0.015078
0.000000
0.000000
0.000000
0.009443
0.000000
0.000000
0.000000
0.024086
0.00000
0.00000
0.00000
Fromme, J.C.
Verdine, G.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
66.321
105.896
41.518
C5 H11 O6 P
198.111
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
ABASIC DIDEOXYRIBOSE
DNA linking
C9 H12 I N2 O8 P
434.078
n
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA 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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Na 1
22.990
SODIUM 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
Fe4 S4
351.640
IRON/SULFUR CLUSTER
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
N
C
N
8
R
C
N
9
N
O
N
10
N
C
N
11
S
C
N
12
N
O
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
N
N
25
N
C
N
26
N
N
N
27
N
C
N
28
N
C
N
29
N
C
N
30
N
O
N
31
N
O
N
32
N
I
N
33
R
C
N
34
N
C
N
35
S
C
N
36
R
C
N
37
N
O
N
38
N
O
N
39
N
C
N
40
N
O
N
41
N
P
N
42
N
O
N
43
N
O
N
44
N
O
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
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
N
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
C
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
N
N
71
S
C
N
72
N
C
N
73
N
O
N
74
N
C
N
75
N
C
N
76
N
C
N
77
N
N
N
78
N
C
N
79
N
N
N
80
N
N
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
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
H
N
96
N
H
N
97
N
N
N
98
S
C
N
99
N
C
N
100
N
O
N
101
N
C
N
102
N
C
N
103
N
O
N
104
N
N
N
105
N
O
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
N
N
115
S
C
N
116
N
C
N
117
N
O
N
118
N
C
N
119
N
C
N
120
N
O
N
121
N
O
N
122
N
O
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
R
C
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
S
N
136
N
O
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
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
Y
156
N
N
Y
157
N
C
Y
158
N
N
Y
159
N
C
Y
160
N
C
N
161
N
N
Y
162
N
N
Y
163
N
C
Y
164
N
N
Y
165
N
C
N
166
N
H
N
167
N
H
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
O
N
181
N
P
N
182
N
O
N
183
N
O
N
184
N
O
N
185
N
C
N
186
R
C
N
187
N
O
N
188
S
C
N
189
N
O
N
190
N
C
N
191
R
C
N
192
N
N
N
193
N
C
N
194
N
O
N
195
N
N
N
196
N
C
N
197
N
N
N
198
N
C
N
199
N
C
N
200
N
H
N
201
N
H
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
O
N
215
N
P
N
216
N
O
N
217
N
O
N
218
N
O
N
219
N
C
N
220
R
C
N
221
N
O
N
222
S
C
N
223
N
O
N
224
N
C
N
225
R
C
Y
226
N
N
Y
227
N
C
Y
228
N
N
Y
229
N
C
N
230
N
C
N
231
N
O
N
232
N
N
N
233
N
C
N
234
N
N
N
235
N
N
Y
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
O
N
252
N
P
N
253
N
O
N
254
N
O
N
255
N
O
N
256
N
C
N
257
R
C
N
258
N
O
N
259
S
C
N
260
N
O
N
261
N
C
N
262
R
C
N
263
N
N
N
264
N
C
N
265
N
O
N
266
N
N
N
267
N
C
N
268
N
O
N
269
N
C
N
270
N
C
N
271
N
C
N
272
N
H
N
273
N
H
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
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
O
N
295
N
N
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
C
N
313
N
C
N
314
N
O
N
315
N
O
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
N
C
N
328
N
C
N
329
N
O
N
330
N
O
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
Y
341
N
C
Y
342
N
N
Y
343
N
C
Y
344
N
C
Y
345
N
N
N
346
N
O
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
O
N
358
N
H
N
359
N
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
S
C
N
365
N
C
N
366
N
C
N
367
N
C
N
368
N
O
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
O
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
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
N
N
405
S
C
N
406
N
C
N
407
N
O
N
408
N
C
N
409
N
C
N
410
N
C
N
411
N
C
N
412
N
N
N
413
N
O
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
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
N
N
430
S
C
N
431
N
C
N
432
N
O
N
433
N
C
N
434
N
C
N
435
N
S
N
436
N
C
N
437
N
O
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
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
NA
N
450
N
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
N
461
N
O
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
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
N
N
474
S
C
N
475
N
C
N
476
N
O
N
477
N
C
N
478
N
C
N
479
N
C
N
480
N
O
