0.019944
0.000000
0.008286
0.000000
0.014609
0.000000
0.000000
0.000000
0.017982
0.00000
0.00000
0.00000
Scott, W.G.
Schultz, E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
112.56
90.00
50.140
68.450
60.220
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 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H15 N5 O11 P2
443.201
n
GUANOSINE-5'-DIPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
C10 H16 N3 O8 P
337.223
n
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
RNA linking
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
N
85
N
N
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
N
N
91
N
C
N
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
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
N
129
N
N
Y
130
N
C
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
H
N
143
N
H
N
144
N
H
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
P
N
151
N
O
N
152
N
O
N
153
N
O
N
154
N
C
N
155
R
C
N
156
N
O
N
157
S
C
N
158
N
O
N
159
R
C
N
160
N
O
N
161
R
C
Y
162
N
N
Y
163
N
C
Y
164
N
N
Y
165
N
C
N
166
N
C
N
167
N
O
N
168
N
N
N
169
N
C
N
170
N
N
N
171
N
N
Y
172
N
C
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
O
N
189
N
H
N
190
N
H
N
191
N
N
N
192
N
C
N
193
N
N
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
O
N
198
N
N
N
199
R
C
N
200
R
C
N
201
N
O
N
202
N
C
N
203
R
C
N
204
R
C
N
205
N
O
N
206
N
O
N
207
N
C
N
208
N
O
N
209
N
P
N
210
N
O
N
211
N
O
N
212
N
O
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
P
N
231
N
O
N
232
N
O
N
233
N
O
N
234
N
C
N
235
R
C
N
236
N
O
N
237
S
C
N
238
N
O
N
239
R
C
N
240
N
O
N
241
R
C
N
242
N
N
N
243
N
C
N
244
N
O
N
245
N
N
N
246
N
C
N
247
N
O
N
248
N
C
N
249
N
C
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
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
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
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
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
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
doub
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
Y
180
N
sing
Y
181
N
sing
Y
182
N
doub
N
183
N
sing
Y
184
N
sing
N
185
N
sing
Y
186
N
doub
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
doub
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
doub
N
203
N
doub
N
204
N
sing
N
205
N
sing
N
206
N
doub
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
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
doub
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
doub
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
doub
N
268
N
sing
N
269
N
doub
N
270
N
sing
N
271
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
70
2256
10.1107/S1399004714010608
25195740
