0.012398
0.000000
0.001435
0.000000
0.026442
0.000000
0.000000
0.000000
0.016253
0.00000
0.00000
0.00000
Rob, A.
Gerlits, O.
Jiang, J.S.
Gan, J.H.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
96.60
90.00
80.660
37.819
61.937
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
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 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
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
O4 P -3
94.971
PHOSPHATE ION
non-polymer
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C10 H14 N5 O6 P Se
410.182
n
2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purine-6-selenol
DNA 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
O
N
147
N
P
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
C
N
152
R
C
N
153
N
O
N
154
S
C
N
155
N
O
N
156
N
C
N
157
R
C
Y
158
N
N
Y
159
N
C
Y
160
N
N
Y
161
N
C
Y
162
N
C
N
163
N
N
Y
164
N
N
Y
165
N
C
Y
166
N
N
Y
167
N
C
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
O
N
183
N
P
N
184
N
O
N
185
N
O
N
186
N
O
N
187
N
C
N
188
R
C
N
189
N
O
N
190
S
C
N
191
N
O
N
192
N
C
N
193
R
C
N
194
N
N
N
195
N
C
N
196
N
O
N
197
N
N
N
198
N
C
N
199
N
N
N
200
N
C
N
201
N
C
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
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
O
N
217
N
P
N
218
N
O
N
219
N
O
N
220
N
O
N
221
N
C
N
222
R
C
N
223
N
O
N
224
S
C
N
225
N
O
N
226
N
C
N
227
R
C
N
228
N
N
N
229
N
C
N
230
N
O
N
231
N
N
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
C
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
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
H
N
252
N
O
N
253
N
P
N
254
N
O
N
255
N
O
N
256
N
O
N
257
N
C
N
258
R
C
N
259
N
O
N
260
S
C
N
261
N
O
N
262
R
C
N
263
N
O
N
264
R
C
Y
265
N
N
Y
266
N
C
Y
267
N
N
Y
268
N
C
N
269
N
C
N
270
N
O
N
271
N
N
N
272
N
C
N
273
N
N
N
274
N
N
Y
275
N
C
N
276
N
H
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
O
N
298
N
N
N
299
N
O
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
N
N
311
S
C
N
312
N
C
N
313
N
O
N
314
N
C
N
315
N
C
N
316
N
C
N
317
N
O
N
318
N
O
N
319
N
O
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
H
N
327
N
H
N
328
N
H
N
329
N
N
N
330
N
C
N
331
N
C
N
332
N
O
N
333
N
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
N
C
Y
344
N
C
Y
345
N
N
Y
346
N
C
Y
347
N
C
Y
348
N
N
N
349
N
O
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
H
N
358
N
H
N
359
N
H
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
S
C
N
368
N
C
N
369
N
C
N
370
N
C
N
371
N
O
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
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
N
C
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
O
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
N
C
N
412
N
C
N
413
N
C
N
414
N
C
N
415
N
N
N
416
N
O
N
417
N
H
N
418
N
H
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
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
N
437
N
C
N
438
N
S
N
439
N
C
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
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
MG
N
453
N
N
N
454
S
C
N
455
N
C
N
456
N
O
N
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
N
464
N
O
N
465
N
H
N
466
N
H
N
467
N
H
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
P
N
477
N
O
N
478
N
O
N
479
N
O
N
480
N
O
N
481
N
N
N
482
S
C
N
483
N
C
N
484
N
O
N
485
N
C
N
486
N
C
N
487
N
C
N
488
N
O
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
O
Y
499
N
C
N
500
N
P
N
501
N
O
N
502
N
O
N
503
N
O
Y
504
N
N
Y
505
N
C
Y
506
N
N
N
507
N
N
Y
508
N
N
Y
509
N
C
N
510
N
SE
Y
511
N
C
Y
512
N
N
Y
513
N
C
N
514
N
C
N
515
N
C
N
516
R
C
N
517
N
O
N
518
R
C
N
519
S
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
532
N
H
N
533
N
H
N
534
N
H
N
535
N
N
N
536
S
C
N
537
N
C
N
538
N
O
N
539
N
C
N
540
N
O
N
541
N
O
N
542
N
H
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
N
N
550
S
C
N
551
N
C
N
552
N
O
N
553
R
C
N
554
N
O
N
555
N
C
N
556
N
O
N
557
N
H
N
558
N
H
N
559
N
H
N
560
N
H
N
561
N
H
N
562
N
H
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
N
N
567
S
C
N
568
N
C
N
569
N
O
N
570
N
C
Y
571
N
C
Y
572
N
C
Y
573
N
C
Y
574
N
N
Y
575
N
C
Y
576
N
C
Y
577
N
C
Y
578
N
C
Y
579
N
C
N
580
N
O
N
581
N
H
N
582
N
H
N
583
N
H
N
584
N
H
N
585
N
H
N
586
N
H
N
587
N
H
N
588
N
H
N
589
N
H
N
590
N
H
N
591
N
H
N
592
N
H
N
593
N
N
N
594
S
C
N
595
N
C
N
596
N
O
N
597
N
C
Y
598
N
C
Y
599
N
C
Y
600
N
C
Y
601
N
C
Y
602
N
C
Y
603
N
C
N
604
N
O
N
605
N
O
N
606
N
H
N
607
N
H
N
608
N
H
N
609
N
H
N
610
N
H
N
611
N
H
N
612
N
H
N
613
N
H
N
614
N
H
N
615
N
H
N
616
N
H
N
617
N
O
N
618
N
P
N
619
N
O
N
620
N
O
N
621
N
O
N
622
N
C
N
623
R
C
N
624
N
O
N
625
S
C
N
626
N
O
N
627
R
C
N
628
N
O
N
629
R
C
N
630
N
N
N
631
N
C
N
632
N
O
N
633
N
N
N
634
N
C
N
635
N
O
N
636
N
C
N
637
N
C
N
638
N
H
N
639
N
H
N
640
N
H
N
641
N
H
N
642
N
H
N
643
N
H
N
644
N
H
N
645
N
H
N
646
N
H
N
647
N
H
N
648
N
H
N
649
N
H
N
650
N
H
N
651
N
N
N
652
S
C
N
653
N
C
N
654
N
O
N
655
N
C
N
656
N
C
N
657
N
C
N
658