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
N
N
491
S
C
N
492
N
C
N
493
N
O
N
494
N
C
N
495
N
O
N
496
N
O
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
FE
N
505
N
FE
N
506
N
FE
N
507
N
FE
N
508
N
S
N
509
N
S
N
510
N
S
N
511
N
S
N
512
N
N
N
513
S
C
N
514
N
C
N
515
N
O
N
516
R
C
N
517
N
O
N
518
N
C
N
519
N
O
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
N
N
530
S
C
N
531
N
C
N
532
N
O
N
533
N
C
Y
534
N
C
Y
535
N
C
Y
536
N
C
Y
537
N
N
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
H
N
556
N
N
N
557
S
C
N
558
N
C
N
559
N
O
N
560
N
C
Y
561
N
C
Y
562
N
C
Y
563
N
C
Y
564
N
C
Y
565
N
C
Y
566
N
C
N
567
N
O
N
568
N
O
N
569
N
H
N
570
N
H
N
571
N
H
N
572
N
H
N
573
N
H
N
574
N
H
N
575
N
H
N
576
N
H
N
577
N
H
N
578
N
H
N
579
N
H
N
580
N
N
N
581
S
C
N
582
N
C
N
583
N
O
N
584
N
C
N
585
N
C
N
586
N
C
N
587
N
O
N
588
N
H
N
589
N
H
N
590
N
H
N
591
N
H
N
592
N
H
N
593
N
H
N
594
N
H
N
595
N
H
N
596
N
H
N
597
N
H
N
598
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
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
doub
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
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
doub
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
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
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
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
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
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
Y
163
N
sing
Y
164
N
sing
Y
165
N
doub
N
166
N
sing
Y
167
N
sing
Y
168
N
sing
Y
169
N
doub
N
170
N
sing
Y
171
N
doub
N
172
N
sing
N
173
N
sing
Y
174
N
sing
Y
175
N
doub
N
176
N
sing
Y
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
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
doub
N
204
N
sing
N
205
N
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
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
sing
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
Y
236
N
sing
Y
237
N
sing
Y
238
N
doub
N
239
N
sing
Y
240
N
sing
N
241
N
sing
Y
242
N
doub
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
doub
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
doub
N
255
N
sing
N
256
N
sing
N
257
N
sing
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
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
doub
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
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
doub
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
doub
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
doub
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
Y
346
N
sing
Y
347
N
doub
Y
348
N
doub
N
349
N
sing
Y
350
N
sing
N
351
N
sing
Y
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
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
doub
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
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
doub
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
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
doub
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
Y
454
N
doub
Y
455
N
sing
Y
456
N
sing
N
457
N
sing
Y
458
N
doub
N
459
N
sing
Y
460
N
doub
N
461
N
sing
Y
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
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
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
doub
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
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
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
doub
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
sing
Y
535
N
doub
Y
536
N
sing
Y
537
N
sing
N
538
N
sing
Y
539
N
doub
Y
540
N
sing
Y
541
N
sing
N
542
N
sing
Y
543
N
sing
Y
544
N
doub
N
545
N
sing
Y
546
N
doub
N
547
N
sing
Y
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
doub
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
Y
563
N
doub
Y
564
N
sing
Y
565
N
sing
N
566
N
sing
Y
567
N
doub
N
568
N
sing
Y
569
N
doub
N
570
N
sing
Y
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
sing
N
579
N
sing
N
580
N
sing
N
581
N
sing
N
582
N
doub
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
sing
N
592
N
sing
N
593
N
sing
UK
Embo J.