Structural and Catalytic Effects of an Invariant Purine Substitution in the Hammerhead Ribozyme: Implications for the Mechanism of Acid-Base Catalysis.
2014
10.2210/pdb3zd4/pdb
pdb_00003zd4
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 315r
SINGLE WAVELENGTH
M
x-ray
1
1.097173
1.0
BL7-1
SSRL
1.097173
SYNCHROTRON
SSRL BEAMLINE BL7-1
13925.326
HAMMERHEAD RIBOZYME, ENZYME STRAND
1
syn
polymer
6333.816
HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
1
syn
polymer
18.015
water
31
nat
water
no
yes
(GDP)GAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC
GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC
A
polyribonucleotide
no
yes
GGCGU(OMC)CUGGUAUCCAAUC(DC)
GGCGUCCUGGUAUCCAAUCC
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
2.35
47.74
G12A MUTATED AND MODELED IN COOT
-6.475
1
19
A
1
B
20
5.134
A_GDP1:DC20_B
1
-3.555
-0.706
-0.057
-0.181
-10.413
1
19
A
2
B
19
1.604
A_G2:C19_B
2
-9.392
-0.502
-0.291
-0.258
-7.328
1
20
A
3
B
18
1.491
A_A3:U18_B
3
-7.186
0.128
0.092
-0.152
-4.307
A
4
B
15
-34.434
A_U4:C15_B
4
-5.425
-1.071
-0.880
-0.017
0.587
1
19
A
5
B
14
-0.212
A_G5:C14_B
5
-14.824
-0.218
0.398
-0.145
-12.525
4
24
A
6
A
28
-94.910
A_U6:A28_A
6
-5.701
4.045
-0.438
-2.263
-12.123
4
24
A
31
B
13
-94.586
A_A31:U13_B
7
-0.153
-4.098
-0.598
-2.150
7.568
1
20
A
9
B
12
4.412
A_U9:A12_B
8
-9.175
-0.219
0.598
-0.088
16.077
1
20
A
10
B
11
6.065
A_A10:U11_B
9
-16.561
-0.009
0.158
-0.067
7.468
1
19
A
11
B
10
4.938
A_C11:G10_B
10
-20.708
0.434
0.035
-0.208
-5.529
1
19
A
12
B
9
4.010
A_C12:G9_B
11
-9.579
0.078
0.253
-0.144
-7.696
1
20
A
13
B
8
2.084
A_A13:U8_B
12
-12.764
0.147
-0.016
-0.217
4.165
1
19
A
14
B
7
0.281
A_G14:C7_B
13
-16.341
0.060
0.475
-0.148
10.147
1
19
A
15
A
20
-2.747
A_C15:G20_A
14
1.399
0.361
-0.492
-0.197
11.301
2
15
A
8
A
26
179.121
A_C8:C26_A
15
5.773
1.949
-0.211
1.895
-0.336
1
19
A
32
A
25
0.271
A_G32:C25_A
16
-6.680
-0.259
0.208
-0.153
-6.564
1
19
A
33
A
24
5.620
A_G33:C24_A
17
-13.656
-0.536
0.101
-0.122
-6.196
1
20
A
34
A
23
-0.211
A_A34:U23_A
18
-10.360
0.010
-0.075
-0.191
-5.279
1
19
A
35
A
22
0.239
A_C35:G22_A
19
-4.847
0.240
0.556
-0.215
-2.557
10
A
36
A
21
-18.004
A_A36:A21_A
20
-13.939
6.430
0.508
-3.797
-20.898
A
37
B
6
-37.287
A_A37:OMC6_B
21
-13.423
-6.116
-1.615
-2.852
29.841
A
38
A
17
83.249
A_A38:G17_A
22
-44.817
-3.879
0.231
3.475
-0.049
1
20
A
39
B
5
3.155
A_A39:U5_B
23
-3.112
-0.383
0.440
0.025
5.528
1
19
A
40
B
4
1.137
A_C40:G4_B
24
-15.948
0.298
0.136
-0.236
-2.075
1
19
A
41
B
3
0.464
A_G41:C3_B
25
-17.244
-0.624
0.094
-0.252
-6.142
1
19
A
42
B
2
0.724
A_C42:G2_B
26
-13.639
0.045
0.332
-0.231
4.489
1
19
A
43
B
1
-1.973
A_C43:G1_B
27
-3.015
0.564
0.091
-0.360
3.243
30.455
A
A
1
2
5.671
B
B
20
19
3.477
2.974
-0.268
-2.142
AA_GDP1G2:C19DC20_BB
1
1.284
-2.449
30.286
-4.690
0.774
2.938
36.195
A
A
2
3
9.066
B
B
19
18
3.188
5.610
