
77
78
27.302
A
A
62
61
3.407
14.624
1.061
-2.099
AA_A77G78:C61U62_AA
23
4.755
-8.877
28.543
-6.148
-1.131
1.676
26.070
B
B
22
23
25.921
B
B
89
88
2.883
11.303
-0.015
-2.154
BB_GTP22G23:U88CCC89_BB
24
-2.168
4.972
23.432
-7.050
-0.403
2.911
38.110
B
B
23
24
10.375
B
B
88
87
3.186
6.741
0.006
-1.332
BB_G23C24:G87U88_BB
25
-0.939
1.445
37.520
-2.842
-0.121
2.451
31.947
B
B
24
25
13.262
B
B
87
86
3.068
7.219
0.172
-2.244
BB_C24C25:G86G87_BB
26
-4.163
7.647
30.868
-5.201
-0.961
2.306
27.996
B
B
25
26
17.097
B
B
86
85
2.995
8.137
0.068
-1.931
BB_C25U26:A85G86_BB
27
3.284
-6.901
26.611
-5.594
0.507
2.600
31.962
B
B
26
27
19.767
B
B
85
84
3.086
10.659
0.089
-0.934
BB_U26U27:A84A85_BB
28
3.909
-7.249
29.927
-3.432
0.475
3.137
41.628
B
B
27
28
17.278
B
B
84
83
3.532
12.042
0.046
-0.656
BB_U27A28:U83A84_BB
29
-8.133
11.669
39.116
-2.266
-0.971
2.615
33.012
B
B
28
29
12.987
B
B
83
82
3.072
7.292
-0.056
-1.571
BB_A28U29:A82U83_BB
30
5.271
-9.389
31.795
-3.862
0.891
2.415
30.230
B
B
29
30
14.605
B
B
82
81
2.862
7.540
0.266
-1.470
BB_U29A30:U81A82_BB
31
-0.169
0.328
29.296
-4.072
-0.538
2.829
34.896
B
B
47
48
11.607
B
B
39
38
3.216
6.917
0.090
-1.706
BB_G47C48:G38C39_BB
32
0.760
-1.275
34.217
-3.824
-0.042
2.441
32.484
B
B
48
49
12.971
B
B
38
37
2.840
7.199
-0.559
-1.526
BB_C48U49:A37G38_BB
33
0.120
-0.215
31.697
-3.759
1.017
2.705
31.530
B
B
49
50
6.074
B
B
37
36
2.838
3.294
0.177
-1.198
BB_U49A50:U36A37_BB
34
0.873
-1.610
31.350
-2.727
-0.187
2.730
34.101
B
B
50
51
20.716
B
B
36
35
3.328
11.904
0.074
-1.175
BB_A50C51:G35U36_BB
35
1.350
-2.349
31.986
-3.814
0.079
3.075
47.947
B
B
51
52
12.216
B
B
35
34
3.377
9.857
0.404
-1.325
BB_C51U52:G34G35_BB
36
3.403
-4.218
46.864
-2.409
-0.228
2.467
50.040
B
B
52
53
-0.974
B
B
34
60
2.685
-0.823
2.825
-1.833
BB_U52G53:C60G34_BB
37
-4.472
5.293
49.847
-2.121
-3.595
3.070
59.522
B
B
53
31
12.126
B
B
60
59
3.177
11.969
-2.221
-0.617
BB_G53C31:G59C60_BB
38
-1.790
1.814
58.389
-1.204
2.151
1.539
32.318
B
B
45
46
35.032
B
B
69
68
3.569
18.104
0.109
-2.358
BB_G45G46:C68C69_BB
39
9.137
-17.679
25.297
-7.067
1.233
3.062
34.487
B
B
46
72
3.878
B
B
68
67
2.957
2.270
-1.360
-2.249
BB_G46U72:A67C68_BB
40
-9.454
16.152
33.128
-4.124
0.915
3.057
27.899
B
B
72
73
7.849
B
B
67
66
3.053
3.757
-1.247
-0.960
BB_U72U73:A66A67_BB
41
-4.476
9.351
27.292
-2.838
1.578
3.159
33.516
B
B
73
74
-0.071
B
B
66
65
3.166
-0.041
0.436
-1.717
BB_U73U74:A65A66_BB
42
-0.686
1.190
33.509
-2.972
-0.865
1.809
30.680
B
B
74
75
32.368
B
B
65
64
3.526
16.282
0.007
-2.299
BB_U74G75:C64A65_BB
43
-0.675
1.342
26.082
-7.182
-0.131
2.860
29.499
B
B
75
76
7.992
B
B
64
63
3.097
4.056