EMJODG
0897
0261-4189
22
3461
3471
10.1093/emboj/cdg311
12840008
Structure of a Trapped Endonuclease III-DNA Covalent Intermediate
2003
10.2210/pdb1p59/pdb
pdb_00001p59
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
IMAGE PLATE
2002-11-20
RIGAKU RAXIS IV
NULL
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
3519.119
5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3'
1
syn
polymer
3414.813
5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3'
1
syn
polymer
26236.789
Endonuclease III
1
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
351.640
IRON/SULFUR CLUSTER
1
syn
non-polymer
18.015
water
31
nat
water
no
yes
(DA)(DA)(DG)(DA)(DC)(DG)(5IU)(DG)(DG)(DA)(DC)
AAGACGUGGAC
B
polydeoxyribonucleotide
no
yes
(DT)(DG)(5IU)(DC)(DC)(DA)(3DR)(DG)(5IU)(DC)(DT)
TGUCCANGUCT
C
polydeoxyribonucleotide
no
no
GSHMLTKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDI
RSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSTAFGVPAIAVDTHVERVSKRLGFCRWDDS
VLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMRKREEKAANQK
GSHMLTKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDI
RSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSTAFGVPAIAVDTHVERVSKRLGFCRWDDS
VLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMRKREEKAANQK
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Geobacillus
Escherichia
sample
NTH
1422
Geobacillus stearothermophilus
562
Escherichia coli
BL21(C41)
PLASMID
PET28
1
2.18
43.58
VAPOR DIFFUSION, HANGING DROP
8.5
PEG 8000, TRIS, BME, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
PEG 8000
1
TRIS
1
BME
1
PEG 8000
2
TRIS
2
BME
2
-16.885
1
20
B
2
C
22
-2.207
B_DA2:DT22_C
1
-5.580
-0.118
-0.255
0.150
-4.412
1
19
B
3
C
21
0.138
B_DG3:DC21_C
2
-13.863
-0.496
0.047
-0.240
2.075
1
20
B
4
C
20
2.313
B_DA4:5IU20_C
3
-4.860
0.188
-0.016
0.287
10.089
1
19
B
5
C
19
-0.094
B_DC5:DG19_C
4
-4.081
0.053
0.033
-0.134
-6.588
1
20
B
7
C
17
5.133
B_5IU7:DA17_C
5
-10.805
0.284
0.415
0.101
-1.054
1
19
B
8
C
16
-2.305
B_DG8:DC16_C
6
-6.222
0.303
-0.059
-0.183
-10.672
1
19
B
9
C
15
4.594
B_DG9:DC15_C
7
-8.758
0.183
-0.254
0.047
-6.308
1
20
B
10
C
14
0.091
B_DA10:5IU14_C
8
-5.731
-0.411
-0.246
0.184
4.474
1
19
B
11
C
13
3.259
B_DC11:DG13_C
9
10.328
0.582
-0.138
-0.259
3.006
32.978
B
B
2
3
3.131
C
C
22
21
3.003
1.776
-0.077
0.126
BB_DA2DG3:DC21DT22_CC
1
-1.499
2.642
32.898
-0.055
-0.098
3.118
38.802
B
B
3
4
1.567
C
C
21
20
3.113
1.041
-0.161
0.127
BB_DG3DA4:5IU20DC21_CC
2
-0.717
1.080
38.782
0.070
0.160
3.058
25.975
B
B
4
5
1.459
C
C
20
19
3.083
0.656
0.329
-0.337
BB_DA4DC5:DG195IU20_CC
3
-1.053
2.343
25.946
-0.919
-1.004
3.159
37.557
B
B
7
8
2.724
C
C
17
16
3.134
1.753
-0.783
0.311
BB_5IU7DG8:DC16DA17_CC
4
-0.754
1.171
37.511
0.263
1.122
3.302
33.770
B
B
8
9
15.270
C
C
16
15
3.559
8.774
0.346
-0.545
BB_DG8DG9:DC15DC16_CC
5
-0.326
0.567
32.640
-2.456
-0.651
3.207
35.862
B
B
9
10
-1.951
C
C
15
14
3.206
-1.200
-0.233
0.190
BB_DG9DA10:5IU14DC15_CC
6
-2.234
3.631
35.775
0.477
0.064
3.096
34.168
B
B
10
11
3.937
C
C
14
13
3.186
2.310
0.690
-0.596
BB_DA10DC11:DG135IU14_CC
7
-1.989
3.389
34.036
-1.366
-1.477
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-07-15
1
1
2008-04-29
1
2
2011-07-13
1
3
2017-10-11
1
4
2023-08-16
_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_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_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.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.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_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