-0.135
-1.444
AA_G2A3:U18C19_BB
2
-0.984
1.591
35.758
-3.067
0.087
3.749
67.233
A
A
3
4
9.081
B
B
18
15
4.213
10.016
3.174
-1.271
AA_A3U4:C15U18_BB
3
-5.896
5.345
66.337
-1.625
-3.148
1.863
36.600
A
A
4
5
18.129
B
B
15
14
3.187
11.030
1.766
-1.675
AA_U4G5:C14C15_BB
4
-11.440
18.802
33.078
-3.902
-4.093
3.453
83.486
A
A
5
6
-1.623
B
A
14
28
3.524
-2.160
-2.690
-1.998
AA_G5U6:A28C14_AB
5
4.165
-3.129
83.378
-1.445
2.127
4.430
-157.496
A
A
6
31
35.221
A
B
28
13
5.282
-68.809
3.272
-3.467
AA_U6A31:U13A28_BA
6
40.992
20.983
-150.465
2.126
1.881
2.526
77.439
A
A
31
9
2.187
B
B
13
12
2.861
2.723
1.563
-1.233
AA_A31U9:A12U13_BB
7
-15.049
12.086
76.148
-1.050
-1.607
2.167
34.683
A
A
9
10
20.371
B
B
12
11
2.791
11.909
-0.384
-1.349
AA_U9A10:U11A12_BB
8
1.077
-1.842
32.616
-3.694
0.773
3.193
36.513
A
A
10
11
9.742
B
B
11
10
3.452
6.077
0.317
-1.376
AA_A10C11:G10U11_BB
9
0.991
-1.588
36.008
-3.055
-0.366
2.427
30.670
A
A
11
12
22.753
B
B
10
9
3.407
11.705
-0.912
-2.197
AA_C11C12:G9G10_BB
10
-4.128
8.025
28.101
-6.304
0.965
2.261
40.260
A
A
12
13
28.355
B
B
9
8
3.072
18.790
-0.055
-1.024
AA_C12A13:U8G9_BB
11
3.518
-5.309
35.599
-3.341
0.427
2.436
27.267
A
A
13
14
16.501
B
B
8
7
2.919
7.675
0.802
-1.447
AA_A13G14:C7U8_BB
12
1.174
-2.523
26.158
-4.672
-1.455
3.226
39.072
A
A
14
15
8.628
B
A
7
20
3.288
5.664
0.304
0.217
AA_G14C15:G20C7_AB
13
12.046
-18.352
36.818
-0.376
1.036
1.349
178.804
A
A
8
32
-77.408
A
A
26
25
1.189
-154.566
-2.442
-2.108
AA_C8G32:C25C26_AA
14
87.002
-43.571
125.925
-0.788
1.371
2.909
32.334
A
A
32
33
11.373
A
A
25
24
3.258
6.279
0.736
-1.877
AA_G32G33:C24C25_AA
15
4.056
-7.347
31.480
-4.432
-0.636
2.821
36.522
A
A
33
34
10.801
A
A
24
23
3.147
6.733
-0.773
-1.546
AA_G33A34:U23C24_AA
16
-0.013
0.021
35.917
-3.323
1.232
2.701
32.979
A
A
34
35
15.380
A
A
23
22
3.198
8.622
0.415
-1.331
AA_A34C35:G22U23_AA
17
-3.166
5.649
31.708
-3.694
-1.227
3.186
56.372
A
A
35
36
4.889
A
A
22
21
3.287
4.608
0.252
-1.344
AA_C35A36:A21G22_AA
18
5.282
-5.604
55.970
-1.681
0.029
3.787
27.404
A
A
36
37
12.921
A
B
21
6
4.069
5.837
1.406
-1.758
AA_A36A37:OMC6A21_BA
19
12.846
-28.435
23.552
-5.581
1.149
3.646
-46.214
A
A
37
38
-50.020
B
A
6
17
1.858
31.941
0.201
-3.957
AA_A37A38:G17OMC6_AB
20
-27.072
-42.396
-20.016
1.717
-2.562
2.900
86.346
A
A
38
39
-13.787
A
B
17
5
3.423
-18.766
0.803
2.523
AA_A38A39:U5G17_BA
21
-3.045
2.237
84.632
2.254
-0.653
2.763
34.025
A
A
39
40
16.526
B
B
5
4
3.198
9.545
-0.261
-1.098
AA_A39C40:G4U5_BB
22
1.447
-2.505
32.666
-3.294
0.661
2.503
33.008
A
A
40
41
22.216
B
B
4
3
3.307
12.331
-0.031
-1.580
AA_C40G41:C3G4_BB
23
-0.509
0.917
30.673
-4.712
-0.026
2.844
38.680
A
A
41
42
16.302
B
B
3
2
3.301
10.667
0.323
-1.289
AA_G41C42:G2C3_BB
24
0.733
-1.121
37.227
-3.203
-0.401
2.681
28.091
A
A
42
43
10.998
B
