0.016481
0.000000
0.000000
0.000000
0.011040
0.000000
0.000000
0.000000
0.021450
0.00000
0.00000
0.00000
Hsiao, Y.-Y.
Yuan, H.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
60.675
90.580
46.621
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
H2 O
18.015
WATER
non-polymer
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
O
N
89
N
P
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
C
N
94
R
C
N
95
N
O
N
96
S
C
N
97
N
O
N
98
N
C
N
99
R
C
Y
100
N
N
Y
101
N
C
Y
102
N
N
Y
103
N
C
Y
104
N
C
N
105
N
N
Y
106
N
N
Y
107
N
C
Y
108
N
N
Y
109
N
C
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
O
N
125
N
P
N
126
N
O
N
127
N
O
N
128
N
O
N
129
N
C
N
130
R
C
N
131
N
O
N
132
S
C
N
133
N
O
N
134
N
C
N
135
R
C
N
136
N
N
N
137
N
C
N
138
N
O
N
139
N
N
N
140
N
C
N
141
N
N
N
142
N
C
N
143
N
C
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
P
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
C
N
164
R
C
N
165
N
O
N
166
S
C
N
167
N
O
N
168
N
C
N
169
R
C
Y
170
N
N
Y
171
N
C
Y
172
N
N
Y
173
N
C
N
174
N
C
N
175
N
O
N
176
N
N
N
177
N
C
N
178
N
N
N
179
N
N
Y
180
N
C
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
N
C
N
206
R
C
N
207
N
N
N
208
N
C
N
209
N
O
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
C
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
229
N
H
N
230
N
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
O
N
239
N
N
N
240
N
O
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
O
N
259
N
O
N
260
N
O
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
H
N
269
N
H
N
270
N
N
N
271
N
C
N
272
N
C
N
273
N
O
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
N
Y
287
N
C
Y
288
N
C
Y
289
N
N
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
O
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
S
C
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
N
N
357
N
O
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
S
N
380
N
C
N
381
N
O
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
MG
N
394
N
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
N
N
418
S
C
N
419
N
C
N
420
N
O
N
421
N
C
N
422
N
C
N
423
N
C
N
424
N
O
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
N
C
N
439
N
O
N
440
N
O
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
N
N
449
S
C
N
450
N
C
N
451
N
O
N
452
R
C
N
453
N
O
N
454
N
C
N
455
N
O
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
N
N
466
S
C
N
467
N
C
N
468
N
O
N
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
N
Y
474
N
C
Y
475
N
C
Y
476
N
C
Y
477
N
C
Y
478
N
C
N
479
N
O
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
N
N
493
S
C
N
494
N
C
N
495
N
O
N
496
N
C
Y
497
N
C
Y
498
N
C
Y
499
N
C
Y
500
N
C
Y
501
N
C
Y
502
N
C
N
503
N
O
N
504
N
O
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
H
N
514
N
H
N
515
N
H
N
516
N
N
N
517
S
C
N
518
N
C
N
519
N
O
N
520
N
C
N
521
N
C
N
522
N
C
N
523
N
O
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
532
N
H
N
533
N
H
N
534
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
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
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
doub
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
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
doub
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
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
Y
106
N
sing
Y
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
110
N
sing
Y
111
N
sing
Y
112
N
doub
N
113
N
sing
Y
114
N
doub
N
115
N
sing
N
116
N
sing
Y
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
doub
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
N
139
N
sing
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
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
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
Y
179
N
sing
Y
180
N
sing
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
doub
N
186
N
doub
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
doub
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
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
doub
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
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
doub
N
239
N
sing
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
doub
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
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
doub
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
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
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
Y
289
N
sing
Y
290
N
doub
Y
291
N
doub
N
292
N
sing
Y
293
N
sing
N
294
N
sing
Y
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
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
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
doub
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
sing
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
doub
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
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
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
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
doub
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
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
doub
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
doub
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
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
doub
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
Y
466
N
doub
Y
467
N
sing
Y
468
N
sing
N
469
N
sing
Y
470
N
doub
Y
471
N
sing
Y
472
N
sing
N
473
N
sing
Y
474
N
sing
Y
475
N
doub
N
476
N
sing
Y
477
N
doub
N
478
N
sing
Y
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
doub
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
Y
494
N
doub
Y
495
N
sing
Y
496
N
sing
N
497
N
sing
Y
498
N
doub
N
499
N
sing
Y
500
N
doub
N
501
N
sing
Y
502
N
sing
N
503
N
sing
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
sing
N
513
N
doub
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
N
524
N
sing
US
Plos Biol.