N
O
N
659
N
H
N
660
N
H
N
661
N
H
N
662
N
H
N
663
N
H
N
664
N
H
N
665
N
H
N
666
N
H
N
667
N
H
N
668
N
H
N
669
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
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
Y
168
N
sing
Y
169
N
sing
Y
170
N
doub
N
171
N
sing
Y
172
N
sing
Y
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
doub
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
doub
N
181
N
sing
Y
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
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
sing
N
208
N
doub
N
209
N
sing
N
210
N
doub
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
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
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
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
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
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
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
sing
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
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
Y
279
N
sing
Y
280
N
sing
Y
281
N
doub
N
282
N
sing
Y
283
N
sing
N
284
N
sing
Y
285
N
doub
N
286
N
doub
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
doub
N
292
N
sing
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
doub
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
doub
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
doub
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
doub
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
doub
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
Y
352
N
sing
Y
353
N
doub
Y
354
N
doub
N
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
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
doub
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
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
doub
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
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
sing
N
410
N
sing
N
411
N
sing
N
412
N
doub
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
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
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
doub
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
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
sing
N
454
N
sing
N
455
N
doub
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
Y
460
N
doub
Y
461
N
sing
Y
462
N
sing
N
463
N
sing
Y
464
N
doub
N
465
N
sing
Y
466
N
doub
N
467
N
sing
Y
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
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
doub
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
Y
495
N
doub
N
496
N
sing
Y
497
N
sing
N
498
N
doub
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
Y
504
N
sing
Y
505
N
sing
Y
506
N
sing
Y
507
N
doub
N
508
N
sing
N
509
N
sing
Y
510
N
doub
Y
511
N
sing
N
512
N
sing
Y
513
N
sing
Y
514
N
doub
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
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
sing
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
sing
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
doub
N
539
N
sing
N
540
N
sing
N
541
N
sing
N
542
N
sing
N
543
N
sing
N
544
N
sing
N
545
N
sing
N
546
N
sing
N
547
N
sing
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
doub
N
552
N
sing
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
sing
N
557
N
sing
N
558
N
sing
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
N
563
N
sing
N
564
N
sing
N
565
N
sing
N
566
N
sing
N
567
N
doub
N
568
N
sing
N
569
N
sing
N
570
N
sing
N
571
N
sing
Y
572
N
doub
Y
573
N
sing
Y
574
N
sing
N
575
N
sing
Y
576
N
doub
Y
577
N
sing
Y
578
N
sing
N
579
N
sing
Y
580
N
sing
Y
581
N
doub
N
582
N
sing
Y
583
N
doub
N
584
N
sing
Y
585
N
sing
N
586
N
sing
N
587
N
sing
N
588
N
sing
N
589
N
sing
N
590
N
sing
N
591
N
sing
N
592
N
sing
N
593
N
sing
N
594
N
sing
N
595
N
doub
N
596
N
sing
N
597
N
sing
N
598
N
sing
N
599
N
sing
Y
600
N
doub
Y
601
N
sing
Y
602
N
sing
N
603
N
sing
Y
604
N
doub
N
605
N
sing
Y
606
N
doub
N
607
N
sing
Y
608
N
sing
N
609
N
sing
N
610
N
sing
N
611
N
sing
N
612
N
sing
N
613
N
sing
N
614
N
sing
N
615
N
doub
N
616
N
sing
N
617
N
sing
N
618
N
sing
N
619
N
sing
N
620
N
sing
N
621
N
sing
N
622
N
sing
N
623
N
sing
N
624
N
sing
N
625
N
sing
N
626
N
sing
N
627
N
sing
N
628
N
sing
N
629
N
sing
N
630
N
sing
N
631
N
sing
N
632
N
sing
N
633
N
sing
N
634
N
sing
N
635
N
sing
N
636
N
sing
N
637
N
sing
N
638
N
sing
N
639
N
doub
N
640
N
sing
N
641
N
sing
N
642
N
sing
N
643
N
doub
N
644
N
sing
N
645
N
doub
N
646
N
sing
N
647
N
sing
N
648
N
sing
N
649
N
sing
N
650
N
sing
N
651
N
sing
N
652
N
sing
N
653
N
sing
N
654
N
doub
N
655
N
sing
N
656
N
sing
N
657
N
sing
N
658
N
sing
N
659
N
sing
N
660
N
sing
N
661
N
sing
N
662
N
sing
N
663
N
sing
N
664
N
sing
N
665
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
70
354
361
10.1107/S1399004713027922
24531469
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.
