0.012390
0.000000
0.001304
-0.000000
0.026611
0.000000
0.000000
-0.000000
0.016135
0.00000
0.00000
0.00000
Fang, Z.
Yang, F.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
96.01
90.00
80.710
37.579
62.319
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 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
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
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
C10 H15 N2 O7 P Se
385.169
n
1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one
2-Se-Thymidine-5'-phosphate
DNA 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
Y
228
N
N
Y
229
N
C
Y
230
N
N
Y
231
N
C
N
232
N
C
N
233
N
O
N
234
N
N
N
235
N
C
N
236
N
N
N
237
N
N
Y
238
N
C
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
H
N
253
N
O
N
254
N
P
N
255
N
O
N
256
N
O
N
257
N
O
N
258
N
C
N
259
R
C
N
260
N
O
N
261
S
C
N
262
N
O
N
263
N
C
N
264
R
C
N
265
N
N
N
266
N
C
N
267
N
O
N
268
N
N
N
269
N
C
N
270
N
O
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
H
N
275
N
H
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
O
N
290
N
P
N
291
N
O
N
292
N
O
N
293
N
O
N
294
N
C
N
295
R
C
N
296
N
O
N
297
S
C
N
298
N
O
N
299
R
C
N
300
N
O
N
301
R
C
Y
302
N
N
Y
303
N
C
Y
304
N
N
Y
305
N
C
N
306
N
C
N
307
N
O
N
308
N
N
N
309
N
C
N
310
N
N
N
311
N
N
Y
312
N
C
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
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
O
N
335
N
N
N
336
N
O
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
N
N
348
S
C
N
349
N
C
N
350
N
O
N
351
N
C
N
352
N
C
N
353
N
C
N
354
N
O
N
355
N
O
N
356
N
O
N
357
N
H
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
N
N
367
N
C
N
368
N
C
N
369
N
O
N
370
N
O
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
Y
381
N
C
Y
382
N
N
Y
383
N
C
Y
384
N
C
Y
385
N
N
N
386
N
O
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
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
O
N
398
N
H
N
399
N
H
N
400
N
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
S
C
N
405
N
C
N
406
N
C
N
407
N
C
N
408
N
O
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
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
N
N
423
S
C
N
424
N
C
N
425
N
O
N
426
N
C
N
427
N
C
N
428
N
C
N
429
N
C
N
430
N
O
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
N
N
445
S
C
N
446
N
C
N
447
N
O
N
448
N
C
N
449
N
C
N
450
N
C
N
451
N
C
N
452
N
N
N
453
N
O
N
454
N
H
N
455
N
H
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
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
N
N
470
S
C
N
471
N
C
N
472
N
O
N
473
N
C
N
474
N
C
N
475
N
S
N
476
N
C
N
477
N
O
N
478
N
H
N
479
N
H
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
MG
N
490
N
N
N
491
S
C
N
492
N
C
N
493
N
O
N
494
N
C
Y
495
N
C
Y
496
N
C
Y
497
N
C