1544-9173
12
e1001803
e1001803
10.1371/journal.pbio.1001803
24594808
Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
2014
10.2210/pdb4kaz/pdb
pdb_00004kaz
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
2011-06-03
RAYONIX MX225HE
SAGITALLY FOCUSED Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.9
1.0
BL44XU
SPring-8
0.9
SYNCHROTRON
SPRING-8 BEAMLINE BL44XU
25719.035
Ribonuclease T
3.1.13.-
1
man
polymer
6052.890
DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
1
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
168
nat
water
Exoribonuclease T, RNase T
no
no
MGSSHHHHHHSSGLVPRGSHMSDNAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHF
HVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKR
NPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV
MGSSHHHHHHSSGLVPRGSHMSDNAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHF
HVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKR
NPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV
A
polypeptide(L)
no
no
(DT)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC)(DT)(DT)(DT)(DA)(DG)(DG)(DG)(DC)(DC)(DC)(DC)
TTGGCCCTCTTTAGGGCCCC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
K-12
sample
b1652, JW1644, rnt
83333
Escherichia coli
562
Escherichia coli
BL21-CodonPlus(DE3)-RIPL
PLASMID
pET-28a
1
2.02
38.99
VAPOR DIFFUSION, HANGING DROP
6
20% v/v 2-Propanol,
0.1 M MES monohydrate,
20% w/v Polyethylene glycol monomethyl ester 2000
, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-4.294
1
19
B
3
B
18
-0.899
B_DG3:DC18_B
1
-2.326
-0.445
0.068
-0.178
8.275
1
19
B
4
B
17
2.041
B_DG4:DC17_B
2
-9.805
-0.256
0.342
-0.117
-7.326
1
19
B
5
B
16
-3.009
B_DC5:DG16_B
3
-8.593
0.284
0.134
-0.188
4.295
1
19
B
6
B
15
2.330
B_DC6:DG15_B
4
-15.010
0.156
-0.046
-0.137
-7.972
1
19
B
7
B
14
-4.933
B_DC7:DG14_B
5
-12.546
-0.765
0.404
0.295
2.805
30.054
B
B
3
4
17.137
B
B
18
17
2.986
8.696
0.013
0.045
BB_DG3DG4:DC17DC18_BB
1
-6.422
12.655
28.084
-1.549
-1.233
3.647
39.578
B
B
4
5
-1.560
B
B
17
16
3.644
-1.056
-0.328
-0.214
BB_DG4DC5:DG16DC17_BB
2
0.041
-0.061
39.564
-0.178
0.490
3.073
33.237
B
B
5
6
8.113
B
B
16
15
3.109
4.624
-0.169
0.054
BB_DC5DC6:DG15DG16_BB
3
1.902
-3.337
32.870
-0.641
0.597
3.722
32.522
B
B
6
7
0.418
B
B
15
14
3.684
0.234
-0.516
0.377
BB_DC6DC7:DG14DG15_BB
4
-4.101
7.341
32.268
0.626
0.107
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2014-03-05
1
1
2014-05-28
1
2
2023-09-20
_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_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-04-23
REL
REL
MG
MAGNESIUM ION
HOH
water
3NGY
PDB
experimental model
MG
1
3
MG
MG
301
A
MG
1
3
MG
MG
101
B
HOH
1
4
HOH
HOH
401
A
HOH
2
4
HOH
HOH
402
A
HOH
3
4
HOH
HOH
403
A
HOH
4
4
HOH
HOH
404
A
HOH
5
4
HOH
HOH
405
A
HOH
7
4
HOH
HOH
406
A
HOH
8
4
HOH
HOH
407
A
HOH
10
4
HOH
HOH
408
A
HOH
11
4
HOH
HOH
409
A
HOH
12
4
HOH
HOH
410
A
HOH
13
4
HOH
HOH
411
A
HOH
14
4
HOH
HOH
412
A
HOH
15
4
HOH
HOH
413
A
HOH
16
4