-0.003
-1.533
BB_G75G76:U63C64_BB
44
-1.196
2.357
29.201
-3.802
-0.227
2.734
41.447
B
B
76
77
8.453
B
B
63
62
3.070
5.956
0.446
-1.862
BB_G76A77:U62U63_BB
45
-3.807
5.403
40.866
-3.199
-0.993
2.681
30.806
B
B
77
78
8.816
B
B
62
61
2.976
4.636
0.739
-2.367
BB_A77G78:C61U62_BB
46
6.131
-11.658
29.854
-5.251
-0.340
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
entity
pdbx_entity_src_syn
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Source and taxonomy
Structure summary
1
0
2011-08-17
1
1
2011-10-26
1
2
2024-02-28
1
3
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_entity.details
RCSB
Y
RCSB
2011-06-23
REL
REL
GMP
GUANOSINE
MG
MAGNESIUM ION
SO4
SULFATE ION
SIN
SUCCINIC ACID
HOH
water
in vitro transcribed RNA
sample
GMP
120
2
GMP
GMP
120
A
MG
228
3
MG
MG
228
A
SO4
211
4
SO4
SO4
211
A
SO4
212
4
SO4
SO4
212
A
SO4
213
4
SO4
SO4
213
A
SO4
216
4
SO4
SO4
216
A
SO4
229
4
SO4
SO4
229
A
SIN
301
5
SIN
SIN
301
A
GMP
120
2
GMP
GMP
120
B
MG
172
3
MG
MG
172
B
MG
175
3
MG
MG
175
B
SO4
214
4
SO4
SO4
214
B
SO4
217
4
SO4
SO4
217
B
SO4
219
4
SO4
SO4
219
B
HOH
69
6
HOH
HOH
90
A
HOH
87
6
HOH
HOH
91
A
HOH
83
6
HOH
HOH
92
A
HOH
171
6
HOH
HOH
171
A
HOH
180
6
HOH
HOH
180
A
HOH
64
6
HOH
HOH
90
B
HOH
174
6
HOH
HOH
174
B
GTP
22
n
1
GTP
22
A
G
23
n
2
G
23
A
C
24
n
3
C
24
A
C
25
n
4
C
25
A
U
26
n
5
U
26
A
U
27
n
6
U
27
A
A
28
n
7
A
28
A
U
29
n
8
U
29
A
A
30
n
9
A
30
A
C
31
n
10
C
31
A
A
32
n
11
A
32
A
G
33
n
12
G
33
A
G
34
n
13
G
34
A
G
35
n
14
G
35
A
U
36
n
15
U
36
A
A
37
n
16
A
37
A
G
38
n
17
G
38
A
C
39
n
18
C
39
A
A
40
n
19
A
40
A
U
41
n
20
U
41
A
A
42
n
21
A
42
A
A
43
n
22
A
43
A
U
44
n
23
U
44
A
G
45
n
24
G
45
A
G
46
n
25
G
46
A
G
47
n
26
G
47
A
C
48
n
27
C
48
A
U
49
n
28
U
49
A
A
50
n
29
A
50
A
C
51
n
30
C
51
A
U
52
n
31
U
52
A
G
53
n
32
G
53
A
A
54
n
33
A
54
A
C
55
n
34
C
55
A
C
56
n
35
C
56
A
C
57
n
36
C
57
A
C
58
n
37
C
58
A
G
59
n
38
G
59
A
C
60
n
39
C
60
A
C
61
n
40
C
61
A
U
62
n
41
U
62
A
U
63
n
42
U
63
A
C
64
n
43
C
64
A
A
65
n
44
A
65
A
A
66
n
45
A
66
A
A
67
n
46
A
67
A
C
68
n
47
C
68
A
C
69
n
48
C
69
A
U
70
n
49
U
70
A
A
71
n
50
A
71
A
U
72
n
51
U
72
A
U
73
n
52
U
73
A
U
74
n
53
U
74
A
G
75
n
54
G
75
A
G
76
n
55
G
76
A
A
77
n
56
A
77
A
G
78
n
57
G
78
A
A
79
n
58
A
79
A
C
80
n
59
C
80
A
U
81
n
60
U
81
A
A
82
n
61
A
82
A
U
83
n
62
U
83
A
A
84
n
63
A
84
A
A
85
n
64
A
85
A
G
86
n
65
G
86
A
G
87
n
66
G
87
A
U
88
n
67
U
88
A
CCC
89
n
68
CCC
89
A
GTP
22
n
1
GTP
22
B
G
23
n
2
G
23
B
C
24
n
3
C
24
B
C
25
n
4
C
25
B
U
26
n
5
U
26
B
U
27
n
6
U
27
B
A
28
n
7
A
28
B
U
29
n
8
U
29
B
A
30
n
9
A
30
B
C
31
n
10
C
31
B
A
32
n
11
A
32
B
G
33
n
12
G
33
B
G
34
n
13
G
34
B
G
35
n