EndoIII-DNA covalent complex with estranged guanine
EndoIII-DNA covalent complex with estranged adenine
Endonuclease III structure
SEQUENCE
AUTHORS INFORMED THAT THE PROTEIN SEQUENCE HAS NOT
YET BEEN PUBLISHED. RESIDUES GLY -2, SER -1 AND HIS
0 ARE CLONING ARTIFACTS.
RCSB
Y
RCSB
2003-04-25
REL
REL
NA
SODIUM ION
SF4
IRON/SULFUR CLUSTER
HOH
water
1ORN
PDB ENTRY 1ORN
PDB
experimental model
NA1
1
4
NA
NA
224
A
FS4
300
5
SF4
SF4
300
A
HOH
9
6
HOH
HOH
12
B
HOH
20
6
HOH
HOH
13
B
HOH
21
6
HOH
HOH
14
B
HOH
2
6
HOH
HOH
23
C
HOH
18
6
HOH
HOH
24
C
HOH
19
6
HOH
HOH
25
C
HOH
22
6
HOH
HOH
26
C
HOH
29
6
HOH
HOH
27
C
HOH
1
6
HOH
HOH
301
A
HOH
3
6
HOH
HOH
302
A
HOH
4
6
HOH
HOH
303
A
HOH
5
6
HOH
HOH
304
A
HOH
6
6
HOH
HOH
305
A
HOH
7
6
HOH
HOH
306
A
HOH
8
6
HOH
HOH
307
A
HOH
10
6
HOH
HOH
308
A
HOH
11
6
HOH
HOH
309
A
HOH
12
6
HOH
HOH
310
A
HOH
13
6
HOH
HOH
311
A
HOH
14
6
HOH
HOH
312
A
HOH
15
6
HOH
HOH
313
A
HOH
16
6
HOH
HOH
314
A
HOH
17
6
HOH
HOH
315
A
HOH
23
6
HOH
HOH
316
A
HOH
24
6
HOH
HOH
317
A
HOH
25
6
HOH
HOH
318
A
HOH
26
6
HOH
HOH
319
A
HOH
27
6
HOH
HOH
320
A
HOH
28
6
HOH
HOH
321
A
HOH
30
6
HOH
HOH
322
A
HOH
31
6
HOH
HOH
323
A
ADE
1
n
1
DA
1
B
ADE
2
n
2
DA
2
B
GUA
3
n
3
DG
3
B
ADE
4
n
4
DA
4
B
CYT
5
n
5
DC
5
B
GUA
6
n
6
DG
6
B
5IU
7
n
7
5IU
7
B
GUA
8
n
8
DG
8
B
GUA
9
n
9
DG
9
B
ADE
10
n
10
DA
10
B
CYT
11
n
11
DC
11
B
n
1
12
C
GUA
13
n
2
DG
13
C
5IU
14
n
3
5IU
14
C
CYT
15
n
4
DC
15
C
CYT
16
n
5
DC
16
C
ADE
17
n
6
DA
17
C
3DR
18
n
7
3DR
18
C
GUA
19
n
8
DG
19
C
5IU
20
n
9
5IU
20
C
CYT
21
n
10
DC
21
C
THY
22
n
11
DT
22
C
n
1
-2
A
n
2
-1
A
n
3
0
A
ALA
1
n
4
MET
1
A
LEU
2
n
5
LEU
2
A
THR
3
n
6
THR
3
A
ALA
4
n
7
LYS
4
A
GLN
5
n
8
GLN
5
A
GLN
6
n
9
GLN
6
A
ILE
7
n
10
ILE
7
A
ARG
8
n
11
ARG
8
A
TYR
9
n
12
TYR
9
A
CYS
10
n
13
CYS
10
A
LEU
11
n
14
LEU
11
A
ALA
12
n
15
ASP
12
A
GLU
13
n
16
GLU
13
A
MET
14
n
17
MET
14
A
ALA
15
n
18
ALA
15
A
LYS
16
n
19
LYS
16
A
MET
17
n
20
MET
17
A
PHE
18
n
21
PHE
18
A
PRO
19
n
22
PRO
19
A
GLY
20
n
23
ASP
20
