0.021834
0.000000
0.000000
0.000000
0.021834
0.000000
0.000000
0.000000
0.011154
0.00000
0.00000
0.00000
Xiong, Y.
Sudarsanakumar, C.
Deng, J.
Pan, B.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
45.800
45.800
89.650
C9 H12 Br N2 O9 P
403.077
n
5-BROMO-URIDINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 I N3 O8 P
449.093
n
5-IODO-CYTIDINE-5'-MONOPHOSPHATE
RNA linking
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 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
P
N
2
N
O
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
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
N
22
N
BR
N
23
N
H
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
O
N
36
S
C
N
37
S
C
N
38
N
O
N
39
R
C
N
40
N
O
N
41
R
C
N
42
N
N
N
43
N
C
N
44
N
C
N
45
N
I
N
46
N
C
N
47
N
N
N
48
N
C
N
49
N
O
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
P
N
54
N
O
N
55
N
O
N
56
N
O
N
57
N
H
N
58
N
H
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
O
N
71
N
P
N
72
N
O
N
73
N
O
N
74
N
O
N
75
N
C
N
76
R
C
N
77
N
O
N
78
S
C
N
79
N
O
N
80
R
C
N
81
N
O
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
Y
87
N
C
N
88
N
N
Y
89
N
N
Y
90
N
C
Y
91
N
N
Y
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
R
C
N
118
N
O
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
N
N
126
N
C
N
127
N
C
N
128
N
H
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
O
N
143
N
P
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
O
N
150
S
C
N
151
N
O
N
152
R
C
N
153
N
O
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
H
N
182
N
H
N
183
N
MG
N
184
N
O
N
185
N
P
N
186
N
O
N
187
N
O
N
188
N
O
N
189
N
C
N
190
R
C
N
191
N
O
N
192
S
C
N
193
N
O
N
194
R
C
N
195
N
O
N
196
R
C
N
197
N
N
N
198
N
C
N
199
N
O
N
200
N
N
N
201
N
C
N
202
N
O
N
203
N
C
N
204
N
C
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
1
N
doub
N
2
N
sing
N
3
N
sing
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
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
doub
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
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
doub
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
doub
N
58
N
sing
N
59
N
sing
N
60
N
doub
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
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
Y
96
N
sing
Y
97
N
sing
Y
98
N
doub
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
doub
N
105
N
sing
N
106
N
sing
Y
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
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
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
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
Y
171
N
sing
Y
172
N
sing
Y
173
N
doub
N
174
N
sing
Y
175
N
sing
N
176
N
sing
Y
177
N
doub
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
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
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
doub
N
220
N
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
To be Published
0353
Crystal Structure of a Bulged RNA from the SL2 Stem-loop of the HIV-1 psi-RNA
10.2210/pdb1jzv/pdb
pdb_00001jzv
