0.012102
0.000000
0.000000
0.000000
0.012102
0.000000
0.000000
0.000000
0.020345
0.00000
0.00000
0.00000
Tereshko, V.
Skripkin, E.
Patel, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
82.634
82.634
49.153
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
Na 1
22.990
SODIUM ION
non-polymer
C21 H39 N7 O12
581.574
STREPTOMYCIN
STREPTOMYCIN A
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
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
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
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
H
N
111
N
O
N
112
N
H
N
113
N
H
N
114
N
MG
N
115
N
NA
N
116
R
C
N
117
N
N
N
118
N
C
N
119
N
N
N
120
N
N
N
121
R
C
N
122
N
O
N
123
S
C
N
124
N
N
N
125
N
C
N
126
N
N
N
127
N
N
N
128
R
C
N
129
N
O
N
130
R
C
N
131
N
O
N
132
S
C
N
133
N
O
N
134
R
C
N
135
S
C
N
136
S
C
N
137
N
O
N
138
N
C
N
139
N
O
N
140
S
C
N
141
N
C
N
142
N
O
N
143
N
O
N
144
S
C
N
145
S
C
N
146
N
N
N
147
N
C
N
148
S
C
N
149
N
O
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
N
O
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
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
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
O
N
196
N
P
N
197
N
O
N
198
N
O
N
199
N
O
N
200
N
C
N
201
R
C
N
202
N
O
N
203
S
C
N
204
N
O
N
205
R
C
N
206
N
O
N
207
R
C
N
208
N
N
N
209
N
C
N
210
N
O
N
211
N
N
N
212
N
C
N
213
N
O
N
214
N
C
N
215
N
C
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
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
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
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
doub
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
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
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
doub
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
sing
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
doub
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
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
N
224
N
sing
N
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
UK
CHEM.BIOL.
CBOLE2
2050
1074-5521
10
175
187
10.1016/S1074-5521(03)00024-3
12618190
Encapsulating Streptomycin within a small 40-mer RNA
2003
10.2210/pdb1ntb/pdb
pdb_00001ntb
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
mirrors
IMAGE PLATE
2002-05-24
RIGAKU RAXIS IV++
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RUH3R
6988.146
5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3'
1
syn
polymer
5762.499
5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'
1
syn
polymer
22.990
SODIUM ION
2
syn
non-polymer
581.574
STREPTOMYCIN
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
6
nat
water
no
no
GGAUCGCAUUUGGACUUCUGCC
GGAUCGCAUUUGGACUUCUGCC
A
polyribonucleotide
no
no
CGGCACCACGGUCGGAUC
CGGCACCACGGUCGGAUC
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
1
3.29
62.62
VAPOR DIFFUSION, HANGING DROP
5.6
MES buffer, Magnesium cloride, sodium cloride, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
MES buffer
1
MgCl2
1
NaCl
1
MPD
1
MgCl2
2
NaCl
2
MPD
2
0.538
1
19
A
2
B
118
-5.197
A_G2:C118_B