14
G
35
B
U
36
n
15
U
36
B
A
37
n
16
A
37
B
G
38
n
17
G
38
B
C
39
n
18
C
39
B
A
40
n
19
A
40
B
U
41
n
20
U
41
B
A
42
n
21
A
42
B
A
43
n
22
A
43
B
U
44
n
23
U
44
B
G
45
n
24
G
45
B
G
46
n
25
G
46
B
G
47
n
26
G
47
B
C
48
n
27
C
48
B
U
49
n
28
U
49
B
A
50
n
29
A
50
B
C
51
n
30
C
51
B
U
52
n
31
U
52
B
G
53
n
32
G
53
B
A
54
n
33
A
54
B
C
55
n
34
C
55
B
C
56
n
35
C
56
B
C
57
n
36
C
57
B
C
58
n
37
C
58
B
G
59
n
38
G
59
B
C
60
n
39
C
60
B
C
61
n
40
C
61
B
U
62
n
41
U
62
B
U
63
n
42
U
63
B
C
64
n
43
C
64
B
A
65
n
44
A
65
B
A
66
n
45
A
66
B
A
67
n
46
A
67
B
C
68
n
47
C
68
B
C
69
n
48
C
69
B
U
70
n
49
U
70
B
A
71
n
50
A
71
B
U
72
n
51
U
72
B
U
73
n
52
U
73
B
U
74
n
53
U
74
B
G
75
n
54
G
75
B
G
76
n
55
G
76
B
A
77
n
56
A
77
B
G
78
n
57
G
78
B
A
79
n
58
A
79
B
C
80
n
59
C
80
B
U
81
n
60
U
81
B
A
82
n
61
A
82
B
U
83
n
62
U
83
B
A
84
n
63
A
84
B
A
85
n
64
A
85
B
G
86
n
65
G
86
B
G
87
n
66
G
87
B
U
88
n
67
U
88
B
CCC
89
n
68
CCC
89
B
0.0241
0.0231
-0.0319
0.1230
0.0523
0.0974
0.2219
-0.1179
-0.1122
-0.0546
0.1691
-0.2160
-0.0954
0.0655
0.2387
0.4770
0.0767
0.0244
0.8071
0.0908
0.3427
refined
0.4428
-1.3913
22.4553
X-RAY DIFFRACTION
0.3478
-0.1187
-0.4324
0.0423
0.1401
0.5510
0.0543
0.1165
-0.0948
-0.2975
0.1990
-0.0725
-0.4050
0.0181
0.1428
0.4718
0.0345
0.0784
0.6741
-0.0301
0.3627
refined
1.4940
0.7691
26.6713
X-RAY DIFFRACTION
0.2746
-0.1983
0.1114
0.8900
-0.2949
0.1165
-0.0690
-0.3583
-0.1310
0.3116
0.1144
0.0115
-0.2457
0.0525
0.5835
0.2651
-0.1303
0.0392
0.4763
-0.0962
0.2456
refined
9.1231
1.8765
-3.9012
X-RAY DIFFRACTION
0.0025
-0.0125
-0.0101
0.2258
0.1681
0.1251
0.1434
-0.0286
-0.0018
0.3396
-0.0280
-0.0667
0.1510
-0.2359
0.1316
0.3953
-0.0581
-0.0016
0.6876
-0.0633
0.2334
refined
-4.6414
-3.0737
-3.3964
X-RAY DIFFRACTION
0.6503
-0.4128
0.2467
2.0796
0.5598
0.3788
0.1336
-0.0229
0.1209
-0.2582
0.0597
-0.3350
-0.1173
0.1272
0.2153
0.4789
-0.0675
0.0872
0.4892
0.2238
0.4561
refined
1.2815
0.5230
-68.6889
X-RAY DIFFRACTION
0.0179
-0.1051
-0.0651
0.6423
0.4065
0.2592
0.0939
-0.0943
0.1207
0.1888
0.0154
-0.2554
0.1711
-0.0101
0.1950
0.2434
-0.1007
-0.0390
0.4231
0.1872
0.3013
refined
2.3500
-0.8187
-72.7823
X-RAY DIFFRACTION
0.2394
0.2563
0.1664
0.4223
0.1051
0.1571
-0.0960
-0.0375
0.1692
-0.2247
0.2561
0.2113
-0.2220
-0.0804
0.2280
0.1517
0.0581
-0.0214
0.1444
-0.0307
0.1864
refined
9.5970
-3.0693
-41.9137
X-RAY DIFFRACTION
0.0559
-0.0592
-0.0008
0.1162
0.0186
0.0590
-0.0623
-0.2075
-0.0047
0.0008
0.1557
-0.1041
0.0115
-0.0746
0.1412
0.0921
0.1090
0.2113
0.8398
-0.0742
0.0867
refined
-4.5634
1.2110
-42.1991
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(chain A and resid 22:30)