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
ADSC QUANTUM 4
MAD
M
x-ray
1
0.9195
1.0
14-BM-D
APS
0.9195
SYNCHROTRON
APS BEAMLINE 14-BM-D
SL2 STEM-LOOP OF THE HIV-1 PSI-RNA
2660.497
5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
2
syn
polymer
2956.655
5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
81
nat
water
no
yes
GGCGAC(5BU)G
GGCGACUG
A,C
polyribonucleotide
no
yes
CAGUACG(5IC)C
CAGUACGCC
B,D
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.09
41.22
VAPOR DIFFUSION, HANGING DROP
6.0
MPD, magnesium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
MPD
1
MgCl2
2
cacodylate
3
-4.792
1
19
A
1
B
17
-3.201
A_G1:C17_B
1
-8.832
-0.221
0.035
-0.223
-4.921
1
19
A
2
B
16
1.326
A_G2:5IC16_B
2
-12.594
-0.522
0.076
-0.104
-0.620
1
19
A
3
B
15
1.263
A_C3:G15_B
3
-6.523
0.194
0.204
-0.185
8.927
1
19
A
4
B
14
2.316
A_G4:C14_B
4
0.354
-0.197
0.305
-0.162
10.080
1
20
A
5
B
12
-7.134
A_A5:U12_B
5
-14.818
0.090
0.077
0.027
8.752
1
19
A
6
B
11
4.043
A_C6:G11_B
6
-18.467
0.335
0.023
-0.093
5.821
1
20
A
7
B
10
2.835
A_5BU7:A10_B
7
-12.291
-0.124
-0.138
-0.116
5.538
1
19
A
8
B
9
-0.291
A_G8:C9_B
8
-7.456
-0.114
0.141
-0.144
-3.107
1
19
C
21
D
37
0.654
C_G21:C37_D
9
-14.951
-0.343
-0.017
-0.234
-10.612
1
19
C
22
D
36
3.748
C_G22:5IC36_D
10
-12.778
-0.620
-0.180
0.003
-4.713
1
19
C
23
D
35
-0.584
C_C23:G35_D
11
-9.240
0.121
-0.078
-0.074
8.079
1
19
C
24
D
34
2.467
C_G24:C34_D
12
0.694
-0.152
0.294
-0.081
9.865
1
20
C
25
D
32
-3.846
C_A25:U32_D
13
-15.159
0.099
0.057
-0.073
7.505
1
19
C
26
D
31
2.380
C_C26:G31_D
14
-18.315
0.405
0.142
-0.201
-3.322
1
20
C
27
D
30
1.938
C_5BU27:A30_D
15
-14.393
-0.258
-0.112
-0.125
-0.903
1
19
C
28
D
29
1.274
C_G28:C29_D
16
-2.730
-0.231
0.196
-0.120
2.798
32.669
A
A
1
2
11.367
B
B
17
16
3.166
6.355
0.160
-1.647
AA_G1G2:5IC16C17_BB
1
0.297
-0.531
32.060
-3.941
-0.237
3.168
33.455
A
A
2
3
0.934
B
B
16
15
3.180
0.538
0.619
-1.687
AA_G2C3:G155IC16_BB
2
0.870
-1.512
33.440
-3.017
-0.936
2.781
24.831
A
A
3
4
2.298
B
B
15
14
2.922
0.987
0.528
-2.104
AA_C3G4:C14G15_BB
3
-2.181
5.079
24.718
-5.153
-1.803
2.798
45.931
A
A
4
5
8.136
B
B
14
12
3.181
6.329
0.832
-2.398
AA_G4A5:U12C14_BB
4
-2.292
2.947
45.461
-3.575
-1.248
2.923
36.611
A
A
5
6
7.212
B
B
12
11
3.168
4.519
0.940
-1.715
AA_A5C6:G11U12_BB
5
-0.685
1.093
36.335
-3.311
-1.584
2.508
29.473
A
A
6
7
17.538
B
B
11
10
3.318
8.792
-0.740
-2.313
AA_C65BU7:A10G11_BB
6
-0.457
0.911
28.155
-6.257
1.365
2.351
32.918
A
A
7
8
22.818
B
B
10
9
3.190
12.605
-0.040
-1.608
AA_5BU7G8:C9A10_BB
7
-2.419
4.379
30.376
-4.738
-0.294
2.471
31.874
C
C
21
22
19.098
D
D
37
36
3.342
10.307
0.081
-2.200
CC_G21G22:5IC36C37_DD
8
-1.167
2.162
30.181
-5.722
-0.342
2.887
34.191
C
C
22
23
11.157
D
D
36
35
3.101
6.519
-0.824
-1.053
CC_G22C23:G355IC36_DD
9
-1.667
2.852
33.542
-2.742
1.158
2.082
26.102
C
C
23
24
15.301
D
D
35
34
2.882
6.811
1.089
-2.064
CC_C23G24:C34G35_DD
10
-3.554
7.983
24.964
-6.012
-3.164
2.333
42.737
C
C
24
25
16.193
D
D
34
32
3.130
11.662
0.998
-2.511
CC_G24A25:U32C34_DD
11
-1.400
1.944
41.164
-4.442
-1.489
2.946
36.821
C
C
25
26
7.248
D
D
32
31
3.183
4.567
0.697
-1.655