Y
498
N
C
Y
499
N
C
Y
500
N
C
N
501
N
O
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
N
N
531
S
C
N
532
N
C
N
533
N
O
N
534
N
C
N
535
N
O
N
536
N
O
N
537
N
H
N
538
N
H
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
H
N
544
N
N
N
545
S
C
N
546
N
C
N
547
N
O
N
548
R
C
N
549
N
O
N
550
N
C
N
551
N
O
N
552
N
H
N
553
N
H
N
554
N
H
N
555
N
H
N
556
N
H
N
557
N
H
N
558
N
H
N
559
N
H
N
560
N
H
N
561
N
N
N
562
S
C
N
563
N
C
N
564
N
O
N
565
N
C
Y
566
N
C
Y
567
N
C
Y
568
N
C
Y
569
N
N
Y
570
N
C
Y
571
N
C
Y
572
N
C
Y
573
N
C
Y
574
N
C
N
575
N
O
N
576
N
H
N
577
N
H
N
578
N
H
N
579
N
H
N
580
N
H
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
N
N
589
S
C
N
590
N
C
N
591
N
O
N
592
N
C
Y
593
N
C
Y
594
N
C
Y
595
N
C
Y
596
N
C
Y
597
N
C
Y
598
N
C
N
599
N
O
N
600
N
O
N
601
N
H
N
602
N
H
N
603
N
H
N
604
N
H
N
605
N
H
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
O
N
613
N
P
N
614
N
O
N
615
N
O
N
616
N
O
N
617
N
C
N
618
R
C
N
619
N
O
N
620
S
C
N
621
N
O
N
622
R
C
N
623
N
O
N
624
R
C
N
625
N
N
N
626
N
C
N
627
N
O
N
628
N
N
N
629
N
C
N
630
N
O
N
631
N
C
N
632
N
C
N
633
N
H
N
634
N
H
N
635
N
H
N
636
N
H
N
637
N
H
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
P
N
647
N
N
N
648
N
C
N
649
N
SE
N
650
N
N
N
651
N
C
N
652
N
O
N
653
N
C
N
654
N
C
N
655
R
C
N
656
N
O
N
657
N
C
N
658
N
O
N
659
S
C
N
660
N
O
N
661
R
C
N
662
N
O
N
663
N
C
N
664
N
O
N
665
N
C
N
666
N
H
N
667
N
H
N
668
N
H
N
669
N
H
N
670
N
H
N
671
N
H
N
672
N
H
N
673
N
H
N
674
N
H
N
675
N
H
N
676
N
H
N
677
N
H
N
678
N
H
N
679
N
H
N
680
N
H
N
681
N
O
N
682
N
N
N
683
S
C
N
684
N
C
N
685
N
O
N
686
N
C
N
687
N
C
N
688
N
C
N
689
N
O
N
690
N
H
N
691
N
H
N
692
N
H
N
693
N
H
N
694
N
H
N
695
N
H
N
696
N
H
N
697
N
H
N
698
N
H
N
699
N
H
N
700
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
Y
241
N
sing
Y
242
N
sing
Y
243
N
doub
N
244
N
sing
Y
245
N
sing
N
246
N
sing
Y
247
N
doub
N
248
N
doub
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
doub
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
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
doub
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
doub
N
287
N
sing
N
288
N
sing
N
289
N
doub
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
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
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
Y
318
N
sing
Y
319
N
sing
Y
320
N
doub
N
321
N
sing
Y
322
N
sing
N
323
N
sing
Y
324
N
doub
N
325
N
doub
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
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
doub
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
doub
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
sing
N
357
N
sing
N
358
N
sing
N
359
N
doub
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
