0.012300
0.000000
0.001458
0.000000
0.026545
0.000000
0.000000
0.000000
0.016144
0.00000
0.00000
0.00000
Gan, J.H.
Abdur, R.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
96.76
90.00
81.301
37.672
62.378
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
C10 H15 N5 O10 P2
427.201
n
2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE
DNA linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
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
P
N
491
N
O
N
492
N
O
N
493
N
O
N
494
N
P
N
495
N
O
N
496
N
O
N
497
N
O
N
498
N
O
N
499
N
C
N
500
R
C
N
501
N
O
N
502
S
C
N
503
N
O
N
504
N
C
N
505
R
C
Y
506
N
N
Y
507
N
C
Y
508
N
N
Y
509
N
C
N
510
N
C
N
511
N
O
N
512
N
N
N
513
N
C
N
514
N
N
N
515
N
N
Y
516
N
C
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
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
N
N
533
S
C
N
534
N
C
N
535
N
O
N
536
N
C
Y
537
N
C
Y
538
N
C
Y
539
N
C
Y
540
N
C
Y
541
N
C
Y
542
N
C
N
543
N
O
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
H
N
555
N
N
N
556
S
C
N
557
N
C
N
558
N
O
N
559
N
C
N
560
N
C
N
561
N
C
N
562
N
O
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
N
567
N
H
N
568
N
H
N
569
N
H
N
570
N
H
N
571
N
H
N
572
N
N
N
573
S
C
N
574
N
C
N
575
N
O
N
576
N
C
N
577
N
O
N
578
N
O
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
N
N
587
S
C
N
588
N
C
N
589
N
O
N
590
R
C
N
591
N
O
N
592
N
C
N
593
N
O
N
594
N
H
N
595
N
H
N
596
N
H
N
597
N
H
N
598
N
H
N
599
N
H
N
600
N
H
N
601
N
H
N
602
N
H
N
603
N
N
N
604
S
C
N
605
N
C
N
606
N
O
N
607
N
C
Y
608
N
C
Y
609
N
C
Y
610
N
C
Y
611
N
N
Y
612
N
C
Y
613
N
C
Y
614
N
C
Y
615
N
C
Y
616
N
C
N
617
N
O
N
618
N
H
N
619
N
H
N
620
N
H
N
621
N
H
N
622
N
H
N
623
N
H
N
624
N
H
N
625
N
H
N
626
N
H
N
627
N
H
N
628
N
H
N
629
N
H
N
630
N
N
N
631
S
C
N
632
N
C
N
633
N
O
N
634
N
C
Y
635
N
C
Y
636
N
C
Y
637
N
C
Y
638
N
C
Y
639
N
C
Y
640
N
C
N
641
N
O
N
642
N
O
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
H
N
652
N
H
N
653
N
H
N
654
N
O
N
655
N
P
N
656
N
O
N
657
N
O
N
658
N
O
N
659
N
C
N
660
R
C
N
661
N
O
N
662
S
C
N
663
N
O
N
664
R
C
N
665
N
O
N
666
R
C
N
667
N
N
N
668
N
C
N
669
N
O
N
670
N
N
N
671
N
C
N
672
N
O
N
673
N
C
N
674
N
C
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
H
N
682
N
H
N
683
N
H
N
684
N
H
N
685
N
H
N
686
N
H
N
687
N
H
N
688
N
N
N
689
S
C
N
690
N
C
N
691
N
O
N
692
N
C
N
693
N
C
N
694
N
C
N
695
N
O
N
696
N
H
N