HOH
HOH
414
A
HOH
17
4
HOH
HOH
415
A
HOH
18
4
HOH
HOH
416
A
HOH
19
4
HOH
HOH
417
A
HOH
20
4
HOH
HOH
418
A
HOH
21
4
HOH
HOH
419
A
HOH
22
4
HOH
HOH
420
A
HOH
23
4
HOH
HOH
421
A
HOH
24
4
HOH
HOH
422
A
HOH
26
4
HOH
HOH
423
A
HOH
27
4
HOH
HOH
424
A
HOH
28
4
HOH
HOH
425
A
HOH
29
4
HOH
HOH
426
A
HOH
30
4
HOH
HOH
427
A
HOH
31
4
HOH
HOH
428
A
HOH
32
4
HOH
HOH
429
A
HOH
34
4
HOH
HOH
430
A
HOH
35
4
HOH
HOH
431
A
HOH
36
4
HOH
HOH
432
A
HOH
37
4
HOH
HOH
433
A
HOH
39
4
HOH
HOH
434
A
HOH
40
4
HOH
HOH
435
A
HOH
41
4
HOH
HOH
436
A
HOH
43
4
HOH
HOH
437
A
HOH
44
4
HOH
HOH
438
A
HOH
45
4
HOH
HOH
439
A
HOH
46
4
HOH
HOH
440
A
HOH
47
4
HOH
HOH
441
A
HOH
48
4
HOH
HOH
442
A
HOH
49
4
HOH
HOH
443
A
HOH
50
4
HOH
HOH
444
A
HOH
51
4
HOH
HOH
445
A
HOH
52
4
HOH
HOH
446
A
HOH
53
4
HOH
HOH
447
A
HOH
54
4
HOH
HOH
448
A
HOH
55
4
HOH
HOH
449
A
HOH
56
4
HOH
HOH
450
A
HOH
58
4
HOH
HOH
451
A
HOH
59
4
HOH
HOH
452
A
HOH
60
4
HOH
HOH
453
A
HOH
61
4
HOH
HOH
454
A
HOH
63
4
HOH
HOH
455
A
HOH
64
4
HOH
HOH
456
A
HOH
65
4
HOH
HOH
457
A
HOH
66
4
HOH
HOH
458
A
HOH
67
4
HOH
HOH
459
A
HOH
68
4
HOH
HOH
460
A
HOH
69
4
HOH
HOH
461
A
HOH
70
4
HOH
HOH
462
A
HOH
71
4
HOH
HOH
463
A
HOH
72
4
HOH
HOH
464
A
HOH
74
4
HOH
HOH
465
A
HOH
75
4
HOH
HOH
466
A
HOH
76
4
HOH
HOH
467
A
HOH
77
4
HOH
HOH
468
A
HOH
78
4
HOH
HOH
469
A
HOH
79
4
HOH
HOH
470
A
HOH
80
4
HOH
HOH
471
A
HOH
82
4
HOH
HOH
472
A
HOH
83
4
HOH
HOH
473
A
HOH
84
4
HOH
HOH
474
A
HOH
85
4
HOH
HOH
475
A
HOH
86
4
HOH
HOH
476
A
HOH
87
4
HOH
HOH
477
A
HOH
88
4
HOH
HOH
478
A
HOH
89
4
HOH
HOH
479
A
HOH
90
4
HOH
HOH
480
A
HOH
91
4
HOH
HOH
481
A
HOH
92
4
HOH
HOH
482
A
HOH
94
4
HOH
HOH
483
A
HOH
95
4
HOH
HOH
484
A
HOH
98
4
HOH
HOH
485
A
HOH
99
4
HOH
HOH
486
A
HOH
100
4
HOH
HOH
487
A
HOH
101
4
HOH
HOH
488
A
HOH
102
4
HOH
HOH
489
A
HOH
103
4
HOH
HOH
490
A
HOH
104
4
HOH
HOH
491
A
HOH
105
4
HOH
HOH
492
A
HOH
106
4
HOH
HOH
493
A
HOH
107
4
HOH
HOH
494
A
HOH
108
4
HOH
HOH
495
A
HOH
109
4
HOH
HOH
496
A
HOH
111
4
HOH
HOH
497
A
HOH
114
4
HOH
HOH
498
A
HOH
115
4
HOH
HOH
499
A
HOH
116
4
HOH
HOH
500
A
HOH
118
4
HOH
HOH
501
A
HOH
119
4
HOH
HOH
502
A
HOH
120
4
HOH
HOH
503
A
HOH
121
4
HOH
HOH
504
A
HOH
122
4
HOH
HOH
505
A
HOH
123
4
HOH
HOH
506
A
HOH
126
4
HOH
HOH
507
A
HOH
127
4
HOH
HOH
508
A
HOH
128
4
HOH
HOH
509
A
HOH
129
4
HOH
HOH
510
A
HOH
130
4
HOH
HOH
511
A
HOH
131
4
HOH
HOH
512
A
HOH
132
4
HOH
HOH
513
A
HOH
133
4
HOH
HOH
514
A
HOH
134
4
HOH
HOH
515
A
HOH
135
4
HOH
HOH
516
A
HOH
136
4
HOH
HOH
517
A
HOH
137
4
HOH
HOH
518
A
HOH
138
4
HOH
HOH
519
A
HOH
139
4
HOH
HOH
520
A
HOH
141
4
HOH
HOH
521
A
HOH
142
4
HOH
HOH
522
A
HOH
143
4
HOH
HOH
523
A
HOH
144
4
HOH
HOH
524
A
HOH
145
4
HOH
HOH
525
A
HOH
147
4
HOH
HOH
526
A
HOH
148
4
HOH
HOH
527
A
HOH
149
4
HOH
HOH
528
A
HOH
150
4
HOH
HOH
529
A
HOH
151
4
HOH
HOH
530
A
HOH
154
4
HOH
HOH
531
A
HOH
155
4
HOH
HOH
532
A
HOH
156
4
HOH
HOH
533
A
HOH
157
4
HOH
HOH
534
A
HOH
158
4
HOH
HOH
535
A
HOH
159
4
HOH
HOH
536
A
HOH
160
4
HOH
HOH
537
A
HOH
161
4
HOH
HOH
538
A
HOH
162
4
HOH