doub
N
368
N
sing
N
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
doub
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
doub
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
Y
391
N
sing
Y
392
N
doub
Y
393
N
doub
N
394
N
sing
Y
395
N
sing
N
396
N
sing
Y
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
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
doub
N
431
N
sing
N
432
N
sing
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
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
doub
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
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
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
sing
N
474
N
sing
N
475
N
doub
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
doub
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
Y
499
N
doub
Y
500
N
sing
Y
501
N
sing
N
502
N
sing
Y
503
N
doub
N
504
N
sing
Y
505
N
doub
N
506
N
sing
Y
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
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
doub
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
doub
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
sing
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
doub
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
sing
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
doub
N
564
N
sing
N
565
N
sing
N
566
N
sing
N
567
N
sing
Y
568
N
doub
Y
569
N
sing
Y
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
sing
Y
577
N
doub
N
578
N
sing
Y
579
N
doub
N
580
N
sing
Y
581
N
sing
N
582
N
sing
N
583
N
sing
N
584
N
sing
N
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
doub
N
592
N
sing
N
593
N
sing
N
594
N
sing
N
595
N
sing
Y
596
N
doub
Y
597
N
sing
Y
598
N
sing
N
599
N
sing
Y
600
N
doub
N
601
N
sing
Y
602
N
doub
N
603
N
sing
Y
604
N
sing
N
605
N
sing
N
606
N
sing
N
607
N
sing
N
608
N
sing
N
609
N
sing
N
610
N
sing
N
611
N
doub
N
612
N
sing
N
613
N
sing
N
614
N
sing
N
615
N
sing
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
doub
N
636
N
sing
N
637
N
sing
N
638
N
sing
N
639
N
doub
N
640
N
sing
N
641
N
doub
N
642
N
sing
N
643
N
sing
N
644
N
sing
N
645
N
sing
N
646
N
sing
N
647
N
sing
N
648
N
doub
N
649
N
sing
N
650
N
sing
N
651
N
sing
N
652
N
doub
N
653
N
sing
N
654
N
sing
N
655
N
doub
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
N
666
N
sing
N
667
N
sing
N
668
N
sing
N
669
N
sing
N
670
N
sing
N
671
N
sing
N
672
N
sing
N
673
N
sing
N
674
N
sing
N
675
N
sing
N
676
N
sing
N
677
N
sing
N
678
N
sing
N
679
N
sing
N
680
N
doub
N
681
N
sing
N
682
N
sing
N
683
N
sing
N
684
N
sing
N
685
N
sing
N
686
N
sing
N
687
N
doub
N
688
N
sing
N
689
N
sing
N
690
N
sing
N
691
N
sing
N
692
N
sing
N
693
N
sing
N
694
N
sing
N
695
N