697
N
H
N
698
N
H
N
699
N
H
N
700
N
H
N
701
N
H
N
702
N
H
N
703
N
H
N
704
N
H
N
705
N
H
N
706
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
doub
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
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
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
sing
N
514
N
sing
N
515
N
sing
Y
516
N
sing
Y
517
N
sing
Y
518
N
doub
N
519
N
sing
Y
520
N
sing
N
521
N
sing
Y
522
N
doub
N
523
N
doub
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
doub
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
Y
543
N
doub
Y
544
N
sing
Y
545
N
sing
N
546
N
sing
Y
547
N
doub
N
548
N
sing
Y
549
N
doub
N
550
N
sing
Y
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
doub
N
562
N
sing
N
563
N
sing
N
564
N
sing
N
565
N
sing
N
566
N
sing
N
567
N
sing
N
568
N
sing
N
569
N
sing
N
570
N
sing
N
571
N
sing
N
572
N
sing
N
573
N
sing
N
574
N
sing
N
575
N
sing
N
576
N
sing
N
577
N
sing
N
578
N
doub
N
579
N
sing
N
580
N
sing
N
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
N
596
N
sing
N
597
N
sing
N
598
N
sing
N
599
N
sing
N
600
N
sing
N
601
N
sing
N
602
N
sing
N
603
N
sing
N
604
N
sing
N
605
N
sing
N
606
N
sing
N
607
N
doub
N
608
N
sing
N
609
N
sing
N
610
N
sing
N
611
N
sing
Y
612
N
doub
Y
613
N
sing
Y
614
N
sing
N
615
N
sing
Y
616
N
doub
Y
617
N
sing
Y
618
N
sing
N
619
N
sing
Y
620
N
sing
Y
621
N
doub
N
622
N
sing
Y
623
N
doub
N
624
N
sing
Y
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
sing
Y
640
N
doub
Y
641
N
sing
Y
642
N
sing
N
643
N
sing
Y
644
N
doub
N
645
N
sing
Y
646
N
doub
N
647
N
sing
Y
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
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
doub
N
680
N
sing
N
681
N
sing
N
682
N
sing
N
683
N
doub
N
684
N
sing
N
685
N
doub
N
686
N
sing
N
687
N
sing
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
doub
N
695
N
sing
N
696
N
sing
N
697
N
sing
N
698
N
sing
N
699
N
sing
N
700
N
sing
N
701
N
sing
N
702
N
sing
N
703
N
sing
N
704
N
sing
N
705
N
sing
To be Published
0353
RNA/DNA hybrid in complex with RNase H catalytic domain mutant D132N
10.2210/pdb3uld/pdb
pdb_00003uld
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
mirrors
CCD
2011-10-25
ADSC QUANTUM 315
mirror
SINGLE WAVELENGTH
M
x-ray
1
0.9765
1.0
5.0.3
ALS
0.9765
SYNCHROTRON
ALS BEAMLINE 5.0.3
16329.478
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