HOH
539
A
HOH
163
4
HOH
HOH
540
A
HOH
166
4
HOH
HOH
541
A
HOH
125
4
HOH
HOH
542
A
HOH
6
4
HOH
HOH
201
B
HOH
9
4
HOH
HOH
202
B
HOH
25
4
HOH
HOH
203
B
HOH
33
4
HOH
HOH
204
B
HOH
38
4
HOH
HOH
205
B
HOH
42
4
HOH
HOH
206
B
HOH
57
4
HOH
HOH
207
B
HOH
62
4
HOH
HOH
208
B
HOH
73
4
HOH
HOH
209
B
HOH
81
4
HOH
HOH
210
B
HOH
93
4
HOH
HOH
211
B
HOH
96
4
HOH
HOH
212
B
HOH
97
4
HOH
HOH
213
B
HOH
110
4
HOH
HOH
214
B
HOH
112
4
HOH
HOH
215
B
HOH
113
4
HOH
HOH
216
B
HOH
117
4
HOH
HOH
217
B
HOH
124
4
HOH
HOH
218
B
HOH
140
4
HOH
HOH
219
B
HOH
146
4
HOH
HOH
220
B
HOH
152
4
HOH
HOH
221
B
HOH
153
4
HOH
HOH
222
B
HOH
164
4
HOH
HOH
223
B
HOH
165
4
HOH
HOH
224
B
HOH
167
4
HOH
HOH
225
B
HOH
168
4
HOH
HOH
226
B
n
1
-19
A
n
2
-18
A
n
3
-17
A
n
4
-16
A
n
5
-15
A
n
6
-14
A
n
7
-13
A
n
8
-12
A
n
9
-11
A
n
10
-10
A
n
11
-9
A
n
12
-8
A
n
13
-7
A
n
14
-6
A
n
15
-5
A
n
16
-4
A
n
17
-3
A
n
18
-2
A
n
19
-1
A
n
20
0
A
n
21
1
A
n
22
2
A
n
23
3
A
n
24
4
A
n
25
5
A
n
26
6
A
n
27
7
A
THR
8
n
28
THR
8
A
GLY
9
n
29
GLY
9
A
LEU
10
n
30
LEU
10
A
CYS
11
n
31
CYS
11
A
ASP
12
n
32
ASP
12
A
ARG
13
n
33
ARG
13
A
PHE
14
n
34
PHE
14
A
ARG
15
n
35
ARG
15
A
GLY
16
n
36
GLY
16
A
PHE
17
n
37
PHE
17
A
TYR
18
n
38
TYR
18
A
PRO
19
n
39
PRO
19
A
VAL
20
n
40
VAL
20
A
VAL
21
n
41
VAL
21
A
ILE
22
n
42
ILE
22
A
ASP
23
n
43
ASP
23
A
VAL
24
n
44
VAL
24
A
GLU
25
n
45
GLU
25
A
THR
26
n
46
THR
26
A
ALA
27
n
47
ALA
27
A
GLY
28
n
48
GLY
28
A
PHE
29
n
49
PHE
29
A
ASN
30
n
50
ASN
30
A
ALA
31
n
51
ALA
31
A
LYS
32
n
52
LYS
32
A
THR
33
n
53
THR
33
A
ASP
34
n
54
ASP
34
A
ALA
35
n
55
ALA
35
A
LEU
36
n
56
LEU
36
A
LEU
37
n
57
LEU
37
A
GLU
38
n
58
GLU
38
A
ILE
39
n
59
ILE
39
A
ALA
40
n
60
ALA
40
A
ALA
41
n
61
ALA
41
A
ILE
42
n
62
ILE
42
A
THR
43
n
63
THR
43
A
LEU
44
n
64
LEU
44
A
LYS
45
n
65
LYS
45
A
MET
46
n
66
MET
46
A
ASP
47
n
67
ASP
47
A
GLU
48
n
68
GLU
48
A
GLN
49
n
69
GLN
49
A
GLY
50
n
70
GLY
50
A
TRP
51
n
71
TRP
51
A
LEU
52
n
72
LEU
52
A
MET
53
n
73
MET
53
A
PRO
54
n
74
PRO
54
A
ASP
55
n
75
ASP
55
A
THR
56
n
76
THR
56
A
THR
57
n
77
THR
57
A
LEU
58
n
78
LEU
58
A
HIS
59
n
79
HIS
59
A
PHE
60
n
80
PHE
60
A
HIS
61
n
81
HIS
61
A
VAL
62
n
82
VAL
62
A
GLU
63
n
83
GLU
63
A
PRO
64
n
84
PRO
64
A
PHE
65
n
85
PHE
65
A
VAL
66
n
86
VAL
66
A
GLY
67
n
87
GLY
67
A
ALA
68
n
88
ALA
68
A
ASN
69
n
89
ASN
69
A
LEU
70
n
90
LEU
70
A
GLN
71
n
91
GLN
71
A
PRO
72
n
92
PRO
72
A
GLU
73
n
93
GLU
73
A
ALA
74
n
94
ALA
74
A
LEU
75
n
95
LEU
75
A
ALA
76
n
96
ALA
76
A
PHE
77
n
97
PHE
77
A
ASN
78
n
98
ASN
78
A
GLY
79
n
99
GLY
79
A
ILE
80
n
100
ILE
80
A
ASP
81
n
101
ASP
81
A
PRO
82
n
102
PRO
82
A
ASN
83
n
103
ASN
83
A
ASP
84
n
104
ASP
84
A
PRO
85
n
105
PRO
85
A
ASP
86
n
106
ASP
86
A
ARG
87
n
107
ARG
87
A
GLY
88
n
108
GLY
88
A
ALA
89
n
109
ALA
89
A
VAL
90
n
110
VAL
90
A
SER
91
n
111
SER
91
A
GLU
92
n
112
GLU
92
A
TYR
93
n
113
TYR
93
A
GLU
94
n
114
GLU
94
A
ALA
95
n
115
ALA
95
A
LEU
96
n
116
LEU
96
A
HIS
97
n
117
HIS
97
A
GLU
98
n
118
GLU
98
A
ILE
99
n
119
ILE
99
A
PHE
100
n
120
PHE
100
A
LYS