2014
10.2210/pdb3twh/pdb
pdb_00003twh
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
2006-08-12
ADSC QUANTUM 210
MIRRORS
MAD
M
x-ray
1
0.9797
1.0
0.9800
1.0
0.9795
1.0
X12C
NSLS
0.9797, 0.9800, 0.9795
SYNCHROTRON
NSLS BEAMLINE X12C
15916.004
Ribonuclease H
3.1.26.4
catalytic domain
D132N
1
man
polymer
1875.189
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
1
syn
polymer
1950.150
DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3')
1
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
18.015
water
136
nat
water
RNase H
no
no
AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIK
WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIK
WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
A
polypeptide(L)
no
no
UCGACA
UCGACA
B
polyribonucleotide
no
yes
(DA)(DT)(SDG)(DT)(DC)(SDG)
ATGTCG
C
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
sample
BH0863, rnhA
86665
Bacillus halodurans
866768
Escherichia coli
BL21-Gold(DE3)pLysS AG
PLASMID
PET15B
2.38
48.25
VAPOR DIFFUSION, HANGING DROP
6.5
0.1 M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
3.113
1
B
2
C
6
8.137
B_C2:SDG6_C
1
-17.264
0.335
0.064
0.200
-8.256
1
19
B
3
C
5
1.237
B_G3:DC5_C
2
-10.139
-0.289
-0.020
-0.116
-15.372
1
20
B
4
C
4
-1.992
B_A4:DT4_C
3
-8.888
0.016
-0.061
-0.149
-13.252
1
B
5
C
3
9.978
B_C5:SDG3_C
4
-3.134
0.147
0.273
0.317
-8.577
1
20
B
6
C
2
1.717
B_A6:DT2_C
5
-8.566
-0.085
-0.045
-0.082
2.775
26.778
B
B
2
3
21.017
C
C
6
5
3.550
9.527
-0.999
-1.590
BB_C2G3:DC5SDG6_CC
1
-0.179
0.395
25.054
-5.903
2.110
3.010
29.847
B
B
3
4
12.941
C
C
5
4
3.423
6.559
0.845
-2.010
BB_G3A4:DT4DC5_CC
2
6.617
-13.055
28.387
-5.279
-0.251
3.395
32.697
B
B
4
5
-3.532
C
C
4
3
3.297
-1.987
0.525
-1.492
BB_A4C5:SDG3DT4_CC
3
1.157
-2.056
32.618
-2.299
-0.727
3.243
21.558
B
B
5
6
1.681
C
C
3
2
3.312
0.613
0.600
-1.890
BB_C5A6:DT2SDG3_CC
4
8.091
-22.164
19.990
-5.309
1.772
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
1
0
2012-10-03
1
1
2014-02-12
1
2
2014-09-24
1
3
2024-02-28
_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_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.pdbx_leaving_atom_flag
_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
BACILLUS HALODURANS RNASE H CATALYTIC DOMAIN MUTANT D132N IN COMPLEX WITH 12-MER RNA/DNA HYBRID
B. HALODURANS RNASE H CATALYTIC DOMAIN D132N MUTANT IN COMPLEX WITH MG2+ AND RNA/DNA HYBRID
RCSB
Y
RCSB
2011-09-21
REL
REL
MG
MAGNESIUM ION
PO4
PHOSPHATE ION
HOH
water
MG
401
4
MG
MG
401
A
MG
402
4
MG
MG
402
A
PO4
7
5
PO4
PO4
7
C
HOH
1
6
HOH
HOH
1
A
HOH
2
6
HOH
HOH
2
A
HOH
3
6
HOH
HOH
3
A
HOH
4
6
HOH
HOH
4
A
HOH
5
6
HOH
HOH
5
A
HOH
6
6
HOH
HOH
6
A
HOH
7
6
HOH
HOH
7
A
HOH
8
6
HOH
HOH
8
A
HOH
9
6
HOH
HOH
9
A
HOH
10
6
HOH
HOH
10
A
HOH
11
6
HOH
HOH
11
A
HOH
12
6
HOH
HOH
12
A
HOH
13
6
HOH
HOH
13
A
HOH
14
6
HOH
HOH
14
A
HOH
15
6
HOH
HOH
15
A
HOH
16
6
HOH
HOH
16
A
HOH
17
6
HOH
HOH
17
A
HOH
18
6
HOH
HOH
18
A
HOH
20
6
HOH
HOH
20
A
HOH
21
6
HOH
HOH
21
A
HOH
22
6
HOH
HOH
22
A
HOH
24
6
HOH
HOH
24
A
HOH
25
6
HOH
HOH
25
A