X-RAY DIFFRACTION
2
(chain A and resid 81:89)
X-RAY DIFFRACTION
3
(chain A and resid 31:47)
X-RAY DIFFRACTION
4
(chain A and resid 61:80)
X-RAY DIFFRACTION
5
(chain B and resid 22:30)
X-RAY DIFFRACTION
6
(chain B and resid 81:89)
X-RAY DIFFRACTION
7
(chain B and resid 31:47)
X-RAY DIFFRACTION
8
(chain X and resid 61:80)
author_defined_assembly
1
monomeric
author_defined_assembly
1
monomeric
A
GTP
22
GUANOSINE-5'-TRIPHOSPHATE
A
GTP
1
G
A
CCC
89
A
CCC
68
C
B
GTP
22
GUANOSINE-5'-TRIPHOSPHATE
B
GTP
1
G
B
CCC
89
B
CCC
68
C
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
PG
GTP
22
B
PG
GTP
1
1
Y
1
B
O1G
GTP
22
B
O1G
GTP
1
1
Y
1
B
O2G
GTP
22
B
O2G
GTP
1
1
Y
1
B
O3G
GTP
22
B
O3G
GTP
1
1
Y
1
A
C4
SIN
301
J
C4
SIN
1
1
N
1
A
O3
SIN
301
J
O3
SIN
1
1
N
1
A
O4
SIN
301
J
O4
SIN
1
1
N
1
-10.51
1.20
119.70
109.19
B
B
B
C3'
O3'
P
GTP
GTP
G
22
22
23
Y
1
-20.01
1.90
104.00
83.99
B
B
B
O3'
P
O5'
GTP
G
G
22
23
23
Y
1
15.05
1.10
110.50
125.55
B
B
B
O3'
P
OP2
GTP
G
G
22
23
23
Y
-8.7938
0.0000
-0.0000
34.9925
-0.0000
-26.1987
0.2751
0.2194
0.2221
2.605
20
520
10910
4.77
89.51
0.46
1
1.89
34.77
0.72
1.00
ML
FLAT BULK SOLVENT MODEL
36.610
0.337
2.605
20
7
3003
88
2908
0
0.006
3328
1.000
5175
22.025
1657
0.059
684
0.007
141
0.5270
0.3960
2.8661
138
2394
85.00
0.3054
0.2590
3.2793
113
2327
82.00
0.2371
0.2013
4.1256
134
2626
91.00
0.2133
0.1699
20.0336
135
3043
99.00
2.6
20
3SKZ
12208
11024
0.066
1
39.0
8.4
90.3
0.209
2.6
2.69
7.8
1046
1
8.9
87.2
data collection
CBASS
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.7_650)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
6
N
N
6
N
N
covale
1.590
both
A
GTP
22
A
O3'
GTP
1
1_555
A
G
23
A
P
G
2
1_555
covale
1.607
both
A
U
88
A
O3'
U
67
1_555
A
CCC
89
A
P
CCC
68
1_555
covale
1.606
both
B
GTP
22
B
O3'
GTP
1
1_555
B
G
23
B
P
G
2
1_555
covale
1.589
both
B
U
88
B
O3'
U
67
1_555
B
CCC
89
B
P
CCC
68
1_555
hydrog
WATSON-CRICK
A
GTP
22
A
N1
GTP
1
1_555
A
CCC
89
A
N3
CCC
68
1_555
hydrog
WATSON-CRICK
A
GTP
22
A
N2
GTP
1
1_555
A
CCC
89
A
O2
CCC
68
1_555
hydrog
WATSON-CRICK
A
GTP
22
A
O6
GTP
1
1_555
A
CCC
89
A
N4
CCC
68
1_555
hydrog
TYPE_28_PAIR
A
G
23
A
N1
G
2
1_555
A
U
88
A
O2
U
67
1_555
hydrog
TYPE_28_PAIR
A
G
23
A
O6
G
2
1_555
A
U
88
A
N3
U
67
1_555
hydrog
WATSON-CRICK
A
C
24
A
N3
C
3
1_555
A
G
87
A
N1
G
66
1_555
hydrog
WATSON-CRICK
A
C
24
A
N4
C
3
1_555
A
G
87
A
O6
G
66
1_555
hydrog
WATSON-CRICK
A
C
24
A
O2
C
3
1_555
A
G
87
A
N2
G
66
1_555
hydrog
WATSON-CRICK
A
C
25
A
N3
C
4
1_555
A
G
86
A
N1
G
65
1_555
hydrog
WATSON-CRICK
A
C
25
A
N4
C
4
1_555
A
G
86
A
O6
G
65
1_555
hydrog
WATSON-CRICK
A
C
25
A
O2
C
4
1_555
A
G
86
A
N2
