0.017676
0.010205
0.000000
0.000000
0.020411
0.000000
0.000000
0.000000
0.011325
0.00000
0.00000
0.00000
Ren, A.
Patel, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
56.573
56.573
88.297
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 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
H18 Ir N6 3
294.400
IRIDIUM HEXAMMINE ION
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
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
N
C
N
84
R
C
Y
85
N
N
Y
86
N
C
Y
87
N
N
Y
88
N
C
N
89
N
C
N
90
N
O
N
91
N
N
N
92
N
C
N
93
N
N
N
94
N
N
Y
95
N
C
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
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
H
N
150
N
H
N
151
N
IR
N
152
N
N
N
153
N
N
N
154
N
N
N
155
N
N
N
156
N
N
N
157
N
N
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
MG
N
177
N
O
N
178
N
P
N
179
N
O
N
180
N
O
N
181
N
O
N
182
N
C
N
183
R
C
N
184
N
O
N
185
S
C
N
186
N
O
N
187
R
C
N
188
N
O
N
189
R
C
N
190
N
N
N
191
N
C
N
192
N
O
N
193
N
N
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
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
H
N
209
N
H
N
210
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
Y
99
N
sing
Y
100
N
sing
Y
101
N
doub
N
102
N
sing
Y
103
N
sing
N
104
N
sing
Y
105
N
doub
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
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
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
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
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
doub
N
214
N
sing
N
215
N
sing
US
Nat.Chem.Biol.
1552-4469
12
702
708
10.1038/nchembio.2125
27398999
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.
2016
10.2210/pdb5k7d/pdb
pdb_00005k7d
100
1
PIXEL
2016-03-15
DECTRIS PILATUS 6M-F
SINGLE WAVELENGTH
M
x-ray
1
1.1052
1.0
24-ID-C
APS
1.1052
SYNCHROTRON
APS BEAMLINE 24-ID-C
15096.936
RNA 47-MER
1
syn
polymer
3514.178
DNA/RNA 11-MER
1
syn
polymer
294.400
IRIDIUM HEXAMMINE ION
2
syn
non-polymer
24.305
MAGNESIUM ION
5
syn
non-polymer
18.015
water
15
nat
water
no
no
CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU
CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU
A
polydeoxyribonucleotide/polyribonucleotide hybrid
no
no
AUCAG(DG)UGCAA
AUCAGGUGCAA
B
polydeoxyribonucleotide/polyribonucleotide hybrid
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
2.18
43.69
VAPOR DIFFUSION, HANGING DROP
0.1 M Na-cacodylate, pH 6.5, Mg(OAc)2 0.2 M and 32% MPD and supplemented with 5 mM Ir(NH3)63+Cl3
293
-5.165
1
22
A
1
A
16
2.560
A_C1:G16_A
1
-3.265
0.122
0.145
-0.777
-5.969
1
19
A
2
A
15
0.931
A_G2:C15_A
2
-14.300
-0.275
-0.139
-0.193
-3.465
1
20
A
3
A
14
2.722
A_U3:A14_A
3
-11.791
0.098
0.024
-0.112
3.833
1
19
A
4
A
13
-0.145
A_G4:C13_A
4
-6.143
-0.301
0.403
-0.312
9.600
1
19
A
5
A
12
-1.573
A_G5:C12_A
5
-1.546
-0.084
0.172
-0.182