B
2
1
2.958
5.269
1.169
-2.188
AA_C42C43:G1G2_BB
25
5.907
-12.331
26.975
-5.598
-1.185
atom_site
atom_site_anisotrop
database_2
pdbx_database_status
pdbx_entity_src_syn
struct_conn
struct_ref
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Other
Database references
Database references
Atomic model
Database references
Derived calculations
Other
Source and taxonomy
Data collection
Refinement description
1
0
2012-12-12
1
1
2013-03-06
1
2
2014-09-10
1
3
2014-09-17
2
0
2022-11-02
2
1
2024-01-31
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_atom_site.type_symbol
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.pdbx_auth_atom_id
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.type_symbol
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_pdbx_entity_src_syn.pdbx_beg_seq_num
_pdbx_entity_src_syn.pdbx_end_seq_num
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref.pdbx_align_begin
HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME
THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME
PDBE
Y
PDBE
2012-11-24
REL
REL
HOH
water
32630
SYNTHETIC CONSTRUCT
sample
1
43
32630
SYNTHETIC CONSTRUCT
sample
1
20
2GOZ
PDB ENTRY 2GOZ
PDB
experimental model
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2001
3
HOH
HOH
2001
B
HOH
2002
3
HOH
HOH
2002
B
HOH
2003
3
HOH
HOH
2003
B
HOH
2004
3
HOH
HOH
2004
B
HOH
2005
3
HOH
HOH
2005
B
HOH
2006
3
HOH
HOH
2006
B
HOH
2007
3
HOH
HOH
2007
B
HOH
2008
3
HOH
HOH
2008
B
HOH
2009
3
HOH
HOH
2009
B
HOH
2010
3
HOH
HOH
2010
B
GDP
1
n
1
GDP
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
U
4
n
4
U
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
A
7
n
7
A
7
A
C
8
n
8
C
8
A
U
9
n
9
U
9
A
A
10
n
10
A
10
A
C
11
n
11
C
11
A
C
12
n
12
C
12
A
A
13
n
13
A
13
A
G
14
n
14
G
14
A
C
15
n
15
C
15
A
U
16
n
16
U
16
A
G
17
n
17
G
17
A
A
18
n
18
A
18
A
U
19
n
19
U
19
A
G
20
n
20
G
20
A
A
21
n
21
A
21
A
G
22
n
22
G
22
A
U
23
n
23
U
23
A
C
24
n
24
C
24
A
C
25
n
25
C
25
A
C
26
n
26
C
26
A
A
27
n
27
A
27
A
A
28
n
28
A
28
A
A
29
n
29
A
29
A
U
30
n
30
U
30
A
A
31
n
31
A
31
A
G
32
n
32
G
32
A
G
33
n
33
G
33
A
A
34
n
34
A
34
A
C
35
n
35
C
35
A
A
36
n
36
A
36
A
A
37
n
37
A
37
A
A
38
n
38
A
38
A
A
39
n
39
A
39
A
C
40
n
40
C
40
A
G
41
n
41
G
41
A
C
42
n
42
C
42
A
C
43
n
43
C
43
A
G
1
n
1
G
1
B
G
2
n
2
G
2
B
C
3
n
3
C
3
B
G
4
n
4
G
4
B
U
5
n
5
U
5
B
OMC
6
n
6
OMC
6
B
C
7
n
7
C
7
B
U
8
n
8
U
8
B
G
9
n
9
G
9
B
G
10
n
10
G
10
B
U
11
n
11
U
11
B
A
12
n
12
A
12
B
U
13
n
13
U
13
B
C
14
n
14
C
14
B
C
15
n
15
C
15
B
A
16
n
16
A
16
B
A
17
n
17
A
17
B
U
18
n
18
U
18
B
C
19
n
19
C
19
B
DC
20
n
20
DC
20
B
5.8229
1.9530
0.0423
2.1739
-0.4410
8.3154
0.3050
-0.1505
-0.3776
0.2587
-0.5892
-0.0871
1.4182
0.4680
0.3637
0.5997
0.0597
-0.0497
0.4442
0.0575
0.3273
refined
-9.5342
18.6015
11.6618