sing
N
696
N
sing
N
697
N
sing
N
698
N
sing
To Be Published
0353
2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant
10.2210/pdb5w7o/pdb
pdb_00005w7o
100
1
PIXEL
2017-05-14
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
5.0.1
ALS
1
SYNCHROTRON
ALS BEAMLINE 5.0.1
1875.189
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
1
syn
polymer
1887.189
DNA (5'-D(*AP*TP*GP*(US3)P*CP*G)-3')
1
syn
polymer
15243.206
Ribonuclease H
3.1.26.4
residues 62-193
D132N
1
man
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
56
nat
water
RNase H
no
no
UCGACA
UCGACA
B
polyribonucleotide
no
yes
(DA)(DT)(DG)(US3)(DC)(DG)
ATGTCG
C
polydeoxyribonucleotide
no
no
EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVK
DKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY
EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVK
DKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY
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
ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
sample
1
132
rnhA, BH0863
272558
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
83333
Escherichia coli K-12
Biological sequence
1
2.48
50.46
VAPOR DIFFUSION, HANGING DROP
0.1M MES pH 6.5, 12%(w/v) PEG 20000
293
-1.705
1
19
B
2
C
6
-3.002
B_C2:DG6_C
1
-6.110
0.013
0.063
-0.149
-19.210
1
19
B
3
C
5
-1.744
B_G3:DC5_C
2
-11.270
-0.206
-0.348
-0.108
-8.024
1
20
B
4
C
4
-1.008
B_A4:US34_C
3
-18.119
0.182
-0.254
-0.016
-10.025
1
19
B
5
C
3
-2.082
B_C5:DG3_C
4
-10.924
0.092
0.286
-0.185
-7.564
1
20
B
6
C
2
0.264
B_A6:DT2_C
5
-6.684
0.083
0.063
-0.147
3.521
39.043
B
B
2
3
7.771
C
C
6
5
3.691
5.153
0.337
-1.112
BB_C2G3:DC5DG6_CC
1
7.039
-10.615
38.093
-2.358
0.443
2.994
33.539
B
B
3
4
8.247
C
C
5
4
3.136
4.741
0.710
-1.084
BB_G3A4:US34DC5_CC
2
2.059
-3.582
33.149
-2.613
-0.911
2.905
31.372
B
B
4
5
16.886
C
C
4
3
3.304
8.975
-0.875
-1.278
BB_A4C5:DG3US34_CC
3
-4.664
8.774
29.735
-4.010
0.762
3.049
26.552
B
B
5
6
7.783
C
C
3
2
3.171
3.541
1.079
-1.863
BB_C5A6:DT2DG3_CC
4
5.252
-11.542
25.798
-4.956
-1.015
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
refine_hist
struct_conn
struct_conn_type
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2017-06-28
1
1
2023-10-04
_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.ptnr1_symmetry
_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.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_refine_hist.d_res_low
_struct_conn.conn_type_id
_struct_conn.id
_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.ptnr1_symmetry
_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_conn.ptnr2_symmetry
_struct_conn_type.id
N
RCSB
Y
RCSB
2017-06-20
REL
REL
MG
MAGNESIUM ION
HOH
water
32630
synthetic construct
sample
32630
synthetic construct
sample
1
6
2G8U