10.454
1
19
A
34
A
11
1.378
A_C34:G11_A
6
-12.867
0.191
-0.086
-0.191
1.290
1
19
A
35
A
10
0.452
A_C35:G10_A
7
-11.487
0.086
0.073
-0.189
-4.000
1
19
A
36
A
9
0.384
A_C36:G9_A
8
-8.239
0.100
0.352
-0.143
-2.636
1
20
A
37
A
8
3.010
A_U37:A8_A
9
-1.237
-0.112
0.194
-0.095
0.029
1
20
A
38
A
7
-1.437
A_A38:U7_A
10
-5.405
0.241
0.332
-0.008
-11.949
A
39
A
6
2.937
A_A39:U6_A
11
-9.478
1.038
0.795
0.168
-1.204
1
19
A
41
A
33
0.500
A_C41:G33_A
12
-2.946
0.188
0.609
-0.213
9.736
A
42
B
53
-3.344
A_G42:DG53_B
13
1.314
-6.840
-1.036
-2.043
25.566
A
43
B
52
11.139
A_U43:G52_B
14
-16.622
-4.146
-1.747
0.583
1.590
A
44
B
51
8.077
A_U44:A51_B
15
-5.269
0.733
0.046
0.453
-0.855
1
19
A
45
B
50
0.320
A_G45:C50_B
16
-9.262
0.450
-0.013
-0.106
5.465
1
20
A
46
B
49
-1.297
A_A46:U49_B
17
-4.037
0.368
0.195
0.155
-9.642
1
20
A
25
B
58
-4.398
A_U25:A58_B
18
1.384
-0.274
0.210
0.091
-6.167
1
20
A
26
B
57
10.834
A_U26:A57_B
19
4.295
-0.325
0.111
-0.065
5.818
1
19
A
27
B
56
6.020
A_G27:C56_B
20
4.222
0.552
-0.053
-0.074
11.299
1
22
A
28
B
55
15.723
A_C28:G55_B
21
-4.044
0.538
-0.363
-0.030
11.284
1
16
A
29
B
54
14.750
A_U29:U54_B
22
-12.598
2.477
0.397
-2.341
2.587
29.388
A
A
1
2
15.475
A
A
16
15
3.145
7.759
-0.106
-1.711
AA_C1G2:C15G16_AA
1
1.372
-2.737
28.334
-4.860
0.472
3.123
33.781
A
A
2
3
7.610
A
A
15
14
3.246
4.410
0.229
-0.708
AA_G2U3:A14C15_AA
2
-0.913
1.575
33.489
-1.916
-0.538
2.449
32.008
A
A
3
4
14.222
A
A
14
13
2.850
7.758
-0.250
-1.399
AA_U3G4:C13A14_AA
3
-2.820
5.169
30.952
-3.692
0.034
2.549
29.572
A
A
4
5
15.620
A
A
13
12
3.214
7.878
-0.775
-1.981
AA_G4G5:C12C13_AA
4
1.307
-2.591
28.497
-5.380
1.767
3.142
48.708
A
A
5
34
4.648
A
A
12
11
3.160
3.829
-1.718
-0.763
AA_G5C34:G11C12_AA
5
-1.459
1.771
48.546
-1.207
1.975
2.418
34.978
A
A
34
35
21.621
A
A
11
10
3.251
12.673
-0.781
-1.980
AA_C34C35:G10G11_AA
6
-4.926
8.404
32.304
-5.021
0.628
2.443
32.010
A
A
35
36
22.527
A
A
10
9
3.244
12.081
-0.761
-1.751
AA_C35C36:G9G10_AA
7
-4.820
8.989
29.311
-5.160
0.587
2.490
33.347
A
A
36
37
22.748
A
A
9
8
3.166
12.739
-0.368
-1.221
AA_C36U37:A8G9_AA
8
-0.683
1.220
30.875
-4.033
0.538
2.484
35.631
A
A
37
38
20.489
A
A
8
7
3.045
12.274
0.597
-1.282
AA_U37A38:U7A8_AA
9
3.663
-6.114
33.319
-3.656
-0.509
2.911
36.124
A
A
38
39
16.269
A
A
7
6
3.301
9.904
1.994
-2.201
AA_A38A39:U6U7_AA
10
7.037
-11.560
34.084
-4.920
-2.242
2.338
57.484
A
A
39
41
3.130
A
A
6
33
2.633
3.003
-1.240
-3.189
AA_A39C41:G33U6_AA
11
6.374
-6.642
57.088
-3.439
1.553
3.813
42.109
A
A
41
42
-4.392
A
B
33
53
3.538
-3.150
4.225
0.695
AA_C41G42:DG53G33_BA
12
3.607
-5.030
41.848
1.333
-5.461
3.037
36.357
A
A
42
43
7.433
B
B
53
52
3.060
4.619
0.571
-0.332
AA_G42U43:G52DG53_BB
13
3.657
-5.886
35.892
-1.136
-0.438
3.527
49.763
A
A
43
44
18.951
B
B
52
51
4.425
15.503
0.347
-1.464
AA_U43U44:A51G52_BB
14
-14.258
17.430
45.345
-3.195
-1.751