1904.208
DNA (5'-D(*AP*TP*GP*TP*CP*(PGN))-3')
1
syn
polymer
24.305
MAGNESIUM ION
4
syn
non-polymer
18.015
water
124
nat
water
RNase H
no
no
GSHMAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQ
TAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
GSHMAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQ
TAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
A
polypeptide(L)
no
no
UCGACA
UCGACA
B
polyribonucleotide
no
yes
(DA)(DT)(DG)(DT)(DC)(PGN)
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
n
n
n
n
sample
rnhA, BH0863
86665
Bacillus halodurans
866768
Escherichia coli
BL21-Gold(DE3)pLysS AG
Plasmid
pET15b
1
2.36
47.85
VAPOR DIFFUSION, SITTING DROP
6.0
0.04 M Magnesium chloride, 0.05 M Sodium cacodylate, 5% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
-2.336
1
19
B
2
C
6
-2.330
B_C2:PGN6_C
1
-6.846
0.149
0.048
-0.177
-16.437
1
19
B
3
C
5
0.967
B_G3:DC5_C
2
-11.742
-0.186
-0.390
-0.132
-11.458
1
20
B
4
C
4
2.550
B_A4:DT4_C
3
-13.677
0.076
-0.137
-0.156
-7.507
1
19
B
5
C
3
-0.779
B_C5:DG3_C
4
-8.621
0.212
0.208
-0.227
-12.050
1
20
B
6
C
2
0.696
B_A6:DT2_C
5
-9.571
0.021
-0.296
-0.125
3.381
37.392
B
B
2
3
11.425
C
C
6
5
3.627
7.253
0.489
-1.138
BB_C2G3:DC5PGN6_CC
1
5.854
-9.223
36.251
-2.815
0.077
3.003
34.187
B
B
3
4
9.933
C
C
5
4
3.257
5.812
0.684
-1.371
BB_G3A4:DT4DC5_CC
2
0.981
-1.676
33.690
-3.218
-1.015
3.051
29.056
B
B
4
5
7.832
C
C
4
3
3.226
3.915
-0.733
-1.425
BB_A4C5:DG3DT4_CC
3
-1.937
3.876
28.733
-3.670
1.051
3.002
27.070
B
B
5
6
13.889
C
C
3
2
3.402
6.325
1.025
-1.970
BB_C5A6:DT2DG3_CC
4
8.824
-19.377
24.835
-5.848
0.097
software
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
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-11-14
1
1
2017-11-08
1
2
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id
_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
SELENIUM DERIVATIZED RNA/DNA HYBRID IN COMPLEX WITH RNASE H CATALYTIC DOMAIN MUTANT D132N
RCSB
Y
RCSB
2011-11-10
REL
REL
MG
MAGNESIUM ION
HOH
water
3TWH
PDB entry 3TWH
PDB
experimental model
MG
1
4
MG
MG
201
A
MG
2
4
MG
MG
202
A
MG
3
4
MG
MG
203
A
MG
4
4
MG
MG
204
A
HOH
1
5
HOH
HOH
301
A
HOH
5
5
HOH
HOH
302
A
HOH
6
5
HOH
HOH
303
A
HOH
7
5
HOH
HOH
304
A
HOH
8
5
HOH
HOH
305
A
HOH
9
5
HOH
HOH
306
A
HOH
10
5
HOH
HOH
307
A
HOH
11
5
HOH
HOH
308
A
HOH
13
5
HOH
HOH
309
A
HOH
15
5
HOH
HOH
310
A
HOH
16
5
HOH
HOH
311
A
HOH
17
5
HOH
HOH