G
65
1_555
hydrog
WATSON-CRICK
A
U
26
A
N3
U
5
1_555
A
A
85
A
N1
A
64
1_555
hydrog
WATSON-CRICK
A
U
26
A
O4
U
5
1_555
A
A
85
A
N6
A
64
1_555
hydrog
WATSON-CRICK
A
U
27
A
N3
U
6
1_555
A
A
84
A
N1
A
63
1_555
hydrog
WATSON-CRICK
A
U
27
A
O4
U
6
1_555
A
A
84
A
N6
A
63
1_555
hydrog
WATSON-CRICK
A
A
28
A
N1
A
7
1_555
A
U
83
A
N3
U
62
1_555
hydrog
WATSON-CRICK
A
A
28
A
N6
A
7
1_555
A
U
83
A
O4
U
62
1_555
hydrog
WATSON-CRICK
A
U
29
A
N3
U
8
1_555
A
A
82
A
N1
A
61
1_555
hydrog
WATSON-CRICK
A
U
29
A
O4
U
8
1_555
A
A
82
A
N6
A
61
1_555
hydrog
WATSON-CRICK
A
A
30
A
N1
A
9
1_555
A
U
81
A
N3
U
60
1_555
hydrog
WATSON-CRICK
A
A
30
A
N6
A
9
1_555
A
U
81
A
O4
U
60
1_555
hydrog
WATSON-CRICK
A
C
31
A
N3
C
10
1_555
A
G
59
A
N1
G
38
1_555
hydrog
WATSON-CRICK
A
C
31
A
N4
C
10
1_555
A
G
59
A
O6
G
38
1_555
hydrog
WATSON-CRICK
A
C
31
A
O2
C
10
1_555
A
G
59
A
N2
G
38
1_555
hydrog
A-G MISPAIR
A
A
32
A
N1
A
11
1_555
A
G
53
A
N2
G
32
1_555
hydrog
G-G MISPAIR
A
G
33
A
N2
G
12
1_555
A
G
34
A
O6
G
13
1_555
hydrog
G-U MISPAIR
A
G
33
A
N2
G
12
1_555
A
U
52
A
O4
U
31
1_555
hydrog
TYPE_28_PAIR
A
G
34
A
N1
G
13
1_555
A
U
52
A
O2
U
31
1_555
hydrog
TYPE_28_PAIR
A
G
34
A
O6
G
13
1_555
A
U
52
A
N3
U
31
1_555
hydrog
WATSON-CRICK
A
G
35
A
N1
G
14
1_555
A
C
51
A
N3
C
30
1_555
hydrog
WATSON-CRICK
A
G
35
A
N2
G
14
1_555
A
C
51
A
O2
C
30
1_555
hydrog
WATSON-CRICK
A
G
35
A
O6
G
14
1_555
A
C
51
A
N4
C
30
1_555
hydrog
WATSON-CRICK
A
U
36
A
N3
U
15
1_555
A
A
50
A
N1
A
29
1_555
hydrog
WATSON-CRICK
A
U
36
A
O4
U
15
1_555
A
A
50
A
N6
A
29
1_555
hydrog
WATSON-CRICK
A
A
37
A
N1
A
16
1_555
A
U
49
A
N3
U
28
1_555
hydrog
WATSON-CRICK
A
A
37
A
N6
A
16
1_555
A
U
49
A
O4
U
28
1_555
hydrog
WATSON-CRICK
A
G
38
A
N1
G
17
1_555
A
C
48
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
38
A
N2
G
17
1_555
A
C
48
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
38
A
O6
G
17
1_555
A
C
48
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
C
39
A
N3
C
18
1_555
A
G
47
A
N1
G
26
1_555
hydrog
WATSON-CRICK
A
C
39
A
N4
C
18
1_555
A
G
47
A
O6
G
26
1_555
hydrog
WATSON-CRICK
A
C
39
A
O2
C
18
1_555
A
G
47
A
N2
G
26
1_555
hydrog
A-G MISPAIR
A
A
42
A
N1
A
21
1_555
A
G
45
A
N2
G
24
1_555
hydrog
WATSON-CRICK
A
G
45
A
N1
G
24
1_555
A
C
69
A
N3
C
48
1_555
hydrog
WATSON-CRICK
A
G
45
A
N2
G
24
1_555
A
C
69
A
O2
C
48
1_555
hydrog
WATSON-CRICK
A
G
45
A
O6
G
24
1_555
A
C
69
A
N4
C
48
1_555
hydrog
WATSON-CRICK
A
G
46
A
N1
G
25
1_555
A
C
68
A
N3
C
47
1_555
hydrog
WATSON-CRICK
A
G
46
A
N2
G
25
1_555
A
C
68
A
O2
C
47
1_555
hydrog
WATSON-CRICK
A
G
46
A
O6
G
25
1_555
A
C
68
A
N4
C
47
1_555
hydrog
WATSON-CRICK
A
G
53
A
N1
G
32
1_555
A
C
60
A
N3
C
39