HOH
28
6
HOH
HOH
28
A
HOH
30
6
HOH
HOH
30
A
HOH
31
6
HOH
HOH
31
A
HOH
32
6
HOH
HOH
32
A
HOH
33
6
HOH
HOH
33
A
HOH
34
6
HOH
HOH
34
A
HOH
35
6
HOH
HOH
35
A
HOH
36
6
HOH
HOH
36
A
HOH
37
6
HOH
HOH
37
A
HOH
38
6
HOH
HOH
38
A
HOH
39
6
HOH
HOH
39
A
HOH
40
6
HOH
HOH
40
A
HOH
41
6
HOH
HOH
41
A
HOH
42
6
HOH
HOH
42
A
HOH
44
6
HOH
HOH
44
A
HOH
45
6
HOH
HOH
45
A
HOH
46
6
HOH
HOH
46
A
HOH
47
6
HOH
HOH
47
A
HOH
48
6
HOH
HOH
48
A
HOH
49
6
HOH
HOH
49
A
HOH
50
6
HOH
HOH
50
A
HOH
51
6
HOH
HOH
51
A
HOH
53
6
HOH
HOH
53
A
HOH
54
6
HOH
HOH
54
A
HOH
55
6
HOH
HOH
55
A
HOH
57
6
HOH
HOH
57
A
HOH
58
6
HOH
HOH
58
A
HOH
59
6
HOH
HOH
197
A
HOH
60
6
HOH
HOH
198
A
HOH
61
6
HOH
HOH
199
A
HOH
62
6
HOH
HOH
200
A
HOH
63
6
HOH
HOH
201
A
HOH
64
6
HOH
HOH
202
A
HOH
66
6
HOH
HOH
203
A
HOH
67
6
HOH
HOH
204
A
HOH
70
6
HOH
HOH
205
A
HOH
71
6
HOH
HOH
206
A
HOH
72
6
HOH
HOH
207
A
HOH
73
6
HOH
HOH
208
A
HOH
74
6
HOH
HOH
209
A
HOH
75
6
HOH
HOH
210
A
HOH
76
6
HOH
HOH
211
A
HOH
78
6
HOH
HOH
212
A
HOH
79
6
HOH
HOH
213
A
HOH
80
6
HOH
HOH
214
A
HOH
82
6
HOH
HOH
215
A
HOH
83
6
HOH
HOH
216
A
HOH
84
6
HOH
HOH
217
A
HOH
85
6
HOH
HOH
218
A
HOH
86
6
HOH
HOH
219
A
HOH
87
6
HOH
HOH
220
A
HOH
88
6
HOH
HOH
221
A
HOH
90
6
HOH
HOH
222
A
HOH
93
6
HOH
HOH
223
A
HOH
94
6
HOH
HOH
224
A
HOH
95
6
HOH
HOH
225
A
HOH
96
6
HOH
HOH
226
A
HOH
97
6
HOH
HOH
227
A
HOH
98
6
HOH
HOH
228
A
HOH
99
6
HOH
HOH
229
A
HOH
100
6
HOH
HOH
230
A
HOH
101
6
HOH
HOH
231
A
HOH
102
6
HOH
HOH
232
A
HOH
103
6
HOH
HOH
233
A
HOH
104
6
HOH
HOH
234
A
HOH
105
6
HOH
HOH
235
A
HOH
106
6
HOH
HOH
236
A
HOH
109
6
HOH
HOH
237
A
HOH
110
6
HOH
HOH
238
A
HOH
111
6
HOH
HOH
239
A
HOH
113
6
HOH
HOH
240
A
HOH
114
6
HOH
HOH
241
A
HOH
116
6
HOH
HOH
242
A
HOH
117
6
HOH
HOH
243
A
HOH
118
6
HOH
HOH
244
A
HOH
119
6
HOH
HOH
245
A
HOH
120
6
HOH
HOH
246
A
HOH
121
6
HOH
HOH
247
A
HOH
122
6
HOH
HOH
248
A
HOH
124
6
HOH
HOH
249
A
HOH
125
6
HOH
HOH
250
A
HOH
127
6
HOH
HOH
251
A
HOH
128
6
HOH
HOH
252
A
HOH
129
6
HOH
HOH
253
A
HOH
130
6
HOH
HOH
254
A
HOH
131
6
HOH
HOH
255
A
HOH
133
6
HOH
HOH
256
A
HOH
134
6
HOH
HOH
257
A
HOH
135
6
HOH
HOH
258
A
HOH
136
6
HOH
HOH
259
A
HOH
19
6
HOH
HOH
19
B
HOH
23
6
HOH
HOH
23
B
HOH
29
6
HOH
HOH
29
B
HOH
56
6
HOH
HOH
56
B
HOH
65
6
HOH
HOH
65
B
HOH
68
6
HOH
HOH
68
B
HOH
69
6
HOH
HOH
69
B
HOH
81
6
HOH
HOH
81
B
HOH
89
6
HOH
HOH
89
B
HOH
91
6
HOH
HOH
91
B
HOH
92
6
HOH
HOH
92
B
HOH
132
6
HOH
HOH
132
B
HOH
26
6
HOH
HOH
26
C
HOH
27
6
HOH
HOH
27
C
HOH
43
6
HOH
HOH
43
C
HOH
52
6
HOH
HOH
52
C
HOH
77
6
HOH
HOH
77
C
HOH
107
6
HOH
HOH
107
C
HOH
108
6
HOH
HOH
108
C
HOH
112
6
HOH
HOH
112
C
HOH
115
6
HOH
HOH
115
C
HOH
123
6
HOH
HOH
123
C
HOH
126
6
HOH
HOH
126
C
n
1
59
A
n
2
60
A
GLU
61
n
3
GLU
61
A
GLU
62
n
4
GLU
62
A
ILE
63
n
5
ILE
63
A
ILE
64
n
6
ILE
64
A
TRP
65
n
7
TRP
65
A
GLU
66
n
8
GLU
66
A
SER
67
n
9
SER
67
A
LEU
68
n
10
LEU
68
A
SER
69
n
11
SER
69
A
VAL
70
n
12
VAL
70
A
ASP
71
n
13
ASP
71
A
VAL
72
n
14
VAL
72
A
GLY
73
n
15
GLY
73
A
SER
74
n
16
SER
74
A
GLN
75
n
17
GLN
75
A
GLY
76
n
18
GLY
76
A
ASN
77
n
19
ASN
77
A
PRO
78
n
20
PRO
78
A
GLY
79
n
21