312
A
HOH
19
5
HOH
HOH
313
A
HOH
20
5
HOH
HOH
314
A
HOH
22
5
HOH
HOH
315
A
HOH
24
5
HOH
HOH
316
A
HOH
25
5
HOH
HOH
317
A
HOH
26
5
HOH
HOH
318
A
HOH
28
5
HOH
HOH
319
A
HOH
29
5
HOH
HOH
320
A
HOH
30
5
HOH
HOH
321
A
HOH
31
5
HOH
HOH
322
A
HOH
32
5
HOH
HOH
323
A
HOH
33
5
HOH
HOH
324
A
HOH
34
5
HOH
HOH
325
A
HOH
38
5
HOH
HOH
326
A
HOH
39
5
HOH
HOH
327
A
HOH
41
5
HOH
HOH
328
A
HOH
44
5
HOH
HOH
329
A
HOH
45
5
HOH
HOH
330
A
HOH
46
5
HOH
HOH
331
A
HOH
47
5
HOH
HOH
332
A
HOH
48
5
HOH
HOH
333
A
HOH
49
5
HOH
HOH
334
A
HOH
51
5
HOH
HOH
335
A
HOH
52
5
HOH
HOH
336
A
HOH
53
5
HOH
HOH
337
A
HOH
54
5
HOH
HOH
338
A
HOH
2
5
HOH
HOH
339
A
HOH
3
5
HOH
HOH
340
A
HOH
4
5
HOH
HOH
341
A
HOH
56
5
HOH
HOH
342
A
HOH
57
5
HOH
HOH
343
A
HOH
58
5
HOH
HOH
344
A
HOH
59
5
HOH
HOH
345
A
HOH
60
5
HOH
HOH
346
A
HOH
61
5
HOH
HOH
347
A
HOH
62
5
HOH
HOH
348
A
HOH
64
5
HOH
HOH
349
A
HOH
65
5
HOH
HOH
350
A
HOH
66
5
HOH
HOH
351
A
HOH
67
5
HOH
HOH
352
A
HOH
68
5
HOH
HOH
353
A
HOH
69
5
HOH
HOH
354
A
HOH
70
5
HOH
HOH
355
A
HOH
73
5
HOH
HOH
356
A
HOH
74
5
HOH
HOH
357
A
HOH
75
5
HOH
HOH
358
A
HOH
76
5
HOH
HOH
359
A
HOH
77
5
HOH
HOH
360
A
HOH
78
5
HOH
HOH
361
A
HOH
79
5
HOH
HOH
362
A
HOH
80
5
HOH
HOH
363
A
HOH
81
5
HOH
HOH
364
A
HOH
82
5
HOH
HOH
365
A
HOH
83
5
HOH
HOH
366
A
HOH
84
5
HOH
HOH
367
A
HOH
86
5
HOH
HOH
368
A
HOH
87
5
HOH
HOH
369
A
HOH
88
5
HOH
HOH
370
A
HOH
89
5
HOH
HOH
371
A
HOH
90
5
HOH
HOH
372
A
HOH
91
5
HOH
HOH
373
A
HOH
92
5
HOH
HOH
374
A
HOH
94
5
HOH
HOH
375
A
HOH
96
5
HOH
HOH
376
A
HOH
97
5
HOH
HOH
377
A
HOH
98
5
HOH
HOH
378
A
HOH
99
5
HOH
HOH
379
A
HOH
100
5
HOH
HOH
380
A
HOH
103
5
HOH
HOH
381
A
HOH
104
5
HOH
HOH
382
A
HOH
105
5
HOH
HOH
383
A
HOH
106
5
HOH
HOH
384
A
HOH
107
5
HOH
HOH
385
A
HOH
108
5
HOH
HOH
386
A
HOH
109
5
HOH
HOH
387
A
HOH
110
5
HOH
HOH
388
A
HOH
111
5
HOH
HOH
389
A
HOH
112
5
HOH
HOH
390
A
HOH
113
5
HOH
HOH
391
A
HOH
114
5
HOH
HOH
392
A
HOH
115
5
HOH
HOH
393
A
HOH
116
5
HOH
HOH
394
A
HOH
120
5
HOH
HOH
395
A
HOH
123
5
HOH
HOH
396
A
HOH
124
5
HOH
HOH
397
A
HOH
14
5
HOH
HOH
101
B
HOH
35
5
HOH
HOH
102
B
HOH
36
5
HOH
HOH
103
B
HOH
42
5
HOH
HOH
104
B
HOH
50
5
HOH
HOH
105
B
HOH
63
5
HOH
HOH
106
B
HOH
71
5
HOH
HOH
107
B
HOH
93
5
HOH
HOH
108
B
HOH
95
5
HOH
HOH
109
B
HOH
117
5
HOH
HOH
110
B
HOH
121
5
HOH
HOH
111
B
HOH
122
5
HOH
HOH
112
B
HOH
12
5
HOH
HOH
101
C
HOH
18
5
HOH
HOH
102
C
HOH
21
5
HOH
HOH
103
C
HOH
23
5
HOH
HOH
104
C
HOH
27
5
HOH
HOH
105