1_555
hydrog
WATSON-CRICK
A
G
53
A
N2
G
32
1_555
A
C
60
A
O2
C
39
1_555
hydrog
WATSON-CRICK
A
G
53
A
O6
G
32
1_555
A
C
60
A
N4
C
39
1_555
hydrog
C-U MISPAIR
A
C
57
A
N4
C
36
1_555
A
U
81
A
O2
U
60
1_555
hydrog
WATSON-CRICK
A
C
61
A
N3
C
40
1_555
A
G
78
A
N1
G
57
1_555
hydrog
WATSON-CRICK
A
C
61
A
N4
C
40
1_555
A
G
78
A
O6
G
57
1_555
hydrog
WATSON-CRICK
A
C
61
A
O2
C
40
1_555
A
G
78
A
N2
G
57
1_555
hydrog
WATSON-CRICK
A
U
62
A
N3
U
41
1_555
A
A
77
A
N1
A
56
1_555
hydrog
WATSON-CRICK
A
U
62
A
O4
U
41
1_555
A
A
77
A
N6
A
56
1_555
hydrog
TYPE_28_PAIR
A
U
63
A
N3
U
42
1_555
A
G
76
A
O6
G
55
1_555
hydrog
TYPE_28_PAIR
A
U
63
A
O2
U
42
1_555
A
G
76
A
N1
G
55
1_555
hydrog
WATSON-CRICK
A
C
64
A
N3
C
43
1_555
A
G
75
A
N1
G
54
1_555
hydrog
WATSON-CRICK
A
C
64
A
N4
C
43
1_555
A
G
75
A
O6
G
54
1_555
hydrog
WATSON-CRICK
A
C
64
A
O2
C
43
1_555
A
G
75
A
N2
G
54
1_555
hydrog
WATSON-CRICK
A
A
65
A
N1
A
44
1_555
A
U
74
A
N3
U
53
1_555
hydrog
WATSON-CRICK
A
A
65
A
N6
A
44
1_555
A
U
74
A
O4
U
53
1_555
hydrog
WATSON-CRICK
A
A
66
A
N1
A
45
1_555
A
U
73
A
N3
U
52
1_555
hydrog
WATSON-CRICK
A
A
66
A
N6
A
45
1_555
A
U
73
A
O4
U
52
1_555
hydrog
WATSON-CRICK
A
A
67
A
N1
A
46
1_555
A
U
72
A
N3
U
51
1_555
hydrog
WATSON-CRICK
A
A
67
A
N6
A
46
1_555
A
U
72
A
O4
U
51
1_555
hydrog
WATSON-CRICK
B
GTP
22
B
N1
GTP
1
1_555
B
CCC
89
B
N3
CCC
68
1_555
hydrog
WATSON-CRICK
B
GTP
22
B
N2
GTP
1
1_555
B
CCC
89
B
O2
CCC
68
1_555
hydrog
WATSON-CRICK
B
GTP
22
B
O6
GTP
1
1_555
B
CCC
89
B
N4
CCC
68
1_555
hydrog
TYPE_28_PAIR
B
G
23
B
N1
G
2
1_555
B
U
88
B
O2
U
67
1_555
hydrog
TYPE_28_PAIR
B
G
23
B
O6
G
2
1_555
B
U
88
B
N3
U
67
1_555
hydrog
WATSON-CRICK
B
C
24
B
N3
C
3
1_555
B
G
87
B
N1
G
66
1_555
hydrog
WATSON-CRICK
B
C
24
B
N4
C
3
1_555
B
G
87
B
O6
G
66
1_555
hydrog
WATSON-CRICK
B
C
24
B
O2
C
3
1_555
B
G
87
B
N2
G
66
1_555
hydrog
WATSON-CRICK
B
C
25
B
N3
C
4
1_555
B
G
86
B
N1
G
65
1_555
hydrog
WATSON-CRICK
B
C
25
B
N4
C
4
1_555
B
G
86
B
O6
G
65
1_555
hydrog
WATSON-CRICK
B
C
25
B
O2
C
4
1_555
B
G
86
B
N2
G
65
1_555
hydrog
U-A PAIR
B
U
26
B
N3
U
5
1_555
B
A
85
B
N1
A
64
1_555
hydrog
WATSON-CRICK
B
U
27
B
N3
U
6
1_555
B
A
84
B
N1
A
63
1_555
hydrog
WATSON-CRICK
B
U
27
B
O4
U
6
1_555
B
A
84
B
N6
A
63
1_555
hydrog
WATSON-CRICK
B
A
28
B
N1
A
7
1_555
B
U
83
B
N3
U
62
1_555
hydrog
WATSON-CRICK
B
A
28
B
N6
A
7
1_555
B
U
83
B
O4
U
62
1_555
hydrog
WATSON-CRICK
B
U
29
B
N3
U
8
1_555
B
A
82
B
N1
A
61
1_555
hydrog
WATSON-CRICK
B
U
29
B
O4
U
8
1_555
B
A
82
B
N6
A
61
1_555
hydrog
WATSON-CRICK
B
A
30
B
N1
A
9
1_555
B
U
81
B
N3
U
60
1_555
hydrog
WATSON-CRICK
B
A
30
B
N6
A
9
1_555
B
U
81
B
O4
U
60
1_555
hydrog
WATSON-CRICK
B
C
31
