0.001969
0.000000
0.000000
0.000000
0.001969
0.000000
0.000000
0.000000
0.001245
0.00000
0.00000
0.00000
Lancaster, L.
Culver, G.M.
Yusupova, G.Z.
Cate, J.H.
Yuspov, M.M.
Noller, H.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
508
508
803
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C5 H11 N O2
117.146
y
VALINE
L-peptide 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
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
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
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
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
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
C
N
131
N
C
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
H
N
146
N
N
N
147
R
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
S
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
O
N
161
N
P
N
162
N
O
N
163
N
O
N
164
N
O
N
165
N
C
N
166
R
C
N
167
N
O
N
168
S
C
N
169
N
O
N
170
R
C
N
171
N
O
N
172
R
C
Y
173
N
N
Y
174
N
C
Y
175
N
N
Y
176
N
C
N
177
N
C
N
178
N
O
N
179
N
N
N
180
N
C
N
181
N
N
N
182
N
N
Y
183
N
C
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
H
N
196
N
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
O
N
206
N
N
N
207
N
O
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
218
N
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
O
N
226
N
O
N
227
N
O
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
N
N
238
N
C
N
239
N
C
N
240
N
O
N
241
N
O
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
Y
252
N
C
Y
253
N
N
Y
254
N
C
Y
255
N
C
Y
256
N
N
N
257
N
O
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
S
C
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
O
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
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
N
N
321
N
O
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
N
C
N
343
N
S
N
344
N
C
N
345
N
O
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
N
368
N
O
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
O
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
N
N
398
S
C
N
399
N
C
N
400
N
O
N
401
N
C
N
402
N
O
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
R
C
N
416
N
O
N
417
N
C
N
418
N
O
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
N
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
N
442
N
O
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
N
466
N
O
N
467
N
O
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
O
N
480
N
P
N
481
N
O
N
482
N
O
N
483
N
O
N
484
N
C
N
485
R
C
N
486
N
O
N
487
S
C
N
488
N
O
N
489
R
C
N
490
N
O
N
491
R
C
N
492
N
N
N
493
N
C
N
494
N
O
N
495
N
N
N
496
N
C
N
497
N
O
N
498
N
C
N
499
N
C
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
H
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
H
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
N
N
514
S
C
N
515
N
C
N
516
N
O
N
517
N
C
N
518
N
C
N
519
N
C
N
520
N
O
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
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
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
doub
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
doub
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
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
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
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
doub
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
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
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
doub
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
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
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
doub
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
Y
182
N
sing
Y
183
N
sing
Y
184
N
doub
N
185
N
sing
Y
186
N
sing
N
187
N
sing
Y
188
N
doub
N
189
N
doub
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
doub
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
doub
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
doub
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
doub
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
doub
N
232
N
sing
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
sing
N
240
N
sing
N
241
N
doub
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
doub
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
Y
255
N
sing
Y
256
N
doub
Y
257
N
doub
N
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
261
N
sing
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
doub
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
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
doub
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
doub
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
doub
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
Y
361
N
doub
Y
362
N
sing
Y
363
N
sing
N
364
N
sing
Y
365
N
doub
N
366
N
sing
Y
367
N
doub
N
368
N
sing
Y
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
doub
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
doub
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
doub
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
Y
430
N
doub
Y
431
N
sing
Y
432
N
sing
N
433
N
sing
Y
434
N
doub
Y
435
N
sing
Y
436
N
sing
N
437
N
sing
Y
438
N
sing
Y
439
N
doub
N
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
doub
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
Y
458
N
doub
Y
459
N
sing
Y
460
N
sing
N
461
N
sing
Y
462
N
doub
N
463
N
sing
Y
464
N
doub
N
465
N
sing
Y
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
doub
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
doub
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
doub
N
502
N
sing
N
503
N
doub
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
doub
N
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
UK
RNA
RNARFU
2122
1355-8382
6
717
729
10.1017/S1355838200000303
10836793
The location of protein S8 and surrounding elements of 16S rRNA in the 70S ribosome from combined use of directed hydroxyl radical probing and X-ray crystallography.