PDB
experimental model
MG
2
4
MG
MG
201
A
MG
3
4
MG
MG
202
A
HOH
16
5
HOH
HOH
101
B
HOH
48
5
HOH
HOH
102
B
HOH
36
5
HOH
HOH
103
B
HOH
2
5
HOH
HOH
104
B
HOH
35
5
HOH
HOH
105
B
HOH
37
5
HOH
HOH
106
B
HOH
43
5
HOH
HOH
107
B
HOH
34
5
HOH
HOH
101
C
HOH
32
5
HOH
HOH
102
C
HOH
6
5
HOH
HOH
103
C
HOH
7
5
HOH
HOH
104
C
HOH
8
5
HOH
HOH
105
C
HOH
47
5
HOH
HOH
106
C
HOH
11
5
HOH
HOH
107
C
HOH
46
5
HOH
HOH
108
C
HOH
42
5
HOH
HOH
109
C
HOH
9
5
HOH
HOH
110
C
HOH
21
5
HOH
HOH
111
C
HOH
57
5
HOH
HOH
112
C
HOH
33
5
HOH
HOH
113
C
HOH
5
5
HOH
HOH
301
A
HOH
30
5
HOH
HOH
302
A
HOH
13
5
HOH
HOH
303
A
HOH
20
5
HOH
HOH
304
A
HOH
4
5
HOH
HOH
305
A
HOH
39
5
HOH
HOH
306
A
HOH
1
5
HOH
HOH
307
A
HOH
51
5
HOH
HOH
308
A
HOH
10
5
HOH
HOH
309
A
HOH
40
5
HOH
HOH
310
A
HOH
14
5
HOH
HOH
311
A
HOH
52
5
HOH
HOH
312
A
HOH
31
5
HOH
HOH
313
A
HOH
17
5
HOH
HOH
314
A
HOH
23
5
HOH
HOH
315
A
HOH
26
5
HOH
HOH
316
A
HOH
55
5
HOH
HOH
317
A
HOH
3
5
HOH
HOH
318
A
HOH
19
5
HOH
HOH
319
A
HOH
12
5
HOH
HOH
320
A
HOH
29
5
HOH
HOH
321
A
HOH
54
5
HOH
HOH
322
A
HOH
25
5
HOH
HOH
323
A
HOH
28
5
HOH
HOH
324
A
HOH
44
5
HOH
HOH
325
A
HOH
56
5
HOH
HOH
326
A
HOH
53
5
HOH
HOH
327
A
HOH
38
5
HOH
HOH
328
A
HOH
50
5
HOH
HOH
329
A
HOH
24
5
HOH
HOH
330
A
HOH
41
5
HOH
HOH
331
A
HOH
45
5
HOH
HOH
332
A
HOH
18
5
HOH
HOH
333
A
HOH
49
5
HOH
HOH
334
A
HOH
22
5
HOH
HOH
335
A
HOH
27
5
HOH
HOH
336
A
U
1
n
1
U
1
B
C
2
n
2
C
2
B
G
3
n
3
G
3
B
A
4
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
DG
3
n
3
DG
3
C
US3
4
n
4
US3
4
C
DC
5
n
5
DC
5
C
DG
6
n
6
DG
6
C
GLU
62
n
1
GLU
62
A
ILE
63
n
2
ILE
63
A
ILE
64
n
3
ILE
64
A
TRP
65
n
4
TRP
65
A
GLU
66
n
5
GLU
66
A
SER
67
n
6
SER
67
A
LEU
68
n
7
LEU
68
A
SER
69
n
8
SER
69
A
VAL
70
n
9
VAL
70
A
ASP
71
n
10
ASP
71
A
VAL
72
n
11
VAL
72
A
GLY
73
n
12
GLY
73
A
SER
74
n
13
SER
74
A
GLN
75
n
14
GLN
75
A
GLY
76
n
15
GLY
76
A
ASN
77
n
16
ASN
77
A
PRO
78
n
17
PRO
78
A
GLY
79
n
18
GLY
79
A
ILE
80
n
19
ILE
80
A
VAL
81
n
20
VAL
81
A
GLU
82
n
21
GLU
82
A
TYR
83
n
22
TYR
83
A
LYS
84
n
23
LYS
84
A
GLY
85
n
24
GLY
85
A
VAL
86
n
25
VAL
86
A
ASP
87
n
26
ASP
87
A
THR
88
n
27
THR
88
A
LYS
89
n
28
LYS
89
A
THR
90
n
29
THR
90
A
GLY
91
n
30
GLY
91
A
GLU
92
n
31
GLU
92
A
VAL
93
n
32
VAL
93
A
LEU
94
n
33
LEU
94
A
PHE
95
n
34
PHE
95
A
GLU
96
n
35
GLU
96
A
ARG
97
n
36
ARG
97
A
GLU
98
n
37
GLU
98
A
PRO
99
n
38
PRO
99
A
ILE
100
n
39
ILE
100
A
PRO
101
n
40
PRO
101
A
ILE
102
n
41
ILE
102
A
GLY
103
n
42
GLY
103
A
THR
104
n
43
THR
104
A
ASN
105
n
44
ASN
105
A
ASN
106
n
45
ASN
106
A
MET
107
n
46
MET
107
A
GLY
108
n
47
GLY
108
A
GLU
109
n
48
GLU
109
A
PHE
110
n
49
PHE
110
A
LEU
111
n
50
LEU
111
A
ALA
112
n
51
ALA
112
A
ILE
113
n
52
ILE
113
A
VAL
114
n
53
VAL
114
A
HIS
115
n
54
HIS
115
A
GLY
116
n
55
GLY
116
A
LEU
117
n
56
LEU
117
A
ARG
118
n
57
ARG
118
A
TYR