A
ALA
21
n
24
ALA
21
A
HIS
22
n
25
HIS
22
A
CYS
23
n
26
CYS
23
A
GLU
24
n
27
GLU
24
A
LEU
25
n
28
LEU
25
A
VAL
26
n
29
VAL
26
A
HIS
27
n
30
HIS
27
A
ARG
28
n
31
ARG
28
A
ASN
29
n
32
ASN
29
A
PRO
30
n
33
PRO
30
A
PHE
31
n
34
PHE
31
A
GLU
32
n
35
GLU
32
A
LEU
33
n
36
LEU
33
A
LEU
34
n
37
LEU
34
A
ILE
35
n
38
ILE
35
A
ALA
36
n
39
ALA
36
A
VAL
37
n
40
VAL
37
A
VAL
38
n
41
VAL
38
A
LEU
39
n
42
LEU
39
A
SER
40
n
43
SER
40
A
ALA
41
n
44
ALA
41
A
GLN
42
n
45
GLN
42
A
CYS
43
n
46
CYS
43
A
THR
44
n
47
THR
44
A
ASP
45
n
48
ASP
45
A
ALA
46
n
49
ALA
46
A
LEU
47
n
50
LEU
47
A
VAL
48
n
51
VAL
48
A
ASN
49
n
52
ASN
49
A
LYS
50
n
53
LYS
50
A
VAL
51
n
54
VAL
51
A
THR
52
n
55
THR
52
A
LYS
53
n
56
LYS
53
A
ARG
54
n
57
ARG
54
A
LEU
55
n
58
LEU
55
A
PHE
56
n
59
PHE
56
A
GLU
57
n
60
GLU
57
A
LYS
58
n
61
LYS
58
A
TYR
59
n
62
TYR
59
A
ARG
60
n
63
ARG
60
A
THR
61
n
64
THR
61
A
PRO
62
n
65
PRO
62
A
HIS
63
n
66
HIS
63
A
ASP
64
n
67
ASP
64
A
TYR
65
n
68
TYR
65
A
ILE
66
n
69
ILE
66
A
ALA
67
n
70
ALA
67
A
VAL
68
n
71
VAL
68
A
PRO
69
n
72
PRO
69
A
LEU
70
n
73
LEU
70
A
GLU
71
n
74
GLU
71
A
GLU
72
n
75
GLU
72
A
LEU
73
n
76
LEU
73
A
GLU
74
n
77
GLU
74
A
GLN
75
n
78
GLN
75
A
ASP
76
n
79
ASP
76
A
ILE
77
n
80
ILE
77
A
ARG
78
n
81
ARG
78
A
SER
79
n
82
SER
79
A
ILE
80
n
83
ILE
80
A
GLY
81
n
84
GLY
81
A
LEU
82
n
85
LEU
82
A
TYR
83
n
86
TYR
83
A
ARG
84
n
87
ARG
84
A
ASN
85
n
88
ASN
85
A
LYS
86
n
89
LYS
86
A
ALA
87
n
90
ALA
87
A
ALA
88
n
91
ARG
88
A
ASN
89
n
92
ASN
89
A
ILE
90
n
93
ILE
90
A
GLN
91
n
94
GLN
91
A
LYS
92
n
95
LYS
92
A
LEU
93
n
96
LEU
93
A
CYS
94
n
97
CYS
94
A
ALA
95
n
98
ALA
95
A
MET
96
n
99
MET
96
A
LEU
97
n
100
LEU
97
A
ILE
98
n
101
ILE
98
A
ASP
99
n
102
ASP
99
A
LYS
100
n
103
LYS
100
A
TYR
101
n
104
TYR
101
A
ASN
102
n
105
ASN
102
A
GLY
103
n
106
GLY
103
A
GLU
104
n
107
GLU
104
A
VAL
105
n
108
VAL
105
A
PRO
106
n
109
PRO
106
A
ARG
107
n
110
ARG
107
A
ASP
108
n
111
ASP
108
A
ARG
109
n
112
ARG
109
A
ASP
110
n
113
ASP
110
A
GLU
111
n
114
GLU