1
-6.520
-0.134
0.338
-0.201
2.388
1
20
A
3
B
117
1.092
A_A3:U117_B
2
-16.245
0.210
-0.207
-0.266
0.734
1
20
A
4
B
116
3.482
A_U4:A116_B
3
-16.940
0.276
0.183
-0.301
-1.348
1
19
A
5
B
115
-1.025
A_C5:G115_B
4
-7.133
-0.081
0.149
-0.283
-6.786
1
19
A
7
B
114
-3.722
A_C7:G114_B
5
1.864
-0.275
-0.084
-0.272
-7.623
1
19
A
13
B
113
0.877
A_G13:C113_B
6
-1.632
-0.575
-0.440
-0.345
-18.198
1
20
A
14
B
112
5.150
A_A14:U112_B
7
-1.466
0.124
-0.819
-0.218
-9.190
1
19
A
15
B
111
-2.001
A_C15:G111_B
8
8.462
0.144
-0.062
-0.203
-28.253
1
19
A
18
B
110
-4.275
A_C18:G110_B
9
1.855
0.004
0.560
-0.244
-2.804
B
108
A
17
-62.150
B_A108:U17_A
10
-0.370
-4.226
-0.563
-1.625
-26.126
2
A
12
B
109
-106.673
A_G12:C109_B
11
20.254
0.201
-0.118
5.874
-4.060
1
20
A
19
B
105
8.188
A_U19:A105_B
12
-3.727
0.118
0.153
0.103
7.333
1
19
A
20
B
104
4.914
A_G20:C104_B
13
-16.209
-0.937
0.181
-0.233
11.775
1
19
A
21
B
103
3.761
A_C21:G103_B
14
-18.246
-0.225
0.290
-0.089
-1.126
1
A
22
B
102
6.976
A_C22:G102_B
15
-19.455
0.690
0.956
-0.134
2.994
33.345
A
A
2
3
7.122
B
B
118
117
3.195
4.075
-0.122
-1.405
AA_G2A3:U117C118_BB
1
1.879
-3.284
33.050
-3.092
0.509
2.797
33.127
A
A
3
4
16.500
B
B
117
116
3.323
9.276
0.288
-1.324
AA_A3U4:A116U117_BB
2
-3.021
5.374
31.697
-3.817
-0.992
2.420
31.502
A
A
4
5
19.617
B
B
116
115
3.180
10.458
-0.313
-1.799
AA_U4C5:G115A116_BB
3
0.369
-0.691
29.755
-5.033
0.638
2.260
38.540
A
A
5
7
17.935
B
B
115
114
3.211
11.662
-0.845
-2.642
AA_C5C7:G114G115_BB
4
1.702
-2.618
36.759
-5.242
1.461
2.707
52.821
A
A
7
13
7.535
B
B
114
113
3.345
6.664
-2.436
-1.959
AA_C7G13:C113G114_BB
5
8.158
-9.224
51.834
-2.605
3.231
3.542
37.746
A
A
13
14
3.009
B
B
113
112
3.710
1.939
-0.222
-1.964
AA_G13A14:U112C113_BB
6
5.382
-8.349
37.325
-3.315
1.118
2.933
31.891
A
A
14
15
6.516
B
B
112
111
3.170
3.572
-0.046
-1.986
AA_A14C15:G111U112_BB
7
-1.507
2.750
31.661
-4.223
-0.173
3.664
46.134
A
A
15
18
-0.723
B
B
111
110
3.745
-0.566
-0.962
-2.926
AA_C15C18:G110G111_BB
8
4.862
-6.215
45.888
-3.679
1.700
-1.462
-168.664
A
B
18
108
23.650
B
A
110
17
-2.725
-45.168
0.126
-2.530
AB_C18A108:U17G110_AB
9
-161.745
-84.690
-39.999
0.876
1.479
2.844
26.203
A
A
19
20
3.263
B
B
105
104
2.926
1.478
-0.704
-1.690
AA_U19G20:C104A105_BB
10
-0.611
1.348
26.155
-4.081
1.408
2.749
38.019
A
A
20
21
7.967
B
B
104
103
2.950
5.172
0.073
-1.257
AA_G20C21:G103C104_BB
11
-2.414
3.719
37.604
-2.506
-0.381
3.066
39.070
A
A
21
22
11.687
B
B
103
102
3.381
7.765
0.479
-1.190
AA_C21C22:G102G103_BB
12
-1.771
2.666
38.281
-2.711
-0.929
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-05-13
1
1
2008-04-29
1
2
2011-07-13
1
3
2024-02-14
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
2.9 A crystal structure of Streptomycin RNA-aptamer (Barium form)
RCSB
Y
RCSB
2003-01-29
REL
REL
NA
SODIUM ION
SRY
STREPTOMYCIN
MG
MAGNESIUM ION
HOH
water
1NTA
Barium form of streptomycin RNA-aptamer
PDB
experimental model
NA
4
3
NA
NA
23
A
NA
5
3
NA
NA
24
A
SRY
6
4
SRY
SRY
25
A
MG
1
5
MG
MG
1
B
HOH
8
6
HOH
HOH
26
A
HOH
10
6
HOH
HOH
27
A
HOH
7
6
HOH
HOH
7
B
HOH
9
6
HOH
HOH
9
B
HOH
11
6
HOH
HOH
11
B
HOH
12
6
HOH
HOH
12
B