2.504
31.494
A
A
44
45
18.374
B
B
51
50
3.140
9.812
-1.141
-1.443
AA_U44G45:C50A51_BB
15
1.276
-2.390
29.937
-4.281
2.313
2.544
26.168
A
A
45
46
11.425
B
B
50
49
2.963
5.132
0.062
-1.776
AA_G45A46:U49C50_BB
16
-2.605
5.800
25.538
-5.110
-0.739
2.966
24.778
A
A
25
26
3.509
B
B
58
57
3.117
1.503
-0.036
-2.287
AA_U25U26:A57A58_BB
17
-2.226
5.197
24.634
-5.755
-0.544
2.429
32.854
A
A
26
27
18.912
B
B
57
56
2.908
10.513
-0.542
-1.145
AA_U26G27:C56A57_BB
18
-1.745
3.138
31.123
-3.536
0.707
2.650
28.525
A
A
27
28
17.049
B
B
56
55
3.105
8.280
0.715
-1.267
AA_G27C28:G55C56_BB
19
1.582
-3.257
27.276
-4.270
-1.126
3.001
38.219
A
A
28
29
5.897
B
B
55
54
3.183
3.851
0.521
-1.199
AA_C28U29:U54G55_BB
20
-3.098
4.744
37.910
-2.291
-1.165
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
1
0
2016-07-13
1
1
2016-07-27
1
2
2016-08-31
1
3
2024-03-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_pdbx_struct_oper_list.symmetry_operation
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
N
RCSB
Y
RCSB
2016-05-26
REL
REL
IRI
IRIDIUM HEXAMMINE ION
MG
MAGNESIUM ION
HOH
water
32630
synthetic construct
sample
1
47
32630
synthetic construct
sample
1
11
IRI
2
3
IRI
IRI
101
A
MG
1
4
MG
MG
102
A
MG
2
4
MG
MG
103
A
MG
4
4
MG
MG
104
A
MG
5
4
MG
MG
105
A
IRI
1
3
IRI
IRI
101
B
MG
3
4
MG
MG
102
B
HOH
4
5
HOH
HOH
201
A
HOH
2
5
HOH
HOH
202
A
HOH
9
5
HOH
HOH
203
A
HOH
3
5
HOH
HOH
204
A
HOH
5
5
HOH
HOH
205
A
HOH
6
5
HOH
HOH
206
A
HOH
14
5
HOH
HOH
207
A
HOH
8
5
HOH
HOH
208
A
HOH
11
5
HOH
HOH
209
A
HOH
10
5
HOH
HOH
210
A
HOH
1
5
HOH
HOH
211
A
HOH
13
5
HOH
HOH
212
A
HOH
15
5
HOH
HOH
213
A
HOH
7
5
HOH
HOH
201
B
HOH
12
5
HOH
HOH
202
B
C
1
n
1
C
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
U
7
n
7
U
7
A
A
8
n
8
A
8
A
G
9
n
9
G
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
C
12
n
12
C
12
A
C
13
n
13
C
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
U
17
n
17
U
17
A
U
18
n
18
U
18
A
A
19
n
19
A
19
A
A
20
n
20
A
20
A
A
21
n
21
A
21
A
U
22
n
22
U
22
A
A
23
n
23
A
23
A
G
24
n
24
G
24
A
U
25
n
25
U
25
A
U
26
n
26
U
26
A
G
27
n
27
G
27
A
C
28
n
28
C
28
A
U
29
n
29
U
29
A
U
30
n
30
U
30
A
A
31
n
31
A
31
A
A
32
n
32
A
32
A
G
33
n
33
G
33
A
C
34
n
34
C
34
A
C
35
n
35
C
35
A
C
36
n
36
C
36
A
U
37
n
37
U
37
A
A
38
n
38
A
38
A
A
39
n
39
A
39
A
G
40
n
40
G
40
A
C
41
n
41
C
41
A
G
42
n
42
G
42
A
U
43
n
43
U
43
A
U
44
n
44
U
44
A
G
45
n
45
G
45
A
A
46
n
46
A
46
A
U
47
n
47
U
47
A
A
48
n
1
A
48
B
U
49
n
2
U
49
B
C
50
n
3
C
50
B
A
51
n
4
A
51
B
G
52
n
5
G
52
B
DG
53
n
6
DG
53
B
U
54
n
7
U
54
B
G
55
n
8
G
55
B
C
56
n
9
C
56
B
A
57
n
10
A
57
B
A
58
n
11
A
58
B
author_and_software_defined_assembly
PISA
2
dimeric
2530
-46
9350
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
A
G
42
A
OP2
G
42
1_555
69.9
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
201
J
O
HOH
1_555
53.6
A
G
42
A
OP2
G
42