101
n
121
LYS
101
A
VAL
102
n
122
VAL
102
A
VAL
103
n
123
VAL
103
A
ARG
104
n
124
ARG
104
A
LYS
105
n
125
LYS
105
A
GLY
106
n
126
GLY
106
A
ILE
107
n
127
ILE
107
A
LYS
108
n
128
LYS
108
A
ALA
109
n
129
ALA
109
A
SER
110
n
130
SER
110
A
GLY
111
n
131
GLY
111
A
CYS
112
n
132
CYS
112
A
ASN
113
n
133
ASN
113
A
ARG
114
n
134
ARG
114
A
ALA
115
n
135
ALA
115
A
ILE
116
n
136
ILE
116
A
MET
117
n
137
MET
117
A
VAL
118
n
138
VAL
118
A
ALA
119
n
139
ALA
119
A
HIS
120
n
140
HIS
120
A
ASN
121
n
141
ASN
121
A
ALA
122
n
142
ALA
122
A
ASN
123
n
143
ASN
123
A
PHE
124
n
144
PHE
124
A
ASP
125
n
145
ASP
125
A
HIS
126
n
146
HIS
126
A
SER
127
n
147
SER
127
A
PHE
128
n
148
PHE
128
A
MET
129
n
149
MET
129
A
MET
130
n
150
MET
130
A
ALA
131
n
151
ALA
131
A
ALA
132
n
152
ALA
132
A
ALA
133
n
153
ALA
133
A
GLU
134
n
154
GLU
134
A
ARG
135
n
155
ARG
135
A
ALA
136
n
156
ALA
136
A
SER
137
n
157
SER
137
A
LEU
138
n
158
LEU
138
A
LYS
139
n
159
LYS
139
A
ARG
140
n
160
ARG
140
A
ASN
141
n
161
ASN
141
A
PRO
142
n
162
PRO
142
A
PHE
143
n
163
PHE
143
A
HIS
144
n
164
HIS
144
A
PRO
145
n
165
PRO
145
A
PHE
146
n
166
PHE
146
A
ALA
147
n
167
ALA
147
A
THR
148
n
168
THR
148
A
PHE
149
n
169
PHE
149
A
ASP
150
n
170
ASP
150
A
THR
151
n
171
THR
151
A
ALA
152
n
172
ALA
152
A
ALA
153
n
173
ALA
153
A
LEU
154
n
174
LEU
154
A
ALA
155
n
175
ALA
155
A
GLY
156
n
176
GLY
156
A
LEU
157
n
177
LEU
157
A
ALA
158
n
178
ALA
158
A
LEU
159
n
179
LEU
159
A
GLY
160
n
180
GLY
160
A
GLN
161
n
181
GLN
161
A
THR
162
n
182
THR
162
A
VAL
163
n
183
VAL
163
A
LEU
164
n
184
LEU
164
A
SER
165
n
185
SER
165
A
LYS
166
n
186
LYS
166
A
ALA
167
n
187
ALA
167
A
CYS
168
n
188
CYS
168
A
GLN
169
n
189
GLN
169
A
THR
170
n
190
THR
170
A
ALA
171
n
191
ALA
171
A
GLY
172
n
192
GLY
172
A
MET
173
n
193
MET
173
A
ASP
174
n
194
ASP
174
A
PHE
175
n
195
PHE
175
A
ASP
176
n
196
ASP
176
A
SER
177
n
197
SER
177
A
THR
178
n
198
THR
178
A
GLN
179
n
199
GLN
179
A
ALA
180
n
200
ALA
180
A
HIS
181
n
201
HIS
181
A
SER
182
n
202
SER
182
A
ALA
183
n
203
ALA
183
A
LEU
184
n
204
LEU
184
A
TYR
185
n
205
TYR
185
A
ASP
186
n
206
ASP
186
A
THR
187
n
207
THR
187
A
GLU
188
n
208
GLU
188
A
ARG
189
n
209
ARG
189
A
THR
190
n
210
THR
190
A
ALA
191
n
211
ALA
191
A
VAL
192
n
212
VAL
192
A
LEU
193
n
213
LEU
193
A
PHE
194
n
214
PHE
194
A
CYS
195
n
215
CYS
195
A
GLU
196
n
216
GLU
196
A
ILE
197
n
217
ILE
197
A
VAL
198
n
218
VAL
198
A
ASN
199
n
219
ASN
199
A
ARG
200
n
220
ARG
200
A
TRP
201
n
221
TRP
201
A
LYS
202
n
222
LYS
202
A
ARG
203
n
223
ARG
203
A
LEU
204
n
224
LEU
204
A
GLY
205
n
225
GLY
205
A
GLY
206
n
226
GLY
206
A
TRP
207
n
227
TRP
207
A
PRO
208
n
228
PRO
208
A
LEU
209
n
229
LEU
209
A
SER
210
n
230
SER
210
A
ALA
211
n
231
ALA
211
A
ALA
212
n
232
ALA
212
A
GLU
213
n
233
GLU
213
A
n
234
214
A
n
235
215
A
DT
1
n
1
DT
1
B
DT
2
n
2
DT
2
B
DG
3
n
3
DG
3
B
DG
4
n
4
DG
4
B
DC
5
n
5
DC
5
B
DC
6
n
6
DC
6
B
DC
7
n
7
DC
7
B
n
8
8
B
n
9
9
B
n
10
10
B
n
11
11
B
n
12
12
B
DA
13
n
13
DA
13
B
DG
14
n
14
DG
14
B
DG