B
N3
C
10
1_555
B
G
59
B
N1
G
38
1_555
hydrog
WATSON-CRICK
B
C
31
B
N4
C
10
1_555
B
G
59
B
O6
G
38
1_555
hydrog
WATSON-CRICK
B
C
31
B
O2
C
10
1_555
B
G
59
B
N2
G
38
1_555
hydrog
TYPE_10_PAIR
B
A
32
B
N1
A
11
1_555
B
G
53
B
N2
G
32
1_555
hydrog
TYPE_10_PAIR
B
A
32
B
N6
A
11
1_555
B
G
53
B
N3
G
32
1_555
hydrog
G-G MISPAIR
B
G
33
B
N2
G
12
1_555
B
G
34
B
O6
G
13
1_555
hydrog
G-U MISPAIR
B
G
33
B
N2
G
12
1_555
B
U
52
B
O4
U
31
1_555
hydrog
TYPE_28_PAIR
B
G
34
B
N1
G
13
1_555
B
U
52
B
O2
U
31
1_555
hydrog
TYPE_28_PAIR
B
G
34
B
O6
G
13
1_555
B
U
52
B
N3
U
31
1_555
hydrog
WATSON-CRICK
B
G
35
B
N1
G
14
1_555
B
C
51
B
N3
C
30
1_555
hydrog
WATSON-CRICK
B
G
35
B
N2
G
14
1_555
B
C
51
B
O2
C
30
1_555
hydrog
WATSON-CRICK
B
G
35
B
O6
G
14
1_555
B
C
51
B
N4
C
30
1_555
hydrog
WATSON-CRICK
B
U
36
B
N3
U
15
1_555
B
A
50
B
N1
A
29
1_555
hydrog
WATSON-CRICK
B
U
36
B
O4
U
15
1_555
B
A
50
B
N6
A
29
1_555
hydrog
WATSON-CRICK
B
A
37
B
N1
A
16
1_555
B
U
49
B
N3
U
28
1_555
hydrog
WATSON-CRICK
B
A
37
B
N6
A
16
1_555
B
U
49
B
O4
U
28
1_555
hydrog
WATSON-CRICK
B
G
38
B
N1
G
17
1_555
B
C
48
B
N3
C
27
1_555
hydrog
WATSON-CRICK
B
G
38
B
N2
G
17
1_555
B
C
48
B
O2
C
27
1_555
hydrog
WATSON-CRICK
B
G
38
B
O6
G
17
1_555
B
C
48
B
N4
C
27
1_555
hydrog
WATSON-CRICK
B
C
39
B
N3
C
18
1_555
B
G
47
B
N1
G
26
1_555
hydrog
WATSON-CRICK
B
C
39
B
N4
C
18
1_555
B
G
47
B
O6
G
26
1_555
hydrog
WATSON-CRICK
B
C
39
B
O2
C
18
1_555
B
G
47
B
N2
G
26
1_555
hydrog
A-G MISPAIR
B
A
42
B
N1
A
21
1_555
B
G
45
B
N2
G
24
1_555
hydrog
WATSON-CRICK
B
G
45
B
N1
G
24
1_555
B
C
69
B
N3
C
48
1_555
hydrog
WATSON-CRICK
B
G
45
B
N2
G
24
1_555
B
C
69
B
O2
C
48
1_555
hydrog
WATSON-CRICK
B
G
45
B
O6
G
24
1_555
B
C
69
B
N4
C
48
1_555
hydrog
WATSON-CRICK
B
G
46
B
N1
G
25
1_555
B
C
68
B
N3
C
47
1_555
hydrog
WATSON-CRICK
B
G
46
B
N2
G
25
1_555
B
C
68
B
O2
C
47
1_555
hydrog
WATSON-CRICK
B
G
46
B
O6
G
25
1_555
B
C
68
B
N4
C
47
1_555
hydrog
WATSON-CRICK
B
G
53
B
N1
G
32
1_555
B
C
60
B
N3
C
39
1_555
hydrog
WATSON-CRICK
B
G
53
B
N2
G
32
1_555
B
C
60
B
O2
C
39
1_555
hydrog
WATSON-CRICK
B
G
53
B
O6
G
32
1_555
B
C
60
B
N4
C
39
1_555
hydrog
C-U MISPAIR
B
C
57
B
N4
C
36
1_555
B
U
81
B
O2
U
60
1_555
hydrog
WATSON-CRICK
B
C
61
B
N3
C
40
1_555
B
G
78
B
N1
G
57
1_555
hydrog
WATSON-CRICK
B
C
61
B
N4
C
40
1_555
B
G
78
B
O6
G
57
1_555
hydrog
WATSON-CRICK
B
C
61
B
O2
C
40
1_555
B
G
78
B
N2
G
57
1_555
hydrog
WATSON-CRICK
B
U
62
B
N3
U
41
1_555
B
A
77
B
N1
A
56
1_555
hydrog
WATSON-CRICK
B
U
62
B
O4
U
41
1_555
B
A
77
B
N6
A
56
1_555
hydrog
TYPE_28_PAIR
B
U
63
B
N3
U
42
1_555
B
G
76
B
O6
G
55
1_555
hydrog
TYPE_28_PAIR
B
U
63
B
O2
U
42
1_555
B
G
76
B
N1
G
55
1_555