GLY
79
A
ILE
80
n
22
ILE
80
A
VAL
81
n
23
VAL
81
A
GLU
82
n
24
GLU
82
A
TYR
83
n
25
TYR
83
A
LYS
84
n
26
LYS
84
A
GLY
85
n
27
GLY
85
A
VAL
86
n
28
VAL
86
A
ASP
87
n
29
ASP
87
A
THR
88
n
30
THR
88
A
LYS
89
n
31
LYS
89
A
THR
90
n
32
THR
90
A
GLY
91
n
33
GLY
91
A
GLU
92
n
34
GLU
92
A
VAL
93
n
35
VAL
93
A
LEU
94
n
36
LEU
94
A
PHE
95
n
37
PHE
95
A
GLU
96
n
38
GLU
96
A
ARG
97
n
39
ARG
97
A
GLU
98
n
40
GLU
98
A
PRO
99
n
41
PRO
99
A
ILE
100
n
42
ILE
100
A
PRO
101
n
43
PRO
101
A
ILE
102
n
44
ILE
102
A
GLY
103
n
45
GLY
103
A
THR
104
n
46
THR
104
A
ASN
105
n
47
ASN
105
A
ASN
106
n
48
ASN
106
A
MET
107
n
49
MET
107
A
GLY
108
n
50
GLY
108
A
GLU
109
n
51
GLU
109
A
PHE
110
n
52
PHE
110
A
LEU
111
n
53
LEU
111
A
ALA
112
n
54
ALA
112
A
ILE
113
n
55
ILE
113
A
VAL
114
n
56
VAL
114
A
HIS
115
n
57
HIS
115
A
GLY
116
n
58
GLY
116
A
LEU
117
n
59
LEU
117
A
ARG
118
n
60
ARG
118
A
TYR
119
n
61
TYR
119
A
LEU
120
n
62
LEU
120
A
LYS
121
n
63
LYS
121
A
GLU
122
n
64
GLU
122
A
ARG
123
n
65
ARG
123
A
ASN
124
n
66
ASN
124
A
SER
125
n
67
SER
125
A
ARG
126
n
68
ARG
126
A
LYS
127
n
69
LYS
127
A
PRO
128
n
70
PRO
128
A
ILE
129
n
71
ILE
129
A
TYR
130
n
72
TYR
130
A
SER
131
n
73
SER
131
A
ASN
132
n
74
ASN
132
A
SER
133
n
75
SER
133
A
GLN
134
n
76
GLN
134
A
THR
135
n
77
THR
135
A
ALA
136
n
78
ALA
136
A
ILE
137
n
79
ILE
137
A
LYS
138
n
80
LYS
138
A
TRP
139
n
81
TRP
139
A
VAL
140
n
82
VAL
140
A
LYS
141
n
83
LYS
141
A
ASP
142
n
84
ASP
142
A
LYS
143
n
85
LYS
143
A
LYS
144
n
86
LYS
144
A
ALA
145
n
87
ALA
145
A
LYS
146
n
88
LYS
146
A
SER
147
n
89
SER
147
A
THR
148
n
90
THR
148
A
LEU
149
n
91
LEU
149
A
VAL
150
n
92
VAL
150
A
ARG
151
n
93
ARG
151
A
ASN
152
n
94
ASN
152
A
GLU
153
n
95
GLU
153
A
GLU
154
n
96
GLU
154
A
THR
155
n
97
THR
155
A
ALA
156
n
98
ALA
156
A
LEU
157
n
99
LEU
157
A
ILE
158
n
100
ILE
158
A
TRP
159
n
101
TRP
159
A
LYS
160
n
102
LYS
160
A
LEU
161
n
103
LEU
161
A
VAL
162
n
104
VAL
162
A
ASP
163
n
105
ASP
163
A
GLU
164
n
106
GLU
164
A
ALA
165
n
107
ALA
165
A
GLU
166
n
108
GLU
166
A
GLU
167
n
109
GLU
167
A
TRP
168
n
110
TRP
168
A
LEU
169
n
111
LEU
169
A
ASN
170
n
112
ASN
170
A
THR
171
n
113
THR
171
A
HIS
172
n
114
HIS
172
A
THR
173
n
115
THR
173
A
TYR
174
n
116
TYR
174
A
GLU
175
n
117
GLU
175
A
THR
176
n
118
THR
176
A
PRO
177
n
119
PRO
177
A
ILE
178
n
120
ILE
178
A
LEU
179
n
121
LEU
179
A
LYS
180
n
122
LYS
180
A
TRP
181
n
123
TRP
181
A
GLN
182
n
124
GLN
182
A
THR
183
n
125
THR
183
A
ASP
184
n
126
ASP
184
A
LYS
185
n
127
LYS
185
A
TRP
186
n
128
TRP
186
A
GLY
187
n
129
GLY
187
A
GLU
188
n
130
GLU
188
A
ILE
189
n
131
ILE
189
A
LYS
190
n
132
LYS
190
A
ALA
191
n
133
ALA
191
A
ASP
192
n
134
ASP
192
A
TYR
193
n
135
TYR
193
A
GLY
194
n
136
GLY
194
A
n
137
195
A
n
138
196
A
U
1
n
1
U
1
B
C
2
n
2
C
2
B
G
3
n
3
G
3
B
A
3
n
4
A
4
B
C
5
n
5
C
5
B
A
6
n
6
A
6
B
DA
1
n
1
DA
1
C
DT
2
n
2
DT
2
C
SDG
3
n
3
SDG
3
C
DT
4
n
4
DT
4
C
DC
5
n
5
DC
5
C
SDG
6
n
6
SDG
6
C
author_and_software_defined_assembly
PISA
3
trimeric
2570
-37
8410
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
55
G
O
HOH
1_555