15
n
15
DG
15
B
DG
16
n
16
DG
16
B
DC
17
n
17
DC
17
B
DC
18
n
18
DC
18
B
DC
19
n
19
DC
19
B
DC
20
n
20
DC
20
B
author_and_software_defined_assembly
PISA
2
dimeric
1880
-33
12070
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
409
E
O
HOH
1_555
97.5
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
410
E
O
HOH
1_555
99.0
A
HOH
409
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
410
E
O
HOH
1_555
99.9
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
419
E
O
HOH
1_555
78.0
A
HOH
409
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
419
E
O
HOH
1_555
175.3
A
HOH
410
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
A
HOH
419
E
O
HOH
1_555
79.9
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
B
DC
19
B
O3'
DC
19
1_555
150.5
A
HOH
409
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
19
B
O3'
DC
19
1_555
93.1
A
HOH
410
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
19
B
O3'
DC
19
1_555
106.1
A
HOH
419
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
19
B
O3'
DC
19
1_555
91.4
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
96.6
A
HOH
409
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
86.5
A
HOH
410
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
162.1
A
HOH
419
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
95.1
B
DC
19
B
O3'
DC
19
1_555
B
MG
101
D
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
56.6
A
GLU
25
A
OE1
GLU
45
1_555
A
MG
301
C
MG
MG
1_555
A
ASP
186
A
OD2
ASP
206
1_555
117.1
A
GLU
25
A
OE1
GLU
45
1_555
A
MG
301
C
MG
MG
1_555
A
HOH
429
E
O
HOH
1_555
156.4
A
ASP
186
A
OD2
ASP
206
1_555
A
MG
301
C
MG
MG
1_555
A
HOH
429
E
O
HOH
1_555
83.5
A
GLU
25
A
OE1
GLU
45
1_555
A
MG
301
C
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
108.0
A
ASP
186
A
OD2
ASP
206
1_555
A
MG
301
C
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
95.4
A
HOH
429
E
O
HOH
1_555
A
MG
301
C
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
79.5
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
A
O
LEU
58
A
O
LEU
78
A
N
ALA
41
A
N
ALA
61
A
O
ILE
42
A
O
ILE
62
A
N
VAL
21
A
N
VAL
41
A
N
TYR
18
A
N
TYR
38
A
O
ARG
114
A
O
ARG
134
A
N
MET
117
A
N
MET
137
A
O
PHE
149
A
O
PHE
169
1
A
HOH
408
E
HOH
1
A
MET
-19
A
MET
1
1
Y
1
A
GLY
-18
A
GLY
2
1
Y
1
A
SER
-17
A
SER
3
1
Y
1
A
SER
-16
A
SER
4
1
Y
1
A
HIS
-15
A
HIS
5
1
Y
1
A
HIS
-14
A
HIS
6
1
Y
1
A
HIS
-13
A
HIS
7
1
Y
1
A
HIS
-12
A
HIS
8
1
Y
1
A
HIS
-11
A
HIS
9
1
Y
1
A
HIS
-10
A
HIS
10
1
Y
1
A
SER
-9
A
SER
11
1
Y
1
A
SER
-8
A
SER
12
1
Y
1
A
GLY
-7
A
GLY
13
1
Y
1
A
LEU
-6
A
LEU
14
1
Y
1
A
VAL
-5
A
VAL
15
1
Y
1
A
PRO
-4
A
PRO
16
1
Y
1
A
ARG
-3
A
ARG
17
1
Y
1
A
GLY
-2
A
GLY
18
1
Y
1
A
SER
-1
A
SER
19
1
Y
1
A
HIS
0
A
HIS
20
1
Y
1
A
MET
1
A
MET
21
1
Y
1
A
SER
2
A
SER
22
1
Y
1
A
ASP
3
A
ASP
23
1
Y
1
A
ASN
4
A
ASN
24
1
Y
1
A
ALA
5
A
ALA
25
1
Y
1
A
GLN
6
A
GLN
26
1
Y
1
A
LEU
7
A
LEU
27
1
Y
1
A
GLU
214
A
GLU
234
1
Y
1
A
VAL
215
A
VAL
235
1
Y
1
B
DT
8
B
DT
8
1
Y
1
B
DC
9
B
DC
9
1
Y
1