hydrog
WATSON-CRICK
B
C
64
B
N3
C
43
1_555
B
G
75
B
N1
G
54
1_555
hydrog
WATSON-CRICK
B
C
64
B
N4
C
43
1_555
B
G
75
B
O6
G
54
1_555
hydrog
WATSON-CRICK
B
C
64
B
O2
C
43
1_555
B
G
75
B
N2
G
54
1_555
hydrog
WATSON-CRICK
B
A
65
B
N1
A
44
1_555
B
U
74
B
N3
U
53
1_555
hydrog
WATSON-CRICK
B
A
65
B
N6
A
44
1_555
B
U
74
B
O4
U
53
1_555
hydrog
WATSON-CRICK
B
A
66
B
N1
A
45
1_555
B
U
73
B
N3
U
52
1_555
hydrog
WATSON-CRICK
B
A
66
B
N6
A
45
1_555
B
U
73
B
O4
U
52
1_555
hydrog
WATSON-CRICK
B
A
67
B
N1
A
46
1_555
B
U
72
B
N3
U
51
1_555
hydrog
WATSON-CRICK
B
A
67
B
N6
A
46
1_555
B
U
72
B
O4
U
51
1_555
hydrog
C-U MISPAIR
B
C
68
B
O2
C
47
1_555
B
U
72
B
N3
U
51
1_555
RNA
three-way junction, riboswitch, 2'-deoxy guanosine, RNA
3SKZ
PDB
1
3SKZ
22
89
3SKZ
22
89
3SKZ
A
1
1
68
22
89
3SKZ
22
89
3SKZ
B
1
1
68
BINDING SITE FOR RESIDUE GMP A 120
A
GMP
120
Software
8
BINDING SITE FOR RESIDUE MG A 228
A
MG
228
Software
2
BINDING SITE FOR RESIDUE SO4 A 211
A
SO4
211
Software
3
BINDING SITE FOR RESIDUE SO4 A 212
A
SO4
212
Software
2
BINDING SITE FOR RESIDUE SO4 A 213
A
SO4
213
Software
4
BINDING SITE FOR RESIDUE SO4 A 216
A
SO4
216
Software
4
BINDING SITE FOR RESIDUE SO4 A 229
A
SO4
229
Software
2
BINDING SITE FOR RESIDUE SIN A 301
A
SIN
301
Software
2
BINDING SITE FOR RESIDUE GMP B 120
B
GMP
120
Software
9
BINDING SITE FOR RESIDUE MG B 172
B
MG
172
Software
4
BINDING SITE FOR RESIDUE SO4 B 214
B
SO4
214
Software
2
BINDING SITE FOR RESIDUE SO4 B 217
B
SO4
217
Software
2
BINDING SITE FOR RESIDUE SO4 B 219
B
SO4
219
Software
3
A
A
30
A
A
9
8
1_555
A
C
31
A
C
10
8
1_555
A
C
55
A
C
34
8
1_555
A
C
57
A
C
36
8
1_555
A
C
58
A
C
37
8
1_555
A
G
59
A
G
38
8
1_555
A
C
80
A
C
59
8
1_555
A
U
81
A
U
60
8
1_555
A
C
58
A
C
37
2
1_555
A
G
59
A
G
38
2
1_555
A
C
24
A
C
3
3
1_555
A
C
25
A
C
4
3
1_555
A
G
86
A
G
65
3
1_555
A
C
64
A
C
43
2
1_555
A
A
65
A
A
44
2
1_555
A
A
30
A
A
9
4
1_555
A
A
79
A
A
58
4
1_555
A
C
80
A
C
59
4
1_555
A
U
81
A
U
60
4
1_555
A
C
39
A
C
18
4
1_555
A
A
40
A
A
19
4
1_555
A
U
41
A
U
20
4
1_555
A
HOH
91
Q
HOH
4
1_555
A
C
68
A
C
47
2
1_555
A
HOH
180
Q
HOH
2
1_555
A
C
57
A
C
36
2
1_555
A
C
58
A
C
37
2
1_555
B
A
30
B
A
9
9
1_555
B
C
31
B
C
10
9
1_555
B
A
54
B
A
33
9
1_555
B
C
55
B
C
34
9
1_555
B
C
57
B
C
36
9
1_555
B
C
58
B
C
37
9
1_555
B
G
59
B
G
38
9
1_555
B
C
80
B
C
59
9
1_555
B
U
81
B
U
60
9
1_555
B
A
32
B
A
11
4
1_555
B
C
61
B
C
40
4
1_555
B
A
77
B
A
56
4
1_555
B
G
78
B
G
57
4
1_555
B
C
24
B
C
3
2
1_555
B
C
25
B
C
4
2
1_555
B
C
64
B
C
43
2
1_555
B
A
65
B
A
44
2
1_555
B
C
39
B
C
18
3
1_555
B
A
40
B
A
19
3
1_555
B
U
41
B
U
20
3
1_555
19
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