2000
10.2210/pdb1emi/pdb
pdb_00001emi
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
105
1
CCD
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
1.1051
1.0
ALS
1.1051
SYNCHROTRON
ALS
COORDINATES FOR THERMUS THERMOPHILUS 16S RRNA BUT SEQUENCE AND NUMBERING IS THAT OF E.COLI 16S RRNA
51921.684
16S RIBOSOMAL RNA
1
nat
polymer
15624.214
RIBOSOMAL PROTEIN S8
1
nat
polymer
no
no
GCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAG
UCUCGUACGAAGACUGACGCUCAGGUGCGUCGACUUGGAGGUUGUGCUUCGUGGCUUCCGGAGCUAACGCGUUAAGUCGA
C
GCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAG
UCUCGUACGAAGACUGACGCUCAGGUGCGUCGACUUGGAGGUUGUGCUUCGUGGCUUCCGGAGCUAACGCGUUAAGUCGA
C
B
polyribonucleotide
no
no
TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHH
IRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW
TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHH
IRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW
A
polypeptide(L)
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
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
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
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
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
Thermus
sample
274
Thermus thermophilus
Thermus
sample
274
Thermus thermophilus
5
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
1
0
2000-06-12
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
P ATOMS ONLY
CA ATOMS ONLY
X-ray crystal structures of 70S ribosome functional complexes
RCSB
Y
RCSB
2000-03-16
REL
G
577
n
1
G
577
B
C
578
n
2
C
578
B
A
579
n
3
A
579
B
C
580
n
4
C
580
B
G
581
n
5
G
581
B
C
582
n
6
C
582
B
A
583
n
7
A
583
B
G
584
n
8
G
584
B
G
585
n
9
G
585
B
C
586
n
10
C
586
B
G
587
n
11
G
587
B
G
588
n
12
G
588
B
U
589
n
13
U
589
B
U
590
n
14
U
590
B
U
591
n
15
U
591
B
G
592
n
16
G
592
B
U
593
n
17
U
593
B
U
594
n
18
U
594
B
A
595
n
19
A
595
B
A
596
n
20
A
596
B
G
597
n
21
G
597
B
U
598
n
22
U
598
B
C
599
n
23
C
599
B
A
600
n
24
A
600
B
G
601
n
25
G
601
B
A
602
n
26
A
602
B
U
603
n
27
U
603
B
G
604
n
28
G
604
B
U
605
n
29
U
605
B
G
606
n
30
G
606
B
A
607
n
31
A
607
B
A
608
n
32
A
608
B
A
609
n
33
A
609
B
U
610
n
34
U
610
B
C
611
n
35
C
611
B
C
612
n
36
C
612
B
C
613
n
37
C
613
B
C
614
n
38
C
614
B
G
615
n
39
G
615
B
G
616
n
40
G
616
B
G