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
U
4
n
4
U
4
A
C
5
n
5
C
5
A
G
6
n
6
G
6
A
C
7
n
7
C
7
A
A
8
n
8
A
8
A
U
9
n
9
U
9
A
U
10
n
10
U
10
A
U
11
n
11
U
11
A
G
12
n
12
G
12
A
G
13
n
13
G
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
U
16
n
16
U
16
A
U
17
n
17
U
17
A
C
18
n
18
C
18
A
U
19
n
19
U
19
A
G
20
n
20
G
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
A
C
101
n
1
C
101
B
G
102
n
2
G
102
B
G
103
n
3
G
103
B
C
104
n
4
C
104
B
A
105
n
5
A
105
B
C
106
n
6
C
106
B
C
107
n
7
C
107
B
A
108
n
8
A
108
B
C
109
n
9
C
109
B
G
110
n
10
G
110
B
G
111
n
11
G
111
B
U
112
n
12
U
112
B
C
113
n
13
C
113
B
G
114
n
14
G
114
B
G
115
n
15
G
115
B
A
116
n
16
A
116
B
U
117
n
17
U
117
B
C
118
n
18
C
118
B
4.4955
0.2268
-0.5570
5.6035
-3.8731
9.3740
-0.4998
0.3799
-0.2448
0.1511
0.5065
-0.3314
0.0325
-0.0659
-0.0066
0.2346
0.2198
0.0239
0.2111
0.0065
0.3656
refined
13.0915
30.3084
0.7858
X-RAY DIFFRACTION
A
1
A
1
A
22
A
22
X-RAY DIFFRACTION
1
author_defined_assembly
2
dimeric
A
C
7
A
OP2
C
7
1_555
A
NA
23
C
NA
NA
1_555
A
A
8
A
O2'
A
8
1_555
113.1
A
C
7
A
OP2
C
7
1_555
A
NA
23
C
NA
NA
1_555
A
U
10
A
OP2
U
10
1_555
125.8
A
A
8
A
O2'
A
8
1_555
A
NA
23
C
NA
NA
1_555
A
U
10
A
OP2
U
10
1_555
98.8
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
A
U
11
A
O4
U
11
1_555
97.6
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
A
HOH
26
G
O
HOH
1_555
85.6
A
U
11
A
O4
U
11
1_555
B
MG
1
F
MG
MG
1_555
A
HOH
26
G
O
HOH
1_555
164.3
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
B
HOH
7
H
O
HOH
1_555
99.4
A
U
11
A
O4
U
11
1_555
B
MG
1
F
MG
MG
1_555
B
HOH
7
H
O
HOH
1_555
100.3
A
HOH
26
G
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
B
HOH
7
H
O
HOH
1_555
64.0
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O5'
C
9
1_555
161.3
A
U
11
A
O4
U
11
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O5'
C
9
1_555
92.2
A
HOH
26
G
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O5'
C
9
1_555
89.3
B
HOH
7
H
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O5'
C
9
1_555
94.4
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
89.4
A
U
11
A
O4
U
11
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
76.3
A
HOH
26
G
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
119.2
B
HOH
7
H
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
170.9
B
C
109
B
O5'
C
9
1_555
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
77.4
A
C
15
A
OP2
C
15
1_555
A
NA
24
D
NA
NA
1_555
A
U
16
A
O4
U
16
1_555
71.6
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
SRY
25
E
SRY
0
N
1
B
HOH
11
H
HOH
0
N
1
B
C3'
U
112
WRONG HAND
1
B
C1'
U
112
PLANAR
1
B
C3'
U
117
PLANAR
1
9.46
1.20
119.70
129.16
A
A
A
C3'
O3'
P
G
G
C
6
6
7
Y
1
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N9
A
A
A
8
8
8
N
1
-19.67
0.80
109.40
89.73
B
B
B
O5'
C5'
C4'
C
C
C
106
106
106
N
1
-10.92
1.60
120.90
109.98
B
B
B
P
O5'
C5'
C
C
C
106
106
106
N
1
7.36
1.20
119.70
127.06
B
B
B
C3'
O3'
P
C
C
A
107
107
108
Y
1
-7.65
0.70
109.70
102.05
B
B
B
C1'
O4'
C4'
U
U
U
112
112
112
N
1
-4.32
0.70
101.30
96.98
B
B
B
C3'
C2'
C1'
U
U
U
112
112
112
N
1
8.16
0.90
107.60
115.76
B
B
B
O4'