B
DT
10
B
DT
10
1
Y
1
B
DT
11
B
DT
11
1
Y
1
B
DT
12
B
DT
12
1
Y
1
A
A
O
O
LYS
HOH
108
510
1.93
1
B
B
O
O
HOH
HOH
224
226
1.99
1
A
A
O
O
HOH
HOH
513
536
2.03
1
A
A
O
O
HOH
HOH
496
508
2.09
1
A
A
O
O
HOH
HOH
501
522
2.11
1
A
A
O
O
HOH
HOH
411
539
2.12
1
A
A
O
O
HOH
HOH
520
523
2.13
1
A
B
O
O
HOH
HOH
506
204
2.13
1
A
A
O
O
HOH
HOH
482
493
2.15
1
2.15
0.30
108.30
110.45
B
B
B
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
-5.24
0.80
109.40
104.16
B
B
B
O5'
C5'
C4'
DT
DT
DT
2
2
2
N
1
-5.84
0.70
102.20
96.36
B
B
B
C4'
C3'
C2'
DT
DT
DT
2
2
2
N
1
-4.83
0.80
102.40
97.57
B
B
B
C3'
C2'
C1'
DG
DG
DG
14
14
14
N
1
1.98
0.30
108.30
110.28
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
3.76
0.30
108.30
112.06
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
3.99
0.30
108.30
112.29
B
B
B
O4'
C1'
N1
DC
DC
DC
19
19
19
N
1
A
ASP
55
-113.76
-95.86
1
A
PHE
146
-142.13
-18.26
1
A
HIS
181
73.08
38.26
0.2185
0.1889
0.1904
0.1904
1.900
28.767
1072
20916
20916
5.13
99.97
0.18
RANDOM
1
0.00
MOLECULAR REPLACEMENT
19.69
0.90
1.11
3NGY
ML
FLAT BULK SOLVENT MODEL
1.900
28.767
168
2056
2
301
1585
0.007
1958
1.148
2715
19.102
716
0.077
302
0.005
305
0.2523
0.2297
1.9866
137
2435
100.00
0.2409
0.2150
2.0913
119
2460
100.00
0.2665
0.2103
2.2223
142
2434
100.00
0.2441
0.1975
2.3938
151
2418
100.00
0.2599
0.2028
2.6345
132
2465
100.00
0.2338
0.1969
3.0154
119
2486
100.00
0.2218
0.1741
3.7977
125
2525
100.00
0.1695
0.1707
28.7702
147
2621
100.00
1.9
30.0
4KAZ
20966
20966
0
0
0.091
1
32.23
8.5
100.0
1.90
1.97
3.92
2070
0.457
1
7.7
100
data collection
HKL-2000
phasing
AMoRE
refinement
PHENIX
(phenix.refine: 1.8.1_1168)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of RNase T in complex with a Y structured DNA
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
GLY
9
A
GLY
29
HELX_P
A
PHE
14
A
PHE
34
1
1
6
A
GLN
71
A
GLN
91
HELX_P
A
GLY
79
A
GLY
99
1
2
9
A
SER
91
A
SER
111
HELX_P
A
GLY
111
A
GLY
131
1
3
21
A
ALA
122
A
ALA
142
HELX_P
A
ALA
136
A
ALA
156
1
4
15
A
THR
151
A
THR
171
HELX_P
A
GLY
160
A
GLY
180
1
5
10
A
VAL
163
A
VAL
183
HELX_P
A
ALA
171
A
ALA
191
1
6
9
A
SER
182
A
SER
202
HELX_P
A
LEU
204
A
LEU
224
1
7
23
metalc
2.293
A
ASP
23
A
OD1
ASP
43
1_555
B
MG
101
D
MG
MG
1_555
metalc
2.373
A
GLU
25
A
OE1
GLU
45
1_555
A
MG
301
C
MG
MG
1_555
metalc
2.289
A
ASP
186
A
OD2
ASP
206
1_555
A
MG
301
C
MG
MG
1_555
metalc
2.547
A
MG
301
C
MG
MG
1_555
A
HOH
429
E
O
HOH
1_555
metalc
2.105
A
MG
301
C
MG
MG
1_555
B
DC
20
B
OP1
DC
20
1_555
metalc
2.245
A
HOH
409
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
metalc
2.318
A
HOH
410
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
metalc
2.442
A
HOH
419
E
O
HOH
1_555
B
MG
101
D
MG
MG
1_555
metalc
2.435
B
DC
19
B
O3'
DC
19
1_555
B
MG
101
D
MG
MG
1_555
metalc
2.657
B
DC
20
B
OP1
DC
20
1_555
B
MG
101
D
MG
MG
1_555
hydrog
WATSON-CRICK
B
DG
3
B
N1
DG
3
1_555
B
DC
18
B
N3
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
3
B
N2
DG
3
1_555
B
DC
18