617
n
41
G
617
B
C
618
n
42
C
618
B
U
619
n
43
U
619
B
C
620
n
44
C
620
B
A
621
n
45
A
621
B
A
622
n
46
A
622
B
C
623
n
47
C
623
B
C
624
n
48
C
624
B
U
625
n
49
U
625
B
G
626
n
50
G
626
B
G
627
n
51
G
627
B
G
628
n
52
G
628
B
A
629
n
53
A
629
B
A
630
n
54
A
630
B
C
631
n
55
C
631
B
U
632
n
56
U
632
B
G
633
n
57
G
633
B
C
634
n
58
C
634
B
A
635
n
59
A
635
B
U
636
n
60
U
636
B
C
637
n
61
C
637
B
U
638
n
62
U
638
B
G
639
n
63
G
639
B
A
640
n
64
A
640
B
U
641
n
65
U
641
B
A
642
n
66
A
642
B
C
643
n
67
C
643
B
U
644
n
68
U
644
B
G
645
n
69
G
645
B
G
646
n
70
G
646
B
C
647
n
71
C
647
B
A
648
n
72
A
648
B
A
649
n
73
A
649
B
G
650
n
74
G
650
B
C
651
n
75
C
651
B
U
652
n
76
U
652
B
U
653
n
77
U
653
B
G
654
n
78
G
654
B
A
655
n
79
A
655
B
G
656
n
80
G
656
B
U
657
n
81
U
657
B
C
658
n
82
C
658
B
U
659
n
83
U
659
B
C
660
n
84
C
660
B
G
661
n
85
G
661
B
U
662
n
86
U
662
B
A
743
n
87
A
743
B
C
744
n
88
C
744
B
G
745
n
89
G
745
B
A
746
n
90
A
746
B
A
747
n
91
A
747
B
G
748
n
92
G
748
B
A
749
n
93
A
749
B
C
750
n
94
C
750
B
U
751
n
95
U
751
B
G
752
n
96
G
752
B
A
753
n
97
A
753
B
C
754
n
98
C
754
B
G
755
n
99
G
755
B
C
756
n
100
C
756
B
U
757
n
101
U
757
B
C
758
n
102
C
758
B
A
759
n
103
A
759
B
G
760
n
104
G
760
B
G
761
n
105
G
761
B
U
762
n
106
U
762
B
G
763
n
107
G
763
B
C
764
n
108
C
764
B
G
821
n
109
G
821
B
U
822
n
110
U
822
B
C
823
n
111
C
823
B
G
824
n
112
G
824
B
A
825
n
113
A
825
B
C
826
n
114
C
826
B
U
827
n
115
U
827
B
U
828
n
116
U
828
B
G
829
n
117
G
829
B
G
830
n
118
G
830
B
A
831
n
119
A
831
B
G
832
n
120
G
832
B
G
833
n
121
G
833
B
U
834
n
122
U
834
B
U
835
n
123
U
835
B
G
836
n
124
G
836
B
U
837
n
125
U
837
B
G
838
n
126
G
838
B
C
841
n
127
C
841
B
U
842
n
128
U
842
B
U
843
n
129
U
843
B
C
848
n
130
C
848
B
G
849
n
131
G
849
B
U
850
n
132
U
850
B
G
851
n
133
G
851
B
G
852
n
134
G
852
B
C
853
n
135
C
853
B
U
854
n
136
U
854
B
U
855
n
137
U
855
B
C
856
n
138
C
856
B
C
857
n
139
C
857
B
G
858
n
140
G
858
B
G
859
n
141
G
859
B
A
860
n
142
A
860
B
G
861
n
143
G
861
B
C
862
n
144
C
862
B
U
863
n
145
U
863
B
A
864
n
146
A
864
B
A
865
n
147
A
865
B
C
866
n
148
C
866
B
G
867
n
149
G
867
B
C
868
n
150
C
868
B
G
869
n
151
G
869
B
U
870
n
152
U
870
B
U
871
n
153
U
871
B
A
872
n
154
A
872
B
A
873
n
155
A
873
B
G
874
n
156
G
874
B
U
875
n
157
U
875
B
C
876
n