CC_A25C26:G31U32_DD
12
-0.804
1.276
36.538
-3.204
-1.206
2.449
29.370
C
C
26
27
20.384
D
D
31
30
3.497
10.124
-0.962
-2.285
CC_C265BU27:A30G31_DD
13
1.916
-3.858
27.541
-6.551
2.284
2.495
33.559
C
C
27
28
18.176
D
D
30
29
3.077
10.331
0.657
-1.377
CC_5BU27G28:C29A30_DD
14
-1.321
2.324
31.946
-3.867
-1.328
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-11-11
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-09-17
REL
REL
MG
MAGNESIUM ION
HOH
water
Solid phase phosphoramidite synthesis
sample
MG
300
3
MG
MG
300
C
HOH
316
4
HOH
HOH
316
A
HOH
319
4
HOH
HOH
319
A
HOH
322
4
HOH
HOH
322
A
HOH
327
4
HOH
HOH
327
A
HOH
328
4
HOH
HOH
328
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
336
4
HOH
HOH
336
A
HOH
342
4
HOH
HOH
342
A
HOH
343
4
HOH
HOH
343
A
HOH
355
4
HOH
HOH
355
A
HOH
361
4
HOH
HOH
361
A
HOH
363
4
HOH
HOH
363
A
HOH
365
4
HOH
HOH
365
A
HOH
368
4
HOH
HOH
368
A
HOH
369
4
HOH
HOH
369
A
HOH
373
4
HOH
HOH
373
A
HOH
307
4
HOH
HOH
307
B
HOH
308
4
HOH
HOH
308
B
HOH
312
4
HOH
HOH
312
B
HOH
314
4
HOH
HOH
314
B
HOH
315
4
HOH
HOH
315
B
HOH
321
4
HOH
HOH
321
B
HOH
326
4
HOH
HOH
326
B
HOH
330
4
HOH
HOH
330
B
HOH
334
4
HOH
HOH
334
B
HOH
335
4
HOH
HOH
335
B
HOH
344
4
HOH
HOH
344
B
HOH
345
4
HOH
HOH
345
B
HOH
346
4
HOH
HOH
346
B
HOH
350
4
HOH
HOH
350
B
HOH
351
4
HOH
HOH
351
B
HOH
352
4
HOH
HOH
352
B
HOH
353
4
HOH
HOH
353
B
HOH
358
4
HOH
HOH
358
B
HOH
359
4
HOH
HOH
359
B
HOH
364
4
HOH
HOH
364
B
HOH
366
4
HOH
HOH
366
B
HOH
367
4
HOH
HOH
367
B
HOH
377
4
HOH
HOH
377
B
HOH
378
4
HOH
HOH
378
B
HOH
301
4
HOH
HOH
301
C
HOH
302
4
HOH
HOH
302
C
HOH
303
4
HOH
HOH
303
C
HOH
304
4
HOH
HOH
304
C
HOH
306
4
HOH
HOH
306
C
HOH
309
4
HOH
HOH
309
C
HOH
313
4
HOH
HOH
313
C
HOH
317
4
HOH
HOH
317
C
HOH
323
4
HOH
HOH
323
C
HOH
324
4
HOH
HOH
324
C
HOH
329
4
HOH
HOH
329
C
HOH
337
4
HOH
HOH
337
C
HOH
338
4
HOH
HOH
338
C
HOH
339
4
HOH
HOH
339
C
HOH
347
4
HOH
HOH
347
C
HOH
357
4
HOH
HOH
357
C
HOH
362
4
HOH
HOH
362
C
HOH
371
4
HOH
HOH
371
C
HOH
305
4
HOH
HOH
305
D
HOH
310
4
HOH
HOH
310
D
HOH
311
4
HOH
HOH
311
D
HOH
318
4
HOH
HOH
318
D
HOH
320
4
HOH
HOH
320
D
HOH
325
4
HOH
HOH
325
D
HOH
331
4
HOH
HOH
331
D
HOH
340
4
HOH
HOH
340
D
HOH
341
4
HOH
HOH
341
D
HOH
348
4
HOH
HOH
348
D
HOH
349
4
HOH
HOH
349
D
HOH
354
4
HOH
HOH
354
D
HOH
356
4
HOH
HOH
356
D
HOH
360
4
HOH
HOH
360
D
HOH
370
4
HOH
HOH
370
D
HOH
372
4
HOH
HOH
372
D
HOH
374
4
HOH
HOH
374
D
HOH
375
4
HOH
HOH
375
D
HOH
376
4
HOH
HOH
376
D
HOH
379
4
HOH
HOH
379
D
HOH
380
4
HOH
HOH
380
D
HOH
381
4
HOH
HOH
381
D
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
C
6
n
6
C
6
A
5BU
7
n
7
5BU
7
A
G
8
n
8
G
8
A
C
9
n
1
C
9
B
A
10
n
2
A
10
B
G
11
n
3
G
11
B
U
12
n
4
U
12
B
A
13
n
5
A
13
B
C
14
n
6
C
14
B
G
15
n
7
G
15
B
5IC
16
n
8
5IC
16
B
C
17
n
9
C
17
B
G
21
n
1
G
21
C
G
22
n
2
G
22
C
C
23
n
3
C
23
C
G
24
n
4
G
24
C
A
25
n
5
A
25
C
C
26
n
6
C
26
C
5BU
27
n
7
5BU
27
C
G
28
n
8
G
28
C
C
29
n
1
C
29
D
A
30
n
2
A
30
D
G
31
n
3
G
31
D
U
32
n
4
U
32
D
A
33
n
5
A
33
D
C
34
n
6
C
34
D
G
35
n
7
G
35
D
5IC
36
n
8
5IC
36
D
C
37
n
9
C
37
D
author_defined_assembly
2
dimeric
author_defined_assembly
2
dimeric
C
HOH
301