X-RAY DIFFRACTION
0.5896
1.2146
0.9685
6.7655
1.8026
1.4247
-0.0108
-0.0107
-0.2627
-0.5724
0.2107
-0.9420
-0.1116
0.1653
-0.2598
0.3042
-0.0041
0.0582
0.3588
-0.0199
0.4791
refined
-11.2177
7.3014
-8.4746
X-RAY DIFFRACTION
3.3811
0.4805
2.6882
5.2670
3.6670
4.1046
-0.6330
0.4047
0.2650
-0.7350
0.8563
-0.1389
-0.9638
0.5514
-0.2880
0.5547
-0.1595
0.0215
0.4813
0.0566
0.4111
refined
-17.7545
10.0028
-21.1917
X-RAY DIFFRACTION
9.4704
-2.7584
-3.9634
8.7572
-0.2352
8.6600
-1.1293
-1.7006
0.3625
1.0332
-0.0925
0.6589
-0.2176
-0.9127
1.1960
0.4933
0.0280
-0.0638
0.7181
-0.1811
0.5702
refined
-18.2220
15.6795
0.3312
X-RAY DIFFRACTION
7.1890
-3.6808
4.4502
8.6537
-1.6796
8.0079
0.0083
-0.3993
0.2379
-0.3373
-0.1489
0.5823
-0.5728
-1.6194
0.1746
0.4401
0.1070
-0.1613
0.6258
-0.0808
0.4785
refined
-22.8271
14.1219
-9.8188
X-RAY DIFFRACTION
5.2889
3.6852
-1.4027
5.8918
-1.1376
0.3828
-1.4455
0.0748
1.0929
-0.5302
0.1727
-0.3188
-2.2335
-1.9499
1.0524
1.1338
0.2002
-0.3708
0.9593
-0.0864
0.6167
refined
-23.5303
17.2769
-24.8286
X-RAY DIFFRACTION
2.9146
-2.6952
2.9942
5.7936
-1.3478
5.4784
0.3934
-0.0758
-0.0892
-0.5746
-0.2651
-0.0807
-0.7925
-0.0265
-0.1376
0.6271
0.0140
0.0163
0.4999
0.0282
0.3101
refined
-31.3871
7.4091
-32.9070
X-RAY DIFFRACTION
3.9599
-1.3778
2.3283
1.0698
-0.1344
2.1025
-0.0626
-0.6905
-0.0826
0.2810
-0.0560
-0.0049
-0.3903
-0.6468
0.1255
0.6249
-0.0341
-0.0238
0.7158
0.1084
0.3262
refined
-30.4950
12.5137
-25.5497
X-RAY DIFFRACTION
0.0526
-0.3828
-0.4311
5.1893
1.5050
3.0583
0.2296
-0.3693
-0.2889
0.7241
-0.2185
-0.6208
0.7800
-0.6640
-0.0468
0.4593
-0.0898
-0.0010
0.4172
0.0825
0.4521
refined
-14.8169
2.4452
-3.7866
X-RAY DIFFRACTION
6.4416
2.3463
0.8041
4.0500
0.8010
9.8534
0.6212
-0.3305
-0.7250
-0.1020
-0.0247
-0.6883
-0.2298
-0.3106
-0.5422
0.3464
0.0749
-0.0350
0.3638
0.0217
0.4943
refined
-0.3432
22.0699
9.4899
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(CHAIN A AND RESID 1:4)
X-RAY DIFFRACTION
2
(CHAIN A AND RESID 5:14)
X-RAY DIFFRACTION
3
(CHAIN A AND RESID 15:25)
X-RAY DIFFRACTION
4
(CHAIN A AND RESID 26:30)
X-RAY DIFFRACTION
5
(CHAIN A AND RESID 31:34)
X-RAY DIFFRACTION
6
(CHAIN A AND RESID 35:38)
X-RAY DIFFRACTION
7
(CHAIN A AND RESID 39:43)
X-RAY DIFFRACTION
8
(CHAIN B AND RESID 1:7)
X-RAY DIFFRACTION
9
(CHAIN B AND RESID 8:15)
X-RAY DIFFRACTION
10
(CHAIN B AND RESID 16:20)
author_and_software_defined_assembly
PISA
2
dimeric
3320
-7.2
10270
A
GDP
1
GUANOSINE-5'-DIPHOSPHATE
A
GDP
1
G
B
OMC
6
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
6
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
A
A
OP1
O
A
HOH
29
2015
2.03
0.2360
0.1820
0.1876
2.200
20.216
907
9162
9.9
95.42
0.33
1
1.44
MOLECULAR REPLACEMENT
30.80
0.90
1.11
PDB ENTRY 2GOZ
ML
FLAT BULK SOLVENT MODEL
2.200