119
n
58
TYR
119
A
LEU
120
n
59
LEU
120
A
LYS
121
n
60
LYS
121
A
GLU
122
n
61
GLU
122
A
ARG
123
n
62
ARG
123
A
ASN
124
n
63
ASN
124
A
SER
125
n
64
SER
125
A
ARG
126
n
65
ARG
126
A
LYS
127
n
66
LYS
127
A
PRO
128
n
67
PRO
128
A
ILE
129
n
68
ILE
129
A
TYR
130
n
69
TYR
130
A
SER
131
n
70
SER
131
A
ASN
132
n
71
ASN
132
A
SER
133
n
72
SER
133
A
GLN
134
n
73
GLN
134
A
THR
135
n
74
THR
135
A
ALA
136
n
75
ALA
136
A
ILE
137
n
76
ILE
137
A
LYS
138
n
77
LYS
138
A
TRP
139
n
78
TRP
139
A
VAL
140
n
79
VAL
140
A
LYS
141
n
80
LYS
141
A
ASP
142
n
81
ASP
142
A
LYS
143
n
82
LYS
143
A
LYS
144
n
83
LYS
144
A
ALA
145
n
84
ALA
145
A
LYS
146
n
85
LYS
146
A
SER
147
n
86
SER
147
A
THR
148
n
87
THR
148
A
LEU
149
n
88
LEU
149
A
VAL
150
n
89
VAL
150
A
ARG
151
n
90
ARG
151
A
ASN
152
n
91
ASN
152
A
GLU
153
n
92
GLU
153
A
GLU
154
n
93
GLU
154
A
THR
155
n
94
THR
155
A
ALA
156
n
95
ALA
156
A
LEU
157
n
96
LEU
157
A
ILE
158
n
97
ILE
158
A
TRP
159
n
98
TRP
159
A
LYS
160
n
99
LYS
160
A
LEU
161
n
100
LEU
161
A
VAL
162
n
101
VAL
162
A
ASP
163
n
102
ASP
163
A
GLU
164
n
103
GLU
164
A
ALA
165
n
104
ALA
165
A
GLU
166
n
105
GLU
166
A
GLU
167
n
106
GLU
167
A
TRP
168
n
107
TRP
168
A
LEU
169
n
108
LEU
169
A
ASN
170
n
109
ASN
170
A
THR
171
n
110
THR
171
A
HIS
172
n
111
HIS
172
A
THR
173
n
112
THR
173
A
TYR
174
n
113
TYR
174
A
GLU
175
n
114
GLU
175
A
THR
176
n
115
THR
176
A
PRO
177
n
116
PRO
177
A
ILE
178
n
117
ILE
178
A
LEU
179
n
118
LEU
179
A
LYS
180
n
119
LYS
180
A
TRP
181
n
120
TRP
181
A
GLN
182
n
121
GLN
182
A
THR
183
n
122
THR
183
A
ASP
184
n
123
ASP
184
A
LYS
185
n
124
LYS
185
A
TRP
186
n
125
TRP
186
A
GLY
187
n
126
GLY
187
A
GLU
188
n
127
GLU
188
A
ILE
189
n
128
ILE
189
A
LYS
190
n
129
LYS
190
A
ALA
191
n
130
ALA
191
A
ASP
192
n
131
ASP
192
A
TYR
193
n
132
TYR
193
A
author_and_software_defined_assembly
PISA
3
trimeric
none
1980
-23
8630
B
A
6
A
O3'
A
6
1_555
A
MG
201
D
MG
MG
1_555
A
ASP
71
C
OD1
ASP
10
1_555
129.2
B
A
6
A
O3'
A
6
1_555
A
MG
201
D
MG
MG
1_555
A
GLU
109
C
OE2
GLU
48
1_555
83.4
A
ASP
71
C
OD1
ASP
10
1_555
A
MG
201
D
MG
MG
1_555
A
GLU
109
C
OE2
GLU
48
1_555
92.9
B
A
6
A
O3'
A
6
1_555
A
MG
201
D
MG
MG
1_555
A
ASN
132
C
OD1
ASN
71
1_555
90.6
A
ASP
71
C
OD1
ASP
10
1_555
A
MG
201
D
MG
MG
1_555
A
ASN
132
C
OD1
ASN
71
1_555
140.1
A
GLU
109
C
OE2
GLU
48
1_555
A
MG
201
D
MG
MG
1_555
A
ASN
132
C
OD1
ASN
71
1_555
95.6
B
A
6
A
O3'
A
6
1_555
A
MG
201
D
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
71.7
A
ASP
71
C
OD1
ASP
10
1_555
A
MG
201
D
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
78.7
A
GLU
109
C
OE2
GLU
48
1_555
A
MG
201
D
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
138.2
A
ASN
132
C
OD1
ASN
71
1_555
A
MG
201
D
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
117.1
B
HOH
102
F
O
HOH