C
HOH
37
5
HOH
HOH
106
C
HOH
40
5
HOH
HOH
107
C
HOH
43
5
HOH
HOH
108
C
HOH
55
5
HOH
HOH
109
C
HOH
72
5
HOH
HOH
110
C
HOH
85
5
HOH
HOH
111
C
HOH
101
5
HOH
HOH
112
C
HOH
102
5
HOH
HOH
113
C
HOH
118
5
HOH
HOH
114
C
HOH
119
5
HOH
HOH
115
C
n
1
55
A
n
2
56
A
n
3
57
A
n
4
58
A
n
5
59
A
n
6
60
A
GLU
61
n
7
GLU
61
A
GLU
62
n
8
GLU
62
A
ILE
63
n
9
ILE
63
A
ILE
64
n
10
ILE
64
A
TRP
65
n
11
TRP
65
A
GLU
66
n
12
GLU
66
A
SER
67
n
13
SER
67
A
LEU
68
n
14
LEU
68
A
SER
69
n
15
SER
69
A
VAL
70
n
16
VAL
70
A
ASP
71
n
17
ASP
71
A
VAL
72
n
18
VAL
72
A
GLY
73
n
19
GLY
73
A
SER
74
n
20
SER
74
A
GLN
75
n
21
GLN
75
A
GLY
76
n
22
GLY
76
A
ASN
77
n
23
ASN
77
A
PRO
78
n
24
PRO
78
A
GLY
79
n
25
GLY
79
A
ILE
80
n
26
ILE
80
A
VAL
81
n
27
VAL
81
A
GLU
82
n
28
GLU
82
A
TYR
83
n
29
TYR
83
A
LYS
84
n
30
LYS
84
A
GLY
85
n
31
GLY
85
A
VAL
86
n
32
VAL
86
A
ASP
87
n
33
ASP
87
A
THR
88
n
34
THR
88
A
LYS
89
n
35
LYS
89
A
THR
90
n
36
THR
90
A
GLY
91
n
37
GLY
91
A
GLU
92
n
38
GLU
92
A
VAL
93
n
39
VAL
93
A
LEU
94
n
40
LEU
94
A
PHE
95
n
41
PHE
95
A
GLU
96
n
42
GLU
96
A
ARG
97
n
43
ARG
97
A
GLU
98
n
44
GLU
98
A
PRO
99
n
45
PRO
99
A
ILE
100
n
46
ILE
100
A
PRO
101
n
47
PRO
101
A
ILE
102
n
48
ILE
102
A
GLY
103
n
49
GLY
103
A
THR
104
n
50
THR
104
A
ASN
105
n
51
ASN
105
A
ASN
106
n
52
ASN
106
A
MET
107
n
53
MET
107
A
GLY
108
n
54
GLY
108
A
GLU
109
n
55
GLU
109
A
PHE
110
n
56
PHE
110
A
LEU
111
n
57
LEU
111
A
ALA
112
n
58
ALA
112
A
ILE
113
n
59
ILE
113
A
VAL
114
n
60
VAL
114
A
HIS
115
n
61
HIS
115
A
GLY
116
n
62
GLY
116
A
LEU
117
n
63
LEU
117
A
ARG
118
n
64
ARG
118
A
TYR
119
n
65
TYR
119
A
LEU
120
n
66
LEU
120
A
LYS
121
n
67
LYS
121
A
GLU
122
n
68
GLU
122
A
ARG
123
n
69
ARG
123
A
ASN
124
n
70
ASN
124
A
SER
125
n
71
SER
125
A
ARG
126
n
72
ARG
126
A
LYS
127
n
73
LYS
127
A
PRO
128
n
74
PRO
128
A
ILE
129
n
75
ILE
129
A
TYR
130
n
76
TYR
130
A
SER
131
n
77
SER
131
A
ASN
132
n
78
ASN
132
A
SER
133
n
79
SER
133
A
GLN
134
n
80
GLN
134
A
THR
135
n
81
THR
135
A
ALA
136
n
82
ALA
136
A
ILE
137
n
83
ILE
137
A
LYS
138
n
84
LYS
138
A
TRP
139
n
85
TRP
139
A
VAL
140
n
86
VAL
140
A
LYS
141
n
87
LYS
141
A
ASP
142
n
88
ASP
142
A
LYS
143
n
89
LYS
143
A
LYS
144
n
90
LYS
144
A
ALA
145
n
91
ALA
145
A
LYS
146
n
92
LYS
146
A
SER
147
n
93
SER
147
A
THR
148
n
94
THR
148
A
LEU
149
n
95
LEU
149
A
VAL
150
n
96
VAL
150
A
ARG
151
n
97
ARG
151
A
ASN
152
n
98
ASN
152
A
GLU
153
n
99
GLU
153
A
GLU
154
n
100
GLU