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
302
H
O
HOH
1_555
90.4
C
HOH
301
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
303
H
O
HOH
1_555
94.2
C
HOH
302
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
303
H
O
HOH
1_555
90.5
C
HOH
301
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
304
H
O
HOH
1_555
168.3
C
HOH
302
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
304
H
O
HOH
1_555
78.8
C
HOH
303
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
304
H
O
HOH
1_555
81.5
C
HOH
301
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
306
H
O
HOH
1_555
100.9
C
HOH
302
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
306
H
O
HOH
1_555
167.3
C
HOH
303
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
306
H
O
HOH
1_555
83.0
C
HOH
304
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
C
HOH
306
H
O
HOH
1_555
89.4
C
HOH
301
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
93.4
C
HOH
302
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
90.5
C
HOH
303
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
172.3
C
HOH
304
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
91.2
C
HOH
306
H
O
HOH
1_555
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
94.5
A
5BU
7
5-BROMO-URIDINE-5'-MONOPHOSPHATE
A
5BU
7
U
B
5IC
16
5-IODO-CYTIDINE-5'-MONOPHOSPHATE
B
5IC
8
C
C
5BU
27
5-BROMO-URIDINE-5'-MONOPHOSPHATE
C
5BU
7
U
D
5IC
36
5-IODO-CYTIDINE-5'-MONOPHOSPHATE
D
5IC
8
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
O2'
5IC
16
B
O2'
5IC
8
1
Y
1
D
O2'
5IC
36
D
O2'
5IC
8
1
Y
1
C
G
24
0.057
SIDE CHAIN
1
D
C
29
0.072
SIDE CHAIN
0.233
0.203
1.7
20
1847
20028
19558
9.4
Random
1
2
MAD
1.7
20
81
800
1
718
0
0.014
1.38
1.7
20
1JZV
19682
-3
0.063
1
98.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
SOLVE
refinement
CNS
1.0
Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA
1
N
N
2
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
covale
1.601
both
A
C
6
A
O3'
C
6
1_555
A
5BU
7
A
P
5BU
7
1_555
covale
1.608
both
A
5BU
7
A
O3'
5BU
7
1_555
A
G
8
A
P
G
8
1_555
covale
1.616
both
B
G
15
B
O3'
G
7
1_555
B
5IC
16
B
P
5IC
8
1_555
covale
1.602
both
B
5IC
16
B
O3'
5IC
8
1_555
B
C
17
B
P
C
9
1_555
covale
1.621
both
C
C
26
C
O3'
C
6
1_555
C
5BU
27
C
P
5BU
7
1_555
covale
1.605
both
C
5BU
27
C
O3'
5BU
7
1_555
C
G
28
C
P
G
8
1_555
covale
1.591
both
D
G
35
D
O3'
G
7
1_555
D
5IC
36
D
P
5IC
8
1_555
covale
1.602
both
D
5IC
36
D
O3'
5IC
8
1_555
D
C
37
D
P
C
9
1_555
metalc
2.202
C
MG
300
E
MG
MG
1_555
C
HOH
301
H
O
HOH
1_555
metalc
2.059
C
MG
300
E
MG
MG
1_555
C
HOH
302
H
O
HOH
1_555
metalc
2.026
C
MG
300
E
MG
MG
1_555
C
HOH
303
H
O
HOH
1_555
metalc
2.263
C
MG
300
E
MG
MG
1_555
C
HOH
304
H
O
HOH
1_555
metalc
2.283
C
MG
300
E
MG
MG
1_555
C
HOH
306
H
O
HOH
1_555
metalc
2.192
C
MG
300
E
MG
MG
1_555
D
HOH
305
I
O
HOH
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
17
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
17
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
17
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
5IC
16
B
N3
5IC
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
5IC
16
B
O2
5IC