B
O2
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
3
B
O6
DG
3
1_555
B
DC
18
B
N4
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N1
DG
4
1_555
B
DC
17
B
N3
DC
17
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N2
DG
4
1_555
B
DC
17
B
O2
DC
17
1_555
hydrog
WATSON-CRICK
B
DG
4
B
O6
DG
4
1_555
B
DC
17
B
N4
DC
17
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N3
DC
5
1_555
B
DG
16
B
N1
DG
16
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N4
DC
5
1_555
B
DG
16
B
O6
DG
16
1_555
hydrog
WATSON-CRICK
B
DC
5
B
O2
DC
5
1_555
B
DG
16
B
N2
DG
16
1_555
hydrog
WATSON-CRICK
B
DC
6
B
N3
DC
6
1_555
B
DG
15
B
N1
DG
15
1_555
hydrog
WATSON-CRICK
B
DC
6
B
N4
DC
6
1_555
B
DG
15
B
O6
DG
15
1_555
hydrog
WATSON-CRICK
B
DC
6
B
O2
DC
6
1_555
B
DG
15
B
N2
DG
15
1_555
hydrog
WATSON-CRICK
B
DC
7
B
N3
DC
7
1_555
B
DG
14
B
N1
DG
14
1_555
hydrog
WATSON-CRICK
B
DC
7
B
N4
DC
7
1_555
B
DG
14
B
O6
DG
14
1_555
hydrog
WATSON-CRICK
B
DC
7
B
O2
DC
7
1_555
B
DG
14
B
N2
DG
14
1_555
Hydrolase/dna
DnaQ, DEDD, exonuclease, DNA repair, Hydrolase-dna complex
A
TRP
207
A
TRP
227
1
A
PRO
208
A
PRO
228
-6.59
RNT_ECOLI
UNP
1
1
P30014
MSDNAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGI
DPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALG
QTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAAEEV
4KAZ
PDB
2
4KAZ
1
215
4KAZ
1
215
P30014
A
1
21
235
1
20
4KAZ
1
20
4KAZ
B
2
1
20
1
initiating methionine
MET
-19
4KAZ
A
P30014
UNP
1
1
expression tag
GLY
-18
4KAZ
A
P30014
UNP
2
1
expression tag
SER
-17
4KAZ
A
P30014
UNP
3
1
expression tag
SER
-16
4KAZ
A
P30014
UNP
4
1
expression tag
HIS
-15
4KAZ
A
P30014
UNP
5
1
expression tag
HIS
-14
4KAZ
A
P30014
UNP
6
1
expression tag
HIS
-13
4KAZ
A
P30014
UNP
7
1
expression tag
HIS
-12
4KAZ
A
P30014
UNP
8
1
expression tag
HIS
-11
4KAZ
A
P30014
UNP
9
1
expression tag
HIS
-10
4KAZ
A
P30014
UNP
10
1
expression tag
SER
-9
4KAZ
A
P30014
UNP
11
1
expression tag
SER
-8
4KAZ
A
P30014
UNP
12
1
expression tag
GLY
-7
4KAZ
A
P30014
UNP
13
1
expression tag
LEU
-6
4KAZ
A
P30014
UNP
14
1
expression tag
VAL
-5
4KAZ
A
P30014
UNP
15
1
expression tag
PRO
-4
4KAZ
A
P30014
UNP
16
1
expression tag
ARG
-3
4KAZ
A
P30014
UNP
17
1
expression tag
GLY
-2
4KAZ
A
P30014
UNP
18
1
expression tag
SER
-1
4KAZ
A
P30014
UNP
19
1
expression tag
HIS
0
4KAZ
A
P30014
UNP
20
5
anti-parallel
anti-parallel
parallel
parallel
A
LEU
52
A
LEU
72
A
HIS
61
A
HIS
81
A
LEU
36
A
LEU
56
A
MET
46
A
MET
66
A
PHE
17
A
PHE
37
A
THR
26
A
THR
46
A
ARG
114
A
ARG
134
A
ALA
119
A
ALA
139
A
PHE
143
A
PHE
163
A
ASP
150
A
ASP
170
BINDING SITE FOR RESIDUE MG A 301
A
MG
301
Software
5
BINDING SITE FOR RESIDUE MG B 101
B
MG
101
Software
6
A
GLU
25
A
GLU
45
5
1_555
A
HIS
181
A
HIS
201
5
1_555
A
ASP
186
A
ASP
206
5
1_555
A
HOH
429
E
HOH
5
1_555
B
DC
20
B
DC
20
5
1_555
A
ASP
23
A
ASP
43
6
1_555
A
HOH
409
E
HOH
6
1_555
A
HOH
410
E
HOH
6
1_555
A
HOH
419
E
HOH
6
1_555
B
DC
19
B
DC
19
6
1_555
B
DC
20
B
DC
20
6
1_555
18
P 21 21 2