154
A
THR
155
n
101
THR
155
A
ALA
156
n
102
ALA
156
A
LEU
157
n
103
LEU
157
A
ILE
158
n
104
ILE
158
A
TRP
159
n
105
TRP
159
A
LYS
160
n
106
LYS
160
A
LEU
161
n
107
LEU
161
A
VAL
162
n
108
VAL
162
A
ASP
163
n
109
ASP
163
A
GLU
164
n
110
GLU
164
A
ALA
165
n
111
ALA
165
A
GLU
166
n
112
GLU
166
A
GLU
167
n
113
GLU
167
A
TRP
168
n
114
TRP
168
A
LEU
169
n
115
LEU
169
A
ASN
170
n
116
ASN
170
A
THR
171
n
117
THR
171
A
HIS
172
n
118
HIS
172
A
THR
173
n
119
THR
173
A
TYR
174
n
120
TYR
174
A
GLU
175
n
121
GLU
175
A
THR
176
n
122
THR
176
A
PRO
177
n
123
PRO
177
A
ILE
178
n
124
ILE
178
A
LEU
179
n
125
LEU
179
A
LYS
180
n
126
LYS
180
A
TRP
181
n
127
TRP
181
A
GLN
182
n
128
GLN
182
A
THR
183
n
129
THR
183
A
ASP
184
n
130
ASP
184
A
LYS
185
n
131
LYS
185
A
TRP
186
n
132
TRP
186
A
GLY
187
n
133
GLY
187
A
GLU
188
n
134
GLU
188
A
ILE
189
n
135
ILE
189
A
LYS
190
n
136
LYS
190
A
ALA
191
n
137
ALA
191
A
ASP
192
n
138
ASP
192
A
TYR
193
n
139
TYR
193
A
n
140
194
A
n
141
195
A
n
142
196
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
DT
4
n
4
DT
4
C
DC
5
n
5
DC
5
C
PGN
6
n
6
PGN
6
C
author_and_software_defined_assembly
PISA
3
trimeric
2670
-37
8580
A
ASP
71
A
A
OD1
ASP
17
1_555
A
MG
201
D
MG
MG
1_555
A
GLU
109
A
OE2
GLU
55
1_555
99.3
A
ASP
71
A
A
OD1
ASP
17
1_555
A
MG
201
D
MG
MG
1_555
A
ASN
132
A
OD1
ASN
78
1_555
138.6
A
GLU
109
A
OE2
GLU
55
1_555
A
MG
201
D
MG
MG
1_555
A
ASN
132
A
OD1
ASN
78
1_555
99.7
A
ASP
71
A
A
OD1
ASP
17
1_555
A
MG
201
D
MG
MG
1_555
B
A
6
B
O3'
A
6
1_555
124.6
A
GLU
109
A
OE2
GLU
55
1_555
A
MG
201
D
MG
MG
1_555
B
A
6
B
O3'
A
6
1_555
95.2
A
ASN
132
A
OD1
ASN
78
1_555
A
MG
201
D
MG
MG
1_555
B
A
6
B
O3'
A
6
1_555
89.8
A
ASP
71
A
A
OD2
ASP
17
1_555
A
MG
202
E
MG
MG
1_555
A
ASP
192
A
OD2
ASP
138
1_555
95.2
A
ASP
71
A
A
OD2
ASP
17
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
366
H
O
HOH
1_555
102.6
A
ASP
192
A
OD2
ASP
138
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
366
H
O
HOH
1_555
82.6
A
ASP
71
A
A
OD2
ASP
17
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
383
H
O
HOH
1_555
82.5
A
ASP
192
A
OD2
ASP
138
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
383
H
O
HOH
1_555
97.6
A
HOH
366
H
O
HOH
1_555
A
MG
202
E
MG
MG
1_555
A
HOH
383
H
O
HOH
1_555
174.9
A
HOH
338
H
O
HOH
1_555
A
MG
203
F
MG
MG
1_555
A
HOH
356
H
O
HOH
1_555
84.6
C
PGN
6
2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE
C
PGN