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
201
J
O
HOH
1_555
120.2
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
202
J
O
HOH
1_555
70.3
A
G
42
A
OP2
G
42
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
202
J
O
HOH
1_555
72.2
A
HOH
201
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
202
J
O
HOH
1_555
71.8
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
204
J
O
HOH
1_555
129.3
A
G
42
A
OP2
G
42
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
204
J
O
HOH
1_555
85.4
A
HOH
201
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
204
J
O
HOH
1_555
114.1
A
HOH
202
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
204
J
O
HOH
1_555
60.0
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
78.7
A
G
42
A
OP2
G
42
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
107.8
A
HOH
201
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
81.0
A
HOH
202
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
147.0
A
HOH
204
J
O
HOH
1_555
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
152.1
A
HOH
203
J
O
HOH
1_555
A
MG
103
E
MG
MG
1_555
A
HOH
208
J
O
HOH
1_555
171.4
A
HOH
203
J
O
HOH
1_555
A
MG
103
E
MG
MG
1_555
A
HOH
211
J
O
HOH
1_555
115.1
A
HOH
208
J
O
HOH
1_555
A
MG
103
E
MG
MG
1_555
A
HOH
211
J
O
HOH
1_555
62.6
A
HOH
209
J
O
HOH
1_555
A
MG
104
F
MG
MG
1_555
A
HOH
212
J
O
HOH
1_555
67.8
A
HOH
207
J
O
HOH
1_555
A
MG
105
G
MG
MG
1_555
A
HOH
210
J
O
HOH
1_555
87.3
A
HOH
207
J
O
HOH
1_555
A
MG
105
G
MG
MG
1_555
A
HOH
213
J
O
HOH
1_555
83.7
A
HOH
210
J
O
HOH
1_555
A
MG
105
G
MG
MG
1_555
A
HOH
213
J
O
HOH
1_555
64.7
B
HOH
201
K
O
HOH
1_555
B
MG
102
I
MG
MG
1_555
B
HOH
202
K
O
HOH
1_555
103.1
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
A
OP2
O
C
HOH
41
201
1.97
1
A
A
O2
N2
C
G
1
16
2.03
1
A
A
O
O
HOH
HOH
202
204
2.09
1
A
A
O
O
HOH
HOH
208
211
2.10
1
A
B
O2
N2
C
G
28
55
2.16
1
5.21
0.70
108.50
113.71
A
A
A
O4'
C1'
N9
A
A
A
19
19
19
N
1
B
B
O3'
C3'
DG
DG
53
53
-0.048
0.006
1.419
1.371
N
0.24
0.19
2.68
49
451
8819
99.8
1
FREE R-VALUE
SAD
2.68
49
15
1271
19
1237
0
2.68
88.3
5K7D
8819
0.038
1
14.9
6.2
99.8
2.68
2.81
1.2
0.618
1
6.4
100
refinement
PHENIX
data reduction
XDS
data scaling
XDS
phasing
AutoSol
N
The structure of native pistol ribozyme, bound to Iridium
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
3
N
N
4
N
N
5
N
N
5
N
N
metalc
2.295
A
C
41
A
OP2
C
41
1_555
A
MG
102
D
MG
MG
1_555
metalc
1.900
A
G
42
A
OP2
G
42
1_555
A
MG
102
D
MG
MG
1_555
metalc
2.053
A
MG
102
D
MG
MG
1_555
A
HOH
201
J
O
HOH
1_555
metalc
2.141
A
MG
102
D
MG
MG
1_555
A
HOH
202
J
O
HOH
1_555
metalc
2.030
A
MG
102
D
MG
MG
1_555
A
HOH
204
J
O
HOH
1_555
metalc
2.233
A
MG
102
D
MG
MG
1_555
A
HOH
205
J
O
HOH
1_555
metalc
2.069
A
MG
103
E
MG
MG
1_555
A
HOH
203
J
O
HOH
1_555
metalc
2.016
A
MG
103
E
MG
MG
1_555
A
HOH
208
J
O
HOH
1_555
metalc
2.031
A
MG
103
E