168.5
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
ASP
71
A
OD2
ASP
13
1_555
85.9
A
HOH
55
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
ASP
71
A
OD2
ASP
13
1_555
98.5
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
ASP
192
A
OD2
ASP
134
1_555
89.6
A
HOH
55
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
ASP
192
A
OD2
ASP
134
1_555
79.0
A
ASP
71
A
OD2
ASP
13
1_555
A
MG
401
D
MG
MG
1_555
A
ASP
192
A
OD2
ASP
134
1_555
103.7
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
100.1
A
HOH
55
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
90.6
A
ASP
71
A
OD2
ASP
13
1_555
A
MG
401
D
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
88.6
A
ASP
192
A
OD2
ASP
134
1_555
A
MG
401
D
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
164.9
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
86.7
A
HOH
55
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
89.3
A
ASP
71
A
OD2
ASP
13
1_555
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
172.0
A
ASP
192
A
OD2
ASP
134
1_555
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
79.4
B
C
5
B
OP1
C
5
1_555
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
89.6
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
A
GLU
109
A
OE2
GLU
51
1_555
125.5
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
A
GLU
109
A
OE1
GLU
51
1_555
87.8
A
GLU
109
A
OE2
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
A
GLU
109
A
OE1
GLU
51
1_555
53.0
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
A
ASN
132
A
OD1
ASN
74
1_555
127.7
A
GLU
109
A
OE2
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
A
ASN
132
A
OD1
ASN
74
1_555
98.5
A
GLU
109
A
OE1
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
A
ASN
132
A
OD1
ASN
74
1_555
100.4
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
B
A
4
B
O3'
A
4
1_555
128.7
A
GLU
109
A
OE2
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
B
A
4
B
O3'
A
4
1_555
82.7
A
GLU
109
A
OE1
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
B
A
4
B
O3'
A
4
1_555
135.3
A
ASN
132
A
OD1
ASN
74
1_555
A
MG
402
E
MG
MG
1_555
B
A
4
B
O3'
A
4
1_555
78.2
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
76.5
A
GLU
109
A
OE2
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
120.9
A
GLU
109
A
OE1
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
153.4
A
ASN
132
A
OD1
ASN
74
1_555
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
106.2
B
A
4
B
O3'
A
4
1_555
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
52.6
C
SDG
3
C
SDG
3
DG
C
SDG
6
C
SDG
6
DG
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
ILE
100
A
O
ILE
42
A
N
VAL
81
A
N
VAL
23
A
O
GLU
82
A
O
GLU
24
A
N
GLY
73
A
N
GLY
15
A
N
LEU
68
A
N
LEU
10
A
O
TYR
130
A
O
TYR
72
A
N
ILE
129
A
N
ILE
71
A
O
LEU
179
A
O
LEU
121
1
A
HOH
210
G
HOH
1
A
ALA
59
A
ALA
1
1
Y
1
A
LYS
60
A
LYS
2
1
Y
1
A
ARG
195
A
ARG
137
1
Y
1
A
LYS
196
A
LYS
138
1
Y
1
-3.79
0.60
121.00
117.21
A
A
A
CB
CG
CD2
TYR
TYR
TYR
83
83
83
N
1
5.72
0.90
118.30
124.02
A
A
A
CB
CG
OD1
ASP
ASP
ASP
142