158
C
876
B
G
877
n
159
G
877
B
A
878
n
160
A
878
B
C
879
n
161
C
879
B
THR
3
n
1
THR
3
A
ASP
4
n
2
ASP
4
A
PRO
5
n
3
PRO
5
A
ILE
6
n
4
ILE
6
A
ALA
7
n
5
ALA
7
A
ASP
8
n
6
ASP
8
A
MET
9
n
7
MET
9
A
LEU
10
n
8
LEU
10
A
THR
11
n
9
THR
11
A
ARG
12
n
10
ARG
12
A
ILE
13
n
11
ILE
13
A
ARG
14
n
12
ARG
14
A
ASN
15
n
13
ASN
15
A
ALA
16
n
14
ALA
16
A
THR
17
n
15
THR
17
A
ARG
18
n
16
ARG
18
A
VAL
19
n
17
VAL
19
A
TYR
20
n
18
TYR
20
A
LYS
21
n
19
LYS
21
A
GLU
22
n
20
GLU
22
A
SER
23
n
21
SER
23
A
THR
24
n
22
THR
24
A
ASP
25
n
23
ASP
25
A
VAL
26
n
24
VAL
26
A
PRO
27
n
25
PRO
27
A
ALA
28
n
26
ALA
28
A
SER
29
n
27
SER
29
A
ARG
30
n
28
ARG
30
A
PHE
31
n
29
PHE
31
A
LYS
32
n
30
LYS
32
A
GLU
33
n
31
GLU
33
A
GLU
34
n
32
GLU
34
A
ILE
35
n
33
ILE
35
A
LEU
36
n
34
LEU
36
A
ARG
37
n
35
ARG
37
A
ILE
38
n
36
ILE
38
A
LEU
39
n
37
LEU
39
A
ALA
40
n
38
ALA
40
A
ARG
41
n
39
ARG
41
A
GLU
42
n
40
GLU
42
A
GLY
43
n
41
GLY
43
A
PHE
44
n
42
PHE
44
A
ILE
45
n
43
ILE
45
A
LYS
46
n
44
LYS
46
A
GLY
47
n
45
GLY
47
A
TYR
48
n
46
TYR
48
A
GLU
49
n
47
GLU
49
A
ARG
50
n
48
ARG
50
A
VAL
51
n
49
VAL
51
A
ASP
52
n
50
ASP
52
A
VAL
53
n
51
VAL
53
A
ASP
54
n
52
ASP
54
A
GLY
55
n
53
GLY
55
A
LYS
56
n
54
LYS
56
A
PRO
57
n
55
PRO
57
A
TYR
58
n
56
TYR
58
A
LEU
59
n
57
LEU
59
A
ARG
60
n
58
ARG
60
A
VAL
61
n
59
VAL
61
A
TYR
62
n
60
TYR
62
A
LEU
63
n
61
LEU
63
A
LYS
64
n
62
LYS
64
A
TYR
65
n
63
TYR
65
A
GLY
66
n
64
GLY
66
A
PRO
67
n
65
PRO
67
A
ARG
68
n
66
ARG
68
A
ARG
69
n
67
ARG
69
A
GLN
70
n
68
GLN
70
A
GLY
71
n
69
GLY
71
A
PRO
72
n
70
PRO
72
A
ASP
73
n
71
ASP
73
A
PRO
74
n
72
PRO
74
A
ARG
75
n
73
ARG
75
A
PRO
76
n
74
PRO
76
A
GLU
77
n
75
GLU
77
A
GLN
78
n
76
GLN
78
A
VAL
79
n
77
VAL
79
A
ILE
80
n
78
ILE
80
A
HIS
81
n
79
HIS
81
A
HIS
82
n
80
HIS
82
A
ILE
83
n
81
ILE
83
A
ARG
84
n
82
ARG
84
A
ARG
85
n
83
ARG
85
A
ILE
86
n
84
ILE
86
A
SER
87
n
85
SER
87
A
LYS
88
n
86
LYS
88
A
PRO
89
n
87
PRO
89
A
GLY
90
n
88
GLY
90
A
ARG
91
n
89
ARG
91
A
ARG
92
n
90
ARG
92
A
VAL
93
n
91
VAL
93
A
TYR
94
n
92
TYR
94
A
VAL
95
n
93
VAL
95
A
GLY
96
n
94
GLY
96
A
VAL
97
n
95
VAL
97
A
LYS
98
n
96
LYS
98
A
GLU
99
n
97
GLU
99
A
ILE
100
n
98
ILE
100
A
PRO
101
n
99
PRO
101
A
ARG
102
n
100
ARG
102
A
VAL
103
n
101
VAL
103
A
ARG
104
n
102
ARG
104
A
ARG
105
n
103
ARG
105
A
GLY
106
n
104
GLY
106
A
LEU
107
n
105
LEU
107
A
GLY
108
n
106