MG
MG
1_555
A
HOH
211
J
O
HOH
1_555
metalc
2.034
A
MG
104
F
MG
MG
1_555
A
HOH
209
J
O
HOH
1_555
metalc
2.053
A
MG
104
F
MG
MG
1_555
A
HOH
212
J
O
HOH
1_555
metalc
2.044
A
MG
105
G
MG
MG
1_555
A
HOH
207
J
O
HOH
1_555
metalc
2.089
A
MG
105
G
MG
MG
1_555
A
HOH
210
J
O
HOH
1_555
metalc
2.062
A
MG
105
G
MG
MG
1_555
A
HOH
213
J
O
HOH
1_555
metalc
2.121
B
MG
102
I
MG
MG
1_555
B
HOH
201
K
O
HOH
1_555
metalc
2.119
B
MG
102
I
MG
MG
1_555
B
HOH
202
K
O
HOH
1_555
hydrog
REVERSED WATSON-CRICK
A
C
1
A
N3
C
1
1_555
A
G
16
A
N2
G
16
1_555
hydrog
REVERSED WATSON-CRICK
A
C
1
A
O2
C
1
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
15
A
N4
C
15
1_555
hydrog
G-U MISPAIR
A
G
2
A
N2
G
2
1_555
A
U
18
A
O4
U
18
1_555
hydrog
WATSON-CRICK
A
U
3
A
N3
U
3
1_555
A
A
14
A
N1
A
14
1_555
hydrog
WATSON-CRICK
A
U
3
A
O4
U
3
1_555
A
A
14
A
N6
A
14
1_555
hydrog
U-A PAIR
A
U
3
A
O2
U
3
1_555
A
A
19
A
N6
A
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
13
A
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
13
A
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
13
A
N4
C
13
1_555
hydrog
TYPE_10_PAIR
A
G
4
A
N2
G
4
1_555
A
A
21
A
N1
A
21
1_555
hydrog
TYPE_10_PAIR
A
G
4
A
N3
G
4
1_555
A
A
21
A
N6
A
21
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
12
A
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
12
A
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
12
A
N4
C
12
1_555
hydrog
TYPE_4_PAIR
A
G
5
A
N2
G
5
1_555
A
G
24
A
N3
G
24
1_555
hydrog
TYPE_4_PAIR
A
G
5
A
N3
G
5
1_555
A
G
24
A
N2
G
24
1_555
hydrog
U-A PAIR
A
U
6
A
N3
U
6
1_555
A
A
39
A
N1
A
39
1_555
hydrog
WATSON-CRICK
A
U
7
A
N3
U
7
1_555
A
A
38
A
N1
A
38
1_555
hydrog
WATSON-CRICK
A
U
7
A
O4
U
7
1_555
A
A
38
A
N6
A
38
1_555
hydrog
WATSON-CRICK
A
A
8
A
N1
A
8
1_555
A
U
37
A
N3
U
37
1_555
hydrog
WATSON-CRICK
A
A
8
A
N6
A
8
1_555
A
U
37
A
O4
U
37
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
36
A
N3
C
36
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
36
A
O2
C
36
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
36
A
N4
C
36
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
35
A
N3
C
35
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
35
A
O2
C
35
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
35
A
N4
C
35
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
A
C
34
A
N3
C
34
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
A
C
34
A
O2
C
34
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
A
C
34
A
N4
C
34
1_555
hydrog
A-A MISPAIR
A
A
14
A
N3
A
14
1_555
A
A
20
A
N6
A
20
1_555
hydrog
C-A MISPAIR
A
C
15
A
O2
C
15
1_555
A
A
19
A
N6
A
19
1_555
hydrog
WATSON-CRICK
A
U
25
A
N3
U
25
1_555
B
A
58
B
N1
A
11
1_555
hydrog
WATSON-CRICK
A
U
25
A
O4
U
25
1_555
B
A
58
B
N6
A
11
1_555
hydrog
WATSON-CRICK
A
U
26
A
N3
U
26
1_555
B
A
57
B
N1
A
10
1_555
hydrog
WATSON-CRICK
A
U
26
A
O4
U
26
1_555
B