4_546
A
MG
202
E
MG
MG
1_555
A
ASP
71
C
OD2
ASP
10
1_555
95.7
B
HOH
102
F
O
HOH
4_546
A
MG
202
E
MG
MG
1_555
A
ASP
192
C
OD1
ASP
131
1_555
146.9
A
ASP
71
C
OD2
ASP
10
1_555
A
MG
202
E
MG
MG
1_555
A
ASP
192
C
OD1
ASP
131
1_555
94.6
B
HOH
102
F
O
HOH
4_546
A
MG
202
E
MG
MG
1_555
A
HOH
303
H
O
HOH
1_555
65.5
A
ASP
71
C
OD2
ASP
10
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
303
H
O
HOH
1_555
71.8
A
ASP
192
C
OD1
ASP
131
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
303
H
O
HOH
1_555
88.2
B
HOH
102
F
O
HOH
4_546
A
MG
202
E
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
85.9
A
ASP
71
C
OD2
ASP
10
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
79.3
A
ASP
192
C
OD1
ASP
131
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
127.0
A
HOH
303
H
O
HOH
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
136.2
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
94
C
O
LEU
33
A
N
GLY
85
C
N
GLY
24
A
N
VAL
81
C
N
VAL
20
A
O
ILE
100
C
O
ILE
39
A
O
LEU
94
C
O
LEU
33
A
N
GLY
85
C
N
GLY
24
A
O
VAL
86
C
O
VAL
25
A
N
SER
69
C
N
SER
8
A
N
LEU
68
C
N
LEU
7
A
O
TYR
130
C
O
TYR
69
A
N
ILE
129
C
N
ILE
68
A
O
LEU
179
C
O
LEU
118
1
A
A
OG1
O
THR
HOH
148
301
2.17
1
-8.31
0.90
105.70
97.39
B
B
B
O5'
P
OP2
A
A
A
4
4
4
N
1
12.68
2.10
111.80
124.48
A
A
A
CG
CD
NE
ARG
ARG
ARG
97
97
97
N
1
6.35
0.90
118.30
124.65
A
A
A
CB
CG
OD1
ASP
ASP
ASP
184
184
184
N
20.647
-0.00
0.00
-0.00
0.00
0.00
0.00
0.953
0.915
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22887
0.18207
0.18445
1.75
50
847
16131
5.0
89.17
2.349
0.075
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.121
0.124
0.80
0.80
1.20
2g8u
MAXIMUM LIKELIHOOD
MASK
1.75
50
56
1379
2
245
1076
0.018
0.018
1372
0.027
0.020
1157
1.868
1.813
1904
1.266
3.005
2702
6.102
5.000
131
36.905
25.098
51
12.468
15.000
202
13.385
15.000
5
0.108
0.200
205
0.012
0.020
1334
0.002
0.020
275
2.006
1.839
527
1.930
1.835
526
2.719
2.738
657
2.719
2.741
658
2.880
2.172
845
2.879
2.173
846
4.307
3.156
1248
5.725
21.349
1696
5.483
21.181
1686
0.353
0.247
1.795
28
613
20
45.36
1.75
50
5W7O
18994
0.024
0.743
1
22.5
3.3
89.6
1.75
1.81
3.7
1030
0.927
0.144
0.876
1
54.2
refinement
REFMAC
5.8.0158
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHASER
N
2-Se-T4-DNA and native RNA 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
5
N
N
5
N
N
A
THR
104
C
THR
43
HELX_P
A
ARG
123
C
ARG
62
1
AA1
20
A
SER
133
C
SER
72
HELX_P
A
LYS
143
C
LYS
82
1
AA2
11
A
THR
155
C
THR
94
HELX_P
A
ASN
170
C
ASN
109
1
AA3
16
A
GLN
182
C
GLN
121
HELX_P
A
GLY
187
C
GLY
126
1
AA4
6
covale
1.624
both
C
DG
3
B
O3'
DG
3
1_555
C
US3
4
B
P
US3
4
1_555
covale
1.613
one
C
US3
4
B
O3'
US3
4
1_555
C
DC
5
B
P
DC
5
1_555
metalc
2.491
B
A
6
A
O3'
A
6
1_555
A
MG
201
D
MG
MG
1_555
metalc