GLY
108
A
ILE
109
n
107
ILE
109
A
ALA
110
n
108
ALA
110
A
ILE
111
n
109
ILE
111
A
LEU
112
n
110
LEU
112
A
SER
113
n
111
SER
113
A
THR
114
n
112
THR
114
A
SER
115
n
113
SER
115
A
LYS
116
n
114
LYS
116
A
GLY
117
n
115
GLY
117
A
VAL
118
n
116
VAL
118
A
LEU
119
n
117
LEU
119
A
THR
120
n
118
THR
120
A
ASP
121
n
119
ASP
121
A
ARG
122
n
120
ARG
122
A
GLU
123
n
121
GLU
123
A
ALA
124
n
122
ALA
124
A
ARG
125
n
123
ARG
125
A
LYS
126
n
124
LYS
126
A
LEU
127
n
125
LEU
127
A
GLY
128
n
126
GLY
128
A
VAL
129
n
127
VAL
129
A
GLY
130
n
128
GLY
130
A
GLY
131
n
129
GLY
131
A
GLU
132
n
130
GLU
132
A
LEU
133
n
131
LEU
133
A
ILE
134
n
132
ILE
134
A
CYS
135
n
133
CYS
135
A
GLU
136
n
134
GLU
136
A
VAL
137
n
135
VAL
137
A
TRP
138
n
136
TRP
138
A
author_defined_assembly
2
dimeric
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
All data collection parameters are as reported for 486D. The RNA
model for the S8 region of 16S rRNA was built manually by fitting to
the 7.8 A X-ray map of the Thermus thermophilus 70S ribosome (Cate et
al., Science 285, 2095-2104, 1999; see PDB 486D) using a single P
pseudoatom for each nucleotide. Note that the nucleotide numbering
corresponds to the nucleotide positions of E.coli 16S rRNA.
Protein S8 from Thermus thermophilus (PDB 1AN7) was fitted to the 7.8
A map of the Thermus thermophilus 70S ribosome by splitting the
protein into N- and C-terminal domains between residues 80 and 81.
The two domains were fit separately, resulting in a small relative
movement compared with the original X-ray structure. Only C-alpha
positions are given in the PDB file.
7.50
1
7.50
0
297
0
161
136
7.50
1EMI
1
phasing
MLPHARE
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL PROTEIN S8.
1
N
N
2
N
N
RIBOSOME
RNA, rRNA, ribosome, ribosomal protein, 16S rRNA, S8
RS8_THET8
UNP
2
3
Q5SHQ2
1EMI
PDB
1
1EMI
3
138
1EMI
3
138
Q5SHQ2
A
1
1
136
577
879
1EMI
577
879
1EMI
B
2
1
161
1
GLU
conflict
ASP
25
1EMI
A
Q5SHQ2
UNP
25
23
1
LYS
conflict
ARG
37
1EMI
A
Q5SHQ2
UNP
37
35
1
GLU
conflict
ASP
52
1EMI
A
Q5SHQ2
UNP
52
50
1
ILE
conflict
VAL
61
1EMI
A
Q5SHQ2
UNP
61
59
1
HIS
conflict
TYR
62
1EMI
A
Q5SHQ2
UNP
62
60
1
LYS
conflict
HIS
81
1EMI
A
Q5SHQ2
UNP
81
79
1
ARG
conflict
LYS
88
1EMI
A
Q5SHQ2
UNP
88
86
1
PRO
conflict
SER
115
1EMI
A
Q5SHQ2
UNP
115
113
97
tetragonal
I 4 2 2