C1'
C2'
U
U
U
112
112
112
N
1
14.13
1.30
114.00
128.13
B
B
B
N1
C1'
C2'
U
U
U
112
112
112
N
1
5.83
0.70
108.50
114.33
B
B
B
O4'
C1'
N1
U
U
U
112
112
112
N
1
6.30
0.60
114.90
121.20
B
B
B
N1
C2
N3
U
U
U
112
112
112
N
1
-5.79
0.60
127.00
121.21
B
B
B
C2
N3
C4
U
U
U
112
112
112
N
1
3.62
0.60
114.60
118.22
B
B
B
N3
C4
C5
U
U
U
112
112
112
N
1
-7.33
0.60
125.90
118.57
B
B
B
C5
C4
O4
U
U
U
112
112
112
N
1
-9.01
1.40
121.20
112.19
B
B
B
C6
N1
C1'
U
U
U
112
112
112
N
1
9.67
1.20
117.70
127.37
B
B
B
C2
N1
C1'
U
U
U
112
112
112
N
1
10.21
1.00
102.60
112.81
B
B
B
C4'
C3'
C2'
U
U
U
117
117
117
N
1
9.53
0.90
107.60
117.13
B
B
B
O4'
C1'
C2'
U
U
U
117
117
117
N
1
7.10
0.70
108.50
115.60
B
B
B
O4'
C1'
N1
U
U
U
117
117
117
N
1
5.41
0.60
114.90
120.31
B
B
B
N1
C2
N3
U
U
U
117
117
117
N
1
-4.95
0.60
127.00
122.05
B
B
B
C2
N3
C4
U
U
U
117
117
117
N
1
-4.21
0.60
125.90
121.69
B
B
B
C5
C4
O4
U
U
U
117
117
117
N
1
-9.93
1.40
121.20
111.27
B
B
B
C6
N1
C1'
U
U
U
117
117
117
N
1
9.51
1.20
117.70
127.21
B
B
B
C2
N1
C1'
U
U
U
117
117
117
N
1
A
A
O5'
C5'
A
A
8
8
-0.070
0.009
1.420
1.350
N
1
A
A
C1'
N1
U
U
11
11
0.107
0.015
1.483
1.590
N
1
A
A
C4
O4
U
U
11
11
0.075
0.008
1.232
1.307
N
1
B
B
O5'
C5'
C
C
106
106
0.185
0.016
1.440
1.625
N
1
B
B
P
OP2
U
U
112
112
0.217
0.017
1.485
1.702
N
1
B
B
P
OP2
U
U
117
117
0.215
0.017
1.485
1.700
N
45.528
0.51
0.00
0.00
0.51
0.00
-1.02
0.946
0.923
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25507
0.20373
0.20847
2.90
20.00
349
3394
9.3
99.84
16.131
0.299
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.396
0.80
0.80
1.40
Barium form of streptomycin RNA-aptamer
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.90
20.00
6
891
43
842
0
0.010
0.021
988
0.002
0.020
327
1.746
2.121
1525
1.710
2.049
854
0.412
0.200
175
0.005
0.020
418
0.003
0.020
4
0.179
0.200
177
0.227
0.200
407
0.110
0.200
198
0.178
0.200
30
0.123
0.200
18
0.225
0.200
10
0.149
0.200
1
0.853
3.000
988
1.372
4.500
1525
0.359
0.3
2.974
22
234
20
2.85
25.0
1NTB
3942
0.045
1
9.3
99.8
0.45
2.85
2.95
99.8
refinement
REFMAC
5.1.13
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
2.9 A crystal structure of Streptomycin RNA-aptamer complex
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
6
N
N
6
N
N
metalc
2.483
A
C
7
A
OP2
C
7
1_555
A
NA
23
C
NA
NA
1_555
metalc
2.497
A
A
8
A
O2'
A
8
1_555
A
NA
23
C
NA
NA
1_555
metalc
2.480
A
U
10
A
OP2
U
10
1_555
A
NA
23
C
NA
NA
1_555
metalc
2.201
A
U
10
A
O2
U
10
1_555
B
MG
1
F
MG
MG
1_555
metalc
2.245
A
U
11
A
O4
U
11
1_555
B
MG
1
F
MG
MG
1_555
metalc
2.248
A
C
15
A
OP2
C
15
1_555
A
NA
24
D
NA
NA
1_555
metalc
2.200
A
U
16
A
O4
U
16
1_555
A
NA
24
D
NA
NA
1_555
metalc
2.090
A
HOH
26
G
O
HOH
1_555
B
MG
1
F
MG
MG
1_555
metalc
2.504
B
MG
1
F
MG
MG
1_555
B
HOH
7
H
O
HOH
1_555
metalc
2.200
B
MG
1
F
MG
MG
1_555
B
C
109
B
O5'
C
9
1_555
metalc
2.191
B
MG
1
F
MG
MG
1_555
B
C
109
B
O4'
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
118
B
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
118
B
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
118
B
N4
C
18
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
B
U
117
B
N3