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
46
A
N
VAL
81
A
N
VAL
27
A
O
VAL
86
A
O
VAL
32
A
N
SER
69
A
N
SER
15
A
N
LEU
68
A
N
LEU
14
A
O
TYR
130
A
O
TYR
76
A
N
ILE
129
A
N
ILE
75
A
O
LEU
179
A
O
LEU
125
1
A
GLY
55
A
GLY
1
1
Y
1
A
SER
56
A
SER
2
1
Y
1
A
HIS
57
A
HIS
3
1
Y
1
A
MET
58
A
MET
4
1
Y
1
A
ALA
59
A
ALA
5
1
Y
1
A
LYS
60
A
LYS
6
1
Y
1
A
GLY
194
A
GLY
140
1
Y
1
A
ARG
195
A
ARG
141
1
Y
1
A
LYS
196
A
LYS
142
1
Y
1
A
A
MG
O
MG
HOH
204
303
1.70
1
A
A
O
O
HOH
HOH
317
389
2.13
1
20.72
1.50
110.10
130.82
A
A
A
CB
CA
C
ALA
ALA
ALA
191
191
191
B
B
N
1
-13.77
1.90
104.00
90.23
B
B
B
O3'
P
O5'
U
C
C
1
2
2
Y
1
-8.18
0.80
109.40
101.22
B
B
B
O5'
C5'
C4'
C
C
C
2
2
2
N
1
-3.29
0.50
129.30
126.01
B
B
B
N1
C2
N3
A
A
A
6
6
6
N
1
-6.60
0.90
105.70
99.10
C
C
C
O5'
P
OP2
DT
DT
DT
2
2
2
N
1
2.50
0.30
108.30
110.80
C
C
C
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
A
A
CA
C
ALA
ALA
191
191
0.408
0.026
1.525
1.933
B
N
1
B
B
O5'
C5'
A
A
4
4
-0.061
0.009
1.420
1.359
N
21.836
0.11
0.00
-0.58
1.03
0.00
-1.27
0.959
0.941
0.23463
0.19366
0.19589
1.60
30
1201
25140
22402
5.1
93.89
2.080
0.072
RANDOM
1
THROUGHOUT
0
FOURIER SYNTHESIS
0.100
0.80
0.80
1.40
PDB entry 3TWH
MAXIMUM LIKELIHOOD
MASK
1.60
30
124
1462
4
249
1085
0.012
0.022
1408
1.560
2.175
1966
5.699
5.000
139
35.193
25.370
54
14.499
15.000
208
13.428
15.000
5
0.096
0.200
221
0.007
0.021
976
0.882
1.500
672
1.639
2.000
1096
2.304
3.000
736
3.540
4.500
867
0.297
0.267
1.639
57
1107
1164
20
62.88
1.6
61.94
3ULD
25140
23657
0
0
0.08
1
16.9
4.8
94.1
0.08
1.6
1.639
16.9
25140
1
4.8
94.1
data collection
HKL-2000
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
High resolution structure of DNA/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
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
THR
104
A
THR
50
HELX_P
A
ARG
123
A
ARG
69
1
1
20
A
SER
133
A
SER
79
HELX_P
A
LYS
143
A
LYS
89
1
2
11
A
THR
155
A
THR
101
HELX_P
A
ASN
170
A
ASN
116
1
3
16
A
GLN
182
A
GLN
128
HELX_P
A
GLY
187
A
GLY
133
1
4
6
covale
1.597
both
C
DC
5
C
O3'
DC
5
1_555
C
PGN
6
C
P
PGN
6
1_555
metalc
2.221
A
A
ASP
71
A
OD1
ASP
17
1_555
A
MG
201
D
MG
MG
1_555
metalc
1.993
A
A
ASP
71
A
OD2
ASP
17
1_555
A
MG
202
E
MG
MG
1_555
metalc
2.089
A
GLU
109
A
OE2
GLU
55
1_555
A
MG
201
D
MG
MG
1_555
metalc
2.071
A
ASN
132
A
OD1
ASN
78
1_555
A
MG
201
D
MG
MG
1_555
metalc
2.473
A
ASP
192
A
OD2
ASP
138
1_555
A
MG
202
E