20.216
31
1374
0
1343
0
0.005
1500
0.938
2331
14.735
746
0.040
311
0.007
63
0.3744
0.2845
2.3377
160
1396
98.00
0.3505
0.2933
2.5179
152
1408
98.00
0.3894
0.2840
2.7707
157
1388
98.00
0.3075
0.2330
3.1703
151
1410
97.00
0.1917
0.1487
3.9892
148
1384
96.00
0.1659
0.1283
20.2172
139
1269
86.00
53.23
2.20
38.35
3ZD4
9191
0.0
0.03
1
16.80
3.9
96.1
0.31
2.20
2.32
3.80
1
4.0
98.2
refinement
PHENIX
(PHENIX.REFINE)
data reduction
iMOSFLM
data scaling
SCALA
phasing
PHASER
Full-Length Hammerhead Ribozyme with G12A substitution at the general base position
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.594
both
A
GDP
1
A
O3'
GDP
1
1_555
A
G
2
A
P
G
2
1_555
covale
1.607
both
B
U
5
B
O3'
U
5
1_555
B
OMC
6
B
P
OMC
6
1_555
covale
1.608
both
B
OMC
6
B
O3'
OMC
6
1_555
B
C
7
B
P
C
7
1_555
covale
1.608
both
B
C
19
B
O3'
C
19
1_555
B
DC
20
B
P
DC
20
1_555
hydrog
WATSON-CRICK
A
GDP
1
A
N1
GDP
1
1_555
B
DC
20
B
N3
DC
20
1_555
hydrog
WATSON-CRICK
A
GDP
1
A
N2
GDP
1
1_555
B
DC
20
B
O2
DC
20
1_555
hydrog
WATSON-CRICK
A
GDP
1
A
O6
GDP
1
1_555
B
DC
20
B
N4
DC
20
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
19
B
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
19
B
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
19
B
N4
C
19
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
B
U
18
B
N3
U
18
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
B
U
18
B
O4
U
18
1_555
hydrog
U-C MISPAIR
A
U
4
A
O4
U
4
1_555
B
C
15
B
N4
C
15
1_555
hydrog
U-A PAIR
A
U
4
A
O2
U
4
1_555
B
A
17
B
N6
A
17
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
B
C
14
B
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
B
C
14
B
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
B
C
14
B
N4
C
14
1_555
hydrog
REVERSED HOOGSTEEN
A
U
6
A
N3
U
6
1_555
A
A
28
A
N7
A
28
1_555
hydrog
REVERSED HOOGSTEEN
A
U
6
A
O2
U
6
1_555
A
A
28
A
N6
A
28
1_555
hydrog
TYPE_15_PAIR
A
C
8
A
N4
C
8
1_555
A
C
26
A
O2
C
26
1_555
hydrog
TYPE_15_PAIR
A
C
8
A
O2
C
8
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
U
9
A
N3
U
9
1_555
B
A
12
B
N1
A
12
1_555
hydrog
WATSON-CRICK
A
U
9
A
O4
U
9
1_555
B
A
12
B
N6
A
12
1_555
hydrog
WATSON-CRICK
A
A
10
A
N1
A
10
1_555
B
U
11
B
N3
U
11
1_555
hydrog
WATSON-CRICK
A
A
10
A
N6
A
10
1_555
B
U
11
B
O4
U
11
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
11
1_555
B
G
10
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
11
1_555
B
G
10
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
11
1_555
B
G
10
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
C
12
A
N3
C
12
1_555
B
G
9
B
N1
G
9
1_555
hydrog
WATSON-CRICK
A
C
12
A
N4
C
12
1_555
B
G
9
B
O6
G
9
1_555
hydrog
WATSON-CRICK
A
C
12
A
O2
C
12
1_555
B
G
9
B
N2
G
9
1_555
hydrog
WATSON-CRICK
A
A
13
A
N1
A
13
1_555
B
U
8
B
N3
U
8
1_555
hydrog
WATSON-CRICK
A
A
13