142
142
N
1
6.18
0.90
118.30
124.48
A
A
A
CB
CG
OD1
ASP
ASP
ASP
184
184
184
N
1
7.03
1.10
110.50
117.53
B
B
B
O3'
P
OP2
C
G
G
2
3
3
Y
1
-7.87
0.90
105.70
97.83
B
B
B
O5'
P
OP2
G
G
G
3
3
3
N
1
-6.12
0.80
109.40
103.28
B
B
B
O5'
C5'
C4'
A
A
A
4
4
4
N
1
-6.27
0.70
101.30
95.03
B
B
B
C3'
C2'
C1'
A
A
A
4
4
4
N
1
-4.30
0.50
129.30
125.00
B
B
B
N1
C2
N3
A
A
A
4
4
4
N
1
3.32
0.50
110.60
113.92
B
B
B
C2
N3
C4
A
A
A
4
4
4
N
1
-6.11
0.70
109.70
103.59
B
B
B
C1'
O4'
C4'
C
C
C
5
5
5
N
1
4.12
0.50
121.00
125.12
B
B
B
C5
C6
N1
C
C
C
5
5
5
N
1
3.05
0.50
106.80
109.85
C
C
C
O4'
C1'
C2'
DA
DA
DA
1
1
1
N
1
6.91
0.60
118.60
125.51
C
C
C
C6
N1
C2
DA
DA
DA
1
1
1
N
1
-4.63
0.50
129.30
124.67
C
C
C
N1
C2
N3
DA
DA
DA
1
1
1
N
1
4.19
0.50
110.70
114.89
C
C
C
C4
C5
N7
DA
DA
DA
1
1
1
N
1
-3.30
0.50
103.90
100.60
C
C
C
C5
N7
C8
DA
DA
DA
1
1
1
N
1
-3.02
0.40
105.80
102.78
C
C
C
N9
C4
C5
DA
DA
DA
1
1
1
N
1
7.84
0.60
118.60
126.44
C
C
C
N1
C6
N6
DA
DA
DA
1
1
1
N
1
-5.45
0.80
123.70
118.25
C
C
C
C5
C6
N6
DA
DA
DA
1
1
1
N
1
-4.60
0.60
122.30
117.70
C
C
C
N3
C2
O2
DT
DT
DT
2
2
2
N
1
9.70
1.50
119.60
129.30
C
C
C
OP1
P
OP2
DT
DT
DT
4
4
4
N
1
-10.70
0.90
105.70
95.00
C
C
C
O5'
P
OP2
DT
DT
DT
4
4
4
N
1
4.84
0.30
108.30
113.14
C
C
C
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-4.45
0.60
115.20
110.75
C
C
C
N3
C4
C5
DT
DT
DT
4
4
4
N
1
4.31
0.60
118.00
122.31
C
C
C
C4
C5
C6
DT
DT
DT
4
4
4
N
1
-3.95
0.60
119.90
115.95
C
C
C
N3
C4
O4
DT
DT
DT
4
4
4
N
1
8.38
0.70
124.90
133.28
C
C
C
C5
C4
O4
DT
DT
DT
4
4
4
N
1
-7.50
0.60
122.90
115.40
C
C
C
C6
C5
C7
DT
DT
DT
4
4
4
N
1
-5.46
0.80
109.40
103.94
C
C
C
O5'
C5'
C4'
DC
DC
DC
5
5
5
N
1
-3.49
0.40
104.50
101.01
C
C
C
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
A
A
CD
OE2
GLU
GLU
109
109
0.080
0.011
1.252
1.332
N
1
B
B
O3'
C3'
G
G
3
3
0.096
0.012
1.427
1.523
N
1
B
B
N7
C8
G
G
3
3
0.045
0.006
1.305
1.350
N
1
C
C
P
O5'
DT
DT
4
4
0.091
0.010
1.593
1.684
N
1
C
C
C4
O4
DT
DT
4
4
0.074
0.009
1.228
1.302
N
1
C
C
C5
C7
DT
DT
4
4
0.053
0.006
1.496
1.549
N
1
C
C
C5'
C4'
DC
DC
5
5
0.067
0.007
1.512
1.579
N
23.980
0.67
0.00
-0.27
-0.01
0.00
-0.72
0.963
0.946
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.20782
0.17541
0.17714
1.79
40
902
16958
16704
5.1
98.45
2.343
0.075
RANDOM
1
THROUGHOUT
MAD
0.114
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
1.79
40
136
1476
6
245
1089
0.026
0.022
1435
2.372
2.174
2003
5.910
5.000
145
37.030
25.179
56
16.588
15.000
221
21.266
15.000
6
0.178
0.200
223
0.012
0.021
997
1.325
1.500
682
2.246
2.000
1114
3.530
3.000
753
5.118
4.500
883
0.340
0.273
1.832
56
1170
20
94.82
1.79
61.53
3TWH
17472
17227
0
0
0.06
1
15.3
7.3
98.6
0.278
1.79
1.86
1707
1
6.3
98.6
data collection
ADSC
Quantum
phasing
SHELXS
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
6
N
N
6
N
N
6
N
N
A
THR
104
A
THR
46
HELX_P
A
ARG
123
A
ARG
65
1
1
20
A
SER
133
A
SER
75
HELX_P
A
LYS
143
A
LYS
85
1
2
11
A
THR
155
A
THR
97
HELX_P
A
ASN
170
A
ASN
112
1
3
16
A
GLN
182
A
GLN
124
HELX_P
A
GLY
187
A
GLY
129
1
4
6
covale
1.624
both
C