MG
MG
1_555
metalc
2.737
A
MG
201
D
MG
MG
1_555
B
A
6
B
O3'
A
6
1_555
metalc
2.009
A
MG
202
E
MG
MG
1_555
A
HOH
366
H
O
HOH
1_555
metalc
1.781
A
MG
202
E
MG
MG
1_555
A
HOH
383
H
O
HOH
1_555
metalc
1.908
A
MG
203
F
MG
MG
1_555
A
HOH
338
H
O
HOH
1_555
metalc
1.915
A
MG
203
F
MG
MG
1_555
A
HOH
356
H
O
HOH
1_555
hydrog
WATSON-CRICK
B
C
2
B
N3
C
2
1_555
C
PGN
6
C
N1
PGN
6
1_555
hydrog
WATSON-CRICK
B
C
2
B
N4
C
2
1_555
C
PGN
6
C
O6
PGN
6
1_555
hydrog
WATSON-CRICK
B
C
2
B
O2
C
2
1_555
C
PGN
6
C
N2
PGN
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
WATSON-CRICK
B
C
5
B
N3
C
5
1_555
C
DG
3
C
N1
DG
3
1_555
hydrog
WATSON-CRICK
B
C
5
B
N4
C
5
1_555
C
DG
3
C
O6
DG
3
1_555
hydrog
WATSON-CRICK
B
C
5
B
O2
C
5
1_555
C
DG
3
C
N2
DG
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
RNase H, DNA/RNA hybrid, ENDONUCLEASE, HYDROLASE, MAGNESIUM, RIBONUCLEASE H, HYDROLASE-RNA-DNA complex
A
ASN
77
A
ASN
23
1
A
PRO
78
A
PRO
24
1.41
RNH1_BACHD
UNP
1
59
Q9KEI9
AKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSDSQTAIK
WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK
3ULD
PDB
2
3ULD
3ULD
PDB
3
3ULD
59
196
3ULD
59
196
Q9KEI9
A
1
5
142
1
6
3ULD
1
6
3ULD
B
2
1
6
1
6
3ULD
1
6
3ULD
C
3
1
6
1
expression tag
GLY
55
3ULD
A
Q9KEI9
UNP
1
1
expression tag
SER
56
3ULD
A
Q9KEI9
UNP
2
1
expression tag
HIS
57
3ULD
A
Q9KEI9
UNP
3
1
expression tag
MET
58
3ULD
A
Q9KEI9
UNP
4
1
ASP
engineered mutation
ASN
132
3ULD
A
Q9KEI9
UNP
132
78
5
anti-parallel
anti-parallel
parallel
parallel
A
VAL
93
A
VAL
39
A
GLY
103
A
GLY
49
A
GLY
79
A
GLY
25
A
ASP
87
A
ASP
33
A
LEU
68
A
LEU
14
A
GLN
75
A
GLN
21
A
ILE
129
A
ILE
75
A
SER
131
A
SER
77
A
ILE
178
A
ILE
124
A
LYS
180
A
LYS
126
BINDING SITE FOR RESIDUE MG A 201
A
MG
201
Software
6
BINDING SITE FOR RESIDUE MG A 202
A
MG
202
Software
6
BINDING SITE FOR RESIDUE MG A 203
A
MG
203
Software
4
BINDING SITE FOR RESIDUE MG A 204
A
MG
204
Software
3
A
ASP
71
A
ASP
17
6
1_555
A
GLU
109
A
GLU
55
6
1_555
A
ASN
132
A
ASN
78
6
1_555
A
HOH
301
H
HOH
6
1_555
A
HOH
302
H
HOH
6
1_555
B
A
6
B
A
6
6
1_555
A
ASP
71
A
ASP
17
6
1_555
A
VAL
72
A
VAL
18
6
1_555
A
ASP
192
A
ASP
138
6
1_555
A
HOH
366
H
HOH
6
1_555
A
HOH
383
H
HOH
6
1_555
B
U
1
B
U
1
6
4_546
A
ARG
118
A
ARG
64
4
1_555
A
TRP
168
A
TRP
114
4
1_555
A
HOH
338
H
HOH
4
1_555
A
HOH
356
H
HOH
4
1_555
A
TYR
83
A
TYR
29
3
1_555
A
ARG
97
A
ARG
43
3
1_555
A
HOH
303
H
HOH
3
1_555
5
C 1 2 1