1.904
B
HOH
102
F
O
HOH
4_546
A
MG
202
E
MG
MG
1_555
metalc
2.229
A
ASP
71
C
OD1
ASP
10
1_555
A
MG
201
D
MG
MG
1_555
metalc
2.420
A
ASP
71
C
OD2
ASP
10
1_555
A
MG
202
E
MG
MG
1_555
metalc
2.316
A
GLU
109
C
OE2
GLU
48
1_555
A
MG
201
D
MG
MG
1_555
metalc
2.155
A
ASN
132
C
OD1
ASN
71
1_555
A
MG
201
D
MG
MG
1_555
metalc
2.054
A
ASP
192
C
OD1
ASP
131
1_555
A
MG
202
E
MG
MG
1_555
metalc
2.574
A
MG
201
D
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
metalc
2.387
A
MG
202
E
MG
MG
1_555
A
HOH
303
H
O
HOH
1_555
metalc
1.761
A
MG
202
E
MG
MG
1_555
A
HOH
320
H
O
HOH
1_555
hydrog
WATSON-CRICK
B
C
2
A
N3
C
2
1_555
C
DG
6
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
B
C
2
A
N4
C
2
1_555
C
DG
6
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
B
C
2
A
O2
C
2
1_555
C
DG
6
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
B
G
3
A
N1
G
3
1_555
C
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
B
G
3
A
N2
G
3
1_555
C
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
B
G
3
A
O6
G
3
1_555
C
DC
5
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
B
A
4
A
N1
A
4
1_555
C
US3
4
B
N3
US3
4
1_555
hydrog
WATSON-CRICK
B
A
4
A
N6
A
4
1_555
C
US3
4
B
O4
US3
4
1_555
hydrog
WATSON-CRICK
B
C
5
A
N3
C
5
1_555
C
DG
3
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
B
C
5
A
N4
C
5
1_555
C
DG
3
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
B
C
5
A
O2
C
5
1_555
C
DG
3
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
B
A
6
A
N1
A
6
1_555
C
DT
2
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
A
6
A
N6
A
6
1_555
C
DT
2
B
O4
DT
2
1_555
HYDROLASE/DNA/RNA
HYDROLASE-DNA-RNA complex
A
ASN
77
C
ASN
16
1
A
PRO
78
C
PRO
17
4.18
5W7O
PDB
1
1
5W7O
5W7O
PDB
2
1
5W7O
RNH1_BACHD
UNP
3
62
Q9KEI9
EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIKWVK
DKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY
1
6
5W7O
1
6
5W7O
B
1
1
6
1
3
5W7O
1
3
5W7O
C
2
1
3
62
193
5W7O
62
193
Q9KEI9
A
3
1
132
3
ASP
engineered mutation
ASN
132
5W7O
A
Q9KEI9
UNP
132
71
3
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
A
VAL
93
C
VAL
32
A
GLU
96
C
GLU
35
A
GLY
79
C
GLY
18
A
ASP
87
C
ASP
26
A
ILE
100
C
ILE
39
A
GLY
103
C
GLY
42
A
VAL
93
C
VAL
32
A
GLU
96
C
GLU
35
A
GLY
79
C
GLY
18
A
ASP
87
C
ASP
26
A
LEU
68
C
LEU
7
A
GLN
75
C
GLN
14
A
ILE
129
C
ILE
68
A
SER
131
C
SER
70
A
ILE
178
C
ILE
117
A
LYS
180
C
LYS
119
binding site for residue MG A 201
A
MG
201
Software
6
binding site for residue MG A 202
A
MG
202
Software
5
A
ASP
71
C
ASP
10
6
1_555
A
GLU
109
C
GLU
48
6
1_555
A
ASN
132
C
ASN
71
6
1_555
A
HOH
318
H
HOH
6
1_555
A
HOH
320
H
HOH
6
1_555
B
A
6
A
A
6
6
1_555
A
ASP
71
C
ASP
10
5
1_555
A
ASP
192
C
ASP
131
5
1_555
A
HOH
303
H
HOH
5
1_555
A
HOH
320
H
HOH
5
1_555
B
HOH
102
F
HOH
5
4_546
5
C 1 2 1