DT
2
C
O3'
DT
2
1_555
C
SDG
3
C
P
SDG
3
1_555
covale
1.629
both
C
SDG
3
C
O3'
SDG
3
1_555
C
DT
4
C
P
DT
4
1_555
covale
1.602
both
C
DC
5
C
O3'
DC
5
1_555
C
SDG
6
C
P
SDG
6
1_555
covale
1.617
one
C
SDG
6
C
O3'
SDG
6
1_555
C
PO4
7
F
P
PO4
1_555
metalc
2.205
A
HOH
36
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.256
A
HOH
55
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.270
A
ASP
71
A
OD2
ASP
13
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.107
A
ASP
71
A
OD1
ASP
13
1_555
A
MG
402
E
MG
MG
1_555
metalc
2.020
A
GLU
109
A
OE2
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
metalc
2.922
A
GLU
109
A
OE1
GLU
51
1_555
A
MG
402
E
MG
MG
1_555
metalc
2.379
A
ASN
132
A
OD1
ASN
74
1_555
A
MG
402
E
MG
MG
1_555
metalc
2.167
A
ASP
192
A
OD2
ASP
134
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.276
A
MG
401
D
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
metalc
2.395
A
MG
401
D
MG
MG
1_555
B
HOH
56
H
O
HOH
1_555
metalc
2.766
A
MG
402
E
MG
MG
1_555
B
A
4
B
O3'
A
4
1_555
metalc
2.657
A
MG
402
E
MG
MG
1_555
B
C
5
B
OP1
C
5
1_555
hydrog
C-SDG PAIR
B
C
2
B
O2
C
2
1_555
C
SDG
6
C
N2
SDG
6
1_555
hydrog
WATSON-CRICK
B
G
3
B
N1
G
3
1_555
C
DC
5
C
N3
DC
5
1_555
hydrog
WATSON-CRICK
B
G
3
B
N2
G
3
1_555
C
DC
5
C
O2
DC
5
1_555
hydrog
WATSON-CRICK
B
G
3
B
O6
G
3
1_555
C
DC
5
C
N4
DC
5
1_555
hydrog
WATSON-CRICK
B
A
4
B
N1
A
4
1_555
C
DT
4
C
N3
DT
4
1_555
hydrog
WATSON-CRICK
B
A
4
B
N6
A
4
1_555
C
DT
4
C
O4
DT
4
1_555
hydrog
C-SDG PAIR
B
C
5
B
O2
C
5
1_555
C
SDG
3
C
N2
SDG
3
1_555
hydrog
WATSON-CRICK
B
A
6
B
N1
A
6
1_555
C
DT
2
C
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
A
6
B
N6
A
6
1_555
C
DT
2
C
O4
DT
2
1_555
Hydrolase/RNA/DNA
SELENIUM-DNA/RNA, RNASE H, ENDONUCLEASE, HYDROLASE, MAGNESIUM, MANGANESE, Metal-binding, SELENIUM-modification, Hydrolase-RNA-DNA complex
A
ASN
77
A
ASN
19
1
A
PRO
78
A
PRO
20
2.91
RNH1_BACHD
UNP
1
59
Q9KEI9
AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIK
WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
3TWH
PDB
2
3TWH
3TWH
PDB
3
3TWH
59
196
3TWH
59
196
Q9KEI9
A
1
1
138
1
6
3TWH
1
6
3TWH
B
2
1
6
1
6
3TWH
1
6
3TWH
C
3
1
6
1
ASP
engineered mutation
ASN
132
3TWH
A
Q9KEI9
UNP
132
74
5
anti-parallel
anti-parallel
parallel
parallel
A
VAL
93
A
VAL
35
A
GLY
103
A
GLY
45
A
GLY
79
A
GLY
21
A
ASP
87
A
ASP
29
A
LEU
68
A
LEU
10
A
GLN
75
A
GLN
17
A
ILE
129
A
ILE
71
A
SER
131
A
SER
73
A
ILE
178
A
ILE
120
A
LYS
180
A
LYS
122
BINDING SITE FOR RESIDUE MG A 401
A
MG
401
Software
6
BINDING SITE FOR RESIDUE MG A 402
A
MG
402
Software
5
BINDING SITE FOR RESIDUE PO4 C 7
C
PO4
7
Software
6
A
HOH
36
G
HOH
6
1_555
A
HOH
55
G
HOH
6
1_555
A
ASP
71
A
ASP
13
6
1_555
A
ASP
192
A
ASP
134
6
1_555
B
C
5
B
C
5
6
1_555
B
HOH
56
H
HOH
6
1_555
A
ASP
71
A
ASP
13
5
1_555
A
GLU
109
A
GLU
51
5
1_555
A
ASN
132
A
ASN
74
5
1_555
B
A
4
B
A
4
5
1_555
B
C
5
B
C
5
5
1_555
A
TRP
139
A
TRP
81
6
1_555
A
LYS
146
A
LYS
88
6
1_555
C
DA
1
C
DA
1
6
4_556
C
SDG
6
C
SDG
6
6
1_555
C
HOH
77
I
HOH
6
1_555
C
HOH
107
I
HOH
6
1_555
5
C 1 2 1