A
N6
A
13
1_555
B
U
8
B
O4
U
8
1_555
hydrog
WATSON-CRICK
A
G
14
A
N1
G
14
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
14
A
N2
G
14
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
14
A
O6
G
14
1_555
B
C
7
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
C
15
A
N3
C
15
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
15
A
N4
C
15
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
15
A
O2
C
15
1_555
A
G
20
A
N2
G
20
1_555
hydrog
G-A MISPAIR
A
G
17
A
N2
G
17
1_555
A
A
38
A
N1
A
38
1_555
hydrog
A-A MISPAIR
A
A
21
A
N6
A
21
1_555
A
A
36
A
N3
A
36
1_555
hydrog
WATSON-CRICK
A
G
22
A
N1
G
22
1_555
A
C
35
A
N3
C
35
1_555
hydrog
WATSON-CRICK
A
G
22
A
N2
G
22
1_555
A
C
35
A
O2
C
35
1_555
hydrog
WATSON-CRICK
A
G
22
A
O6
G
22
1_555
A
C
35
A
N4
C
35
1_555
hydrog
WATSON-CRICK
A
U
23
A
N3
U
23
1_555
A
A
34
A
N1
A
34
1_555
hydrog
WATSON-CRICK
A
U
23
A
O4
U
23
1_555
A
A
34
A
N6
A
34
1_555
hydrog
WATSON-CRICK
A
C
24
A
N3
C
24
1_555
A
G
33
A
N1
G
33
1_555
hydrog
WATSON-CRICK
A
C
24
A
N4
C
24
1_555
A
G
33
A
O6
G
33
1_555
hydrog
WATSON-CRICK
A
C
24
A
O2
C
24
1_555
A
G
33
A
N2
G
33
1_555
hydrog
WATSON-CRICK
A
C
25
A
N3
C
25
1_555
A
G
32
A
N1
G
32
1_555
hydrog
WATSON-CRICK
A
C
25
A
N4
C
25
1_555
A
G
32
A
O6
G
32
1_555
hydrog
WATSON-CRICK
A
C
25
A
O2
C
25
1_555
A
G
32
A
N2
G
32
1_555
hydrog
A-U PAIR
A
A
28
A
N3
A
28
1_555
A
U
30
A
N3
U
30
1_555
hydrog
REVERSED HOOGSTEEN
A
A
31
A
N6
A
31
1_555
B
U
13
B
O2
U
13
1_555
hydrog
REVERSED HOOGSTEEN
A
A
31
A
N7
A
31
1_555
B
U
13
B
N3
U
13
1_555
hydrog
A-OMC MISPAIR
A
A
37
A
N6
A
37
1_555
B
OMC
6
B
O2
OMC
6
1_555
hydrog
A-OMC MISPAIR
A
A
38
A
N6
A
38
1_555
B
OMC
6
B
O2
OMC
6
1_555
hydrog
WATSON-CRICK
A
A
39
A
N1
A
39
1_555
B
U
5
B
N3
U
5
1_555
hydrog
WATSON-CRICK
A
A
39
A
N6
A
39
1_555
B
U
5
B
O4
U
5
1_555
hydrog
WATSON-CRICK
A
C
40
A
N3
C
40
1_555
B
G
4
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
40
A
N4
C
40
1_555
B
G
4
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
40
A
O2
C
40
1_555
B
G
4
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
G
41
A
N1
G
41
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
41
A
N2
G
41
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
41
A
O6
G
41
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
C
42
A
N3
C
42
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
42
A
N4
C
42
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
C
42
A
O2
C
42
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
C
43
A
N3
C
43
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
43
A
N4
C
43
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
43
A
O2
C
43
1_555
B
G
1
B
N2
G
1
1_555
RNA
RNA, GENERAL BASE CATALYSIS
3ZD4
PDB
1
1
3ZD4
3ZD4
PDB
2
1
3ZD4
1
43
3ZD4
1
43
3ZD4
A
1
1
43
1
20
3ZD4
1
20
3ZD4
B
2
1
20
5
C 1 2 1