U
17
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
B
U
117
B
O4
U
17
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
B
A
116
B
N1
A
16
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
B
A
116
B
N6
A
16
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
B
G
115
B
N1
G
15
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
B
G
115
B
O6
G
15
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
B
G
115
B
N2
G
15
1_555
hydrog
TYPE_6_PAIR
A
G
6
A
N1
G
6
1_555
A
G
13
A
O6
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
6
A
N2
G
6
1_555
A
G
13
A
N7
G
13
1_555
hydrog
G-C PAIR
A
G
6
A
O6
G
6
1_555
B
C
113
B
N4
C
13
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
114
B
N1
G
14
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
114
B
O6
G
14
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
114
B
N2
G
14
1_555
hydrog
G-C PAIR
A
G
12
A
N1
G
12
1_555
B
C
109
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
13
A
N1
G
13
1_555
B
C
113
B
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
13
A
N2
G
13
1_555
B
C
113
B
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
13
A
O6
G
13
1_555
B
C
113
B
N4
C
13
1_555
hydrog
WATSON-CRICK
A
A
14
A
N1
A
14
1_555
B
U
112
B
N3
U
12
1_555
hydrog
WATSON-CRICK
A
A
14
A
N6
A
14
1_555
B
U
112
B
O4
U
12
1_555
hydrog
WATSON-CRICK
A
C
15
A
N3
C
15
1_555
B
G
111
B
N1
G
11
1_555
hydrog
WATSON-CRICK
A
C
15
A
N4
C
15
1_555
B
G
111
B
O6
G
11
1_555
hydrog
WATSON-CRICK
A
C
15
A
O2
C
15
1_555
B
G
111
B
N2
G
11
1_555
hydrog
U-C MISPAIR
A
U
16
A
O2
U
16
1_555
A
C
18
A
N4
C
18
1_555
hydrog
U-A PAIR
A
U
17
A
O2
U
17
1_555
B
A
108
B
N6
A
8
1_555
hydrog
WATSON-CRICK
A
C
18
A
N3
C
18
1_555
B
G
110
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
18
A
N4
C
18
1_555
B
G
110
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
18
A
O2
C
18
1_555
B
G
110
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
U
19
A
N3
U
19
1_555
B
A
105
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
U
19
A
O4
U
19
1_555
B
A
105
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
G
20
A
N1
G
20
1_555
B
C
104
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
G
20
A
N2
G
20
1_555
B
C
104
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
G
20
A
O6
G
20
1_555
B
C
104
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
C
21
A
N3
C
21
1_555
B
G
103
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
21
A
N4
C
21
1_555
B
G
103
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
21
A
O2
C
21
1_555
B
G
103
B
N2
G
3
1_555
hydrog
C-G PAIR
A
C
22
A
O2
C
22
1_555
B
G
102
B
N1
G
2
1_555
RNA
Streptomycin RNA-Aptamer, Magnesium form, RNA
1NTB
PDB
1
1NTB
1NTB
PDB
2
1NTB
1
22
1NTB
1
22
1NTB
A
1
1
22
101
118
1NTB
101
118
1NTB
B
2
1
18
BINDING SITE FOR RESIDUE MG B 1
B
MG
1
Software
5
BINDING SITE FOR RESIDUE NA A 23
A
NA
23
Software
3
BINDING SITE FOR RESIDUE NA A 24
A
NA
24
Software
2
A
U
10
A
U
10
5
1_555
A
U
11
A
U
11
5
1_555
A
HOH
26
G
HOH
5
1_555
B
HOH
7
H
HOH
5
1_555
B
C
109
B
C
9
5
1_555
A
C
7
A
C
7
3
1_555
A
A
8
A
A
8
3
1_555
A
U
10
A
U
10
3
1_555
A
C
15
A
C
15
2
1_555
A
U
16
A
U
16
2
1_555
79
I 4