A
57
B
N6
A
10
1_555
hydrog
WATSON-CRICK
A
G
27
A
N1
G
27
1_555
B
C
56
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
27
A
N2
G
27
1_555
B
C
56
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
27
A
O6
G
27
1_555
B
C
56
B
N4
C
9
1_555
hydrog
REVERSED WATSON-CRICK
A
C
28
A
N3
C
28
1_555
B
G
55
B
N2
G
8
1_555
hydrog
REVERSED WATSON-CRICK
A
C
28
A
O2
C
28
1_555
B
G
55
B
N1
G
8
1_555
hydrog
TYPE_16_PAIR
A
U
29
A
N3
U
29
1_555
B
U
54
B
O4
U
7
1_555
hydrog
TYPE_16_PAIR
A
U
29
A
O2
U
29
1_555
B
U
54
B
N3
U
7
1_555
hydrog
G-G MISPAIR
A
G
33
A
O6
G
33
1_555
A
G
40
A
N2
G
40
1_555
hydrog
WATSON-CRICK
A
G
33
A
N1
G
33
1_555
A
C
41
A
N3
C
41
1_555
hydrog
WATSON-CRICK
A
G
33
A
N2
G
33
1_555
A
C
41
A
O2
C
41
1_555
hydrog
WATSON-CRICK
A
G
33
A
O6
G
33
1_555
A
C
41
A
N4
C
41
1_555
hydrog
A-C MISPAIR
A
A
39
A
N1
A
39
1_555
A
C
41
A
N4
C
41
1_555
hydrog
G-G MISPAIR
A
G
40
A
N2
G
40
1_555
A
G
42
A
O6
G
42
1_555
hydrog
G-DG MISPAIR
A
G
42
A
O6
G
42
1_555
B
DG
53
B
N2
DG
6
1_555
hydrog
U-G MISPAIR
A
U
43
A
O4
U
43
1_555
B
G
52
B
N2
G
5
1_555
hydrog
U-DG MISPAIR
A
U
43
A
O4
U
43
1_555
B
DG
53
B
N2
DG
6
1_555
hydrog
U-A PAIR
A
U
44
A
N3
U
44
1_555
B
A
51
B
N1
A
4
1_555
hydrog
WATSON-CRICK
A
G
45
A
N1
G
45
1_555
B
C
50
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
45
A
N2
G
45
1_555
B
C
50
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
45
A
O6
G
45
1_555
B
C
50
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
A
46
A
N1
A
46
1_555
B
U
49
B
N3
U
2
1_555
hydrog
WATSON-CRICK
A
A
46
A
N6
A
46
1_555
B
U
49
B
O4
U
2
1_555
RNA/DNA
ribozyme, RNA structure, pistol, RNA-DNA complex
5K7D
PDB
1
1
5K7D
5K7D
PDB
2
1
5K7D
1
47
5K7D
1
47
5K7D
A
1
1
47
48
58
5K7D
48
58
5K7D
B
2
1
11
binding site for residue IRI A 101
A
IRI
101
Software
7
binding site for residue MG A 102
A
MG
102
Software
6
binding site for residue MG A 103
A
MG
103
Software
4
binding site for residue MG A 104
A
MG
104
Software
4
binding site for residue MG A 105
A
MG
105
Software
4
binding site for residue IRI B 101
B
IRI
101
Software
3
binding site for residue MG B 102
B
MG
102
Software
4
A
G
5
A
G
5
7
1_555
A
U
7
A
U
7
7
1_555
A
A
8
A
A
8
7
1_555
A
G
9
A
G
9
7
1_555
A
G
10
A
G
10
7
1_555
A
G
11
A
G
11
7
1_555
A
C
34
A
C
34
7
1_555
A
C
41
A
C
41
6
1_555
A
G
42
A
G
42
6
1_555
A
HOH
201
J
HOH
6
1_555
A
HOH
202
J
HOH
6
1_555
A
HOH
204
J
HOH
6
1_555
A
HOH
205
J
HOH
6
1_555
A
G
33
A
G
33
4
1_555
A
HOH
203
J
HOH
4
1_555
A
HOH
208
J
HOH
4
1_555
A
HOH
211
J
HOH
4
1_555
A
U
37
A
U
37
4
1_555
A
A
38
A
A
38
4
1_555
A
HOH
209
J
HOH
4
1_555
A
HOH
212
J
HOH
4
1_555
A
A
23
A
A
23
4
1_555
A
HOH
207
J
HOH
4
1_555
A
HOH
210
J
HOH
4
1_555
A
HOH
213
J
HOH
4
1_555
B
G
52
B
G
5
3
1_555
B
DG
53
B
DG
6
3
1_555
B
MG
102
I
MG
3
1_555
B
DG
53
B
DG
6
4
1_555
B
IRI
101
H
IRI
4
1_555
B
HOH
201
K
HOH
4
1_555
B
HOH
202
K
HOH
4
1_555
154
P 32 2 1