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
5IC
16
B
N4
5IC
8
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
B
G
15
B
N1
G
7
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
15
B
O6
G
7
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
15
B
N2
G
7
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
B
C
14
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
B
C
14
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
B
C
14
B
N4
C
6
1_555
hydrog
WATSON-CRICK
A
A
5
A
N1
A
5
1_555
B
U
12
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
5
1_555
B
U
12
B
O4
U
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
B
G
11
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
B
G
11
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
B
G
11
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
5BU
7
A
N3
5BU
7
1_555
B
A
10
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
5BU
7
A
O4
5BU
7
1_555
B
A
10
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
B
C
9
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
B
C
9
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
B
C
9
B
N4
C
1
1_555
hydrog
G-A MISPAIR
B
G
11
B
N2
G
3
1_555
D
A
33
D
N3
A
5
1_555
hydrog
A-G MISPAIR
B
A
13
B
N3
A
5
1_555
D
G
31
D
N2
G
3
1_555
hydrog
WATSON-CRICK
C
G
21
C
N1
G
1
1_555
D
C
37
D
N3
C
9
1_555
hydrog
WATSON-CRICK
C
G
21
C
N2
G
1
1_555
D
C
37
D
O2
C
9
1_555
hydrog
WATSON-CRICK
C
G
21
C
O6
G
1
1_555
D
C
37
D
N4
C
9
1_555
hydrog
WATSON-CRICK
C
G
22
C
N1
G
2
1_555
D
5IC
36
D
N3
5IC
8
1_555
hydrog
WATSON-CRICK
C
G
22
C
N2
G
2
1_555
D
5IC
36
D
O2
5IC
8
1_555
hydrog
WATSON-CRICK
C
G
22
C
O6
G
2
1_555
D
5IC
36
D
N4
5IC
8
1_555
hydrog
WATSON-CRICK
C
C
23
C
N3
C
3
1_555
D
G
35
D
N1
G
7
1_555
hydrog
WATSON-CRICK
C
C
23
C
N4
C
3
1_555
D
G
35
D
O6
G
7
1_555
hydrog
WATSON-CRICK
C
C
23
C
O2
C
3
1_555
D
G
35
D
N2
G
7
1_555
hydrog
WATSON-CRICK
C
G
24
C
N1
G
4
1_555
D
C
34
D
N3
C
6
1_555
hydrog
WATSON-CRICK
C
G
24
C
N2
G
4
1_555
D
C
34
D
O2
C
6
1_555
hydrog
WATSON-CRICK
C
G
24
C
O6
G
4
1_555
D
C
34
D
N4
C
6
1_555
hydrog
WATSON-CRICK
C
A
25
C
N1
A
5
1_555
D
U
32
D
N3
U
4
1_555
hydrog
WATSON-CRICK
C
A
25
C
N6
A
5
1_555
D
U
32
D
O4
U
4
1_555
hydrog
WATSON-CRICK
C
C
26
C
N3
C
6
1_555
D
G
31
D
N1
G
3
1_555
hydrog
WATSON-CRICK
C
C
26
C
N4
C
6
1_555
D
G
31
D
O6
G
3
1_555
hydrog
WATSON-CRICK
C
C
26
C
O2
C
6
1_555
D
G
31
D
N2
G
3
1_555
hydrog
WATSON-CRICK
C
5BU
27
C
N3
5BU
7
1_555
D
A
30
D
N1
A
2
1_555
hydrog
WATSON-CRICK
C
5BU
27
C
O4
5BU
7
1_555
D
A
30
D
N6
A
2
1_555
hydrog
WATSON-CRICK
C
G
28
C
N1
G
8
1_555
D
C
29
D
N3
C
1
1_555
hydrog
WATSON-CRICK
C
G
28
C
N2
G
8
1_555
D
C
29
D
O2
C
1
1_555
hydrog
WATSON-CRICK
C
G
28
C
O6
G
8
1_555
D
C
29
D
N4
C
1
1_555
RNA
A-bulge, A-RNA, HIV-1 SL2, RNA
1JZV
PDB
1
1JZV
1JZV
PDB
2
1JZV
1
8
1JZV
1
8
1JZV
A
1
1
8
9
17
1JZV
9
17
1JZV
B
2
1
9
21
28
1JZV
21
28
1JZV
C
1
1
8
29
37
1JZV
29
37
1JZV
D
2
1
9
BINDING SITE FOR RESIDUE MG C 300
C
MG
300
Software
6
C
HOH
301
H
HOH
6
1_555
C
HOH
302
H
HOH
6
1_555
C
HOH
303
H
HOH
6
1_555
C
HOH
304
H
HOH
6
1_555
C
HOH
306
H
HOH
6
1_555
D
HOH
305
I
HOH
6
1_555
92
P 41 21 2