111
A
LEU
112
n
115
LEU
112
A
MET
113
n
116
MET
113
A
LYS
114
n
117
LYS
114
A
LEU
115
n
118
LEU
115
A
PRO
116
n
119
PRO
116
A
GLY
117
n
120
GLY
117
A
VAL
118
n
121
VAL
118
A
GLY
119
n
122
GLY
119
A
ARG
120
n
123
ARG
120
A
LYS
121
n
124
LYS
121
A
THR
122
n
125
THR
122
A
ALA
123
n
126
ALA
123
A
ASN
124
n
127
ASN
124
A
VAL
125
n
128
VAL
125
A
VAL
126
n
129
VAL
126
A
VAL
127
n
130
VAL
127
A
SER
128
n
131
SER
128
A
THR
129
n
132
THR
129
A
ALA
130
n
133
ALA
130
A
PHE
131
n
134
PHE
131
A
GLY
132
n
135
GLY
132
A
VAL
133
n
136
VAL
133
A
PRO
134
n
137
PRO
134
A
ALA
135
n
138
ALA
135
A
ILE
136
n
139
ILE
136
A
ALA
137
n
140
ALA
137
A
VAL
138
n
141
VAL
138
A
ASP
139
n
142
ASP
139
A
THR
140
n
143
THR
140
A
HIS
141
n
144
HIS
141
A
VAL
142
n
145
VAL
142
A
GLU
143
n
146
GLU
143
A
ARG
144
n
147
ARG
144
A
VAL
145
n
148
VAL
145
A
SER
146
n
149
SER
146
A
LYS
147
n
150
LYS
147
A
ARG
148
n
151
ARG
148
A
LEU
149
n
152
LEU
149
A
GLY
150
n
153
GLY
150
A
PHE
151
n
154
PHE
151
A
CYS
152
n
155
CYS
152
A
ARG
153
n
156
ARG
153
A
TRP
154
n
157
TRP
154
A
ASP
155
n
158
ASP
155
A
ASP
156
n
159
ASP
156
A
SER
157
n
160
SER
157
A
VAL
158
n
161
VAL
158
A
LEU
159
n
162
LEU
159
A
ALA
160
n
163
GLU
160
A
VAL
161
n
164
VAL
161
A
GLU
162
n
165
GLU
162
A
LYS
163
n
166
LYS
163
A
THR
164
n
167
THR
164
A
LEU
165
n
168
LEU
165
A
MET
166
n
169
MET
166
A
LYS
167
n
170
LYS
167
A
ILE
168
n
171
ILE
168
A
ILE
169
n
172
ILE
169
A
PRO
170
n
173
PRO
170
A
LYS
171
n
174
LYS
171
A
GLU
172
n
175
GLU
172
A
GLU
173
n
176
GLU
173
A
TRP
174
n
177
TRP
174
A
SER
175
n
178
SER
175
A
ILE
176
n
179
ILE
176
A
THR
177
n
180
THR
177
A
HIS
178
n
181
HIS
178
A
HIS
179
n
182
HIS
179
A
ARG
180
n
183
ARG
180
A
MET
181
n
184
MET
181
A
ILE
182
n
185
ILE
182
A
PHE
183
n
186
PHE
183
A
PHE
184
n
187
PHE
184
A
GLY
185
n
188
GLY
185
A
ARG
186
n
189
ARG
186
A
TYR
187
n
190
TYR
187
A
HIS
188
n
191
HIS
188
A
CYS
189
n
192
CYS
189
A
LYS
190
n
193
LYS
190
A
ALA
191
n
194
ALA
191
A
GLY
192
n
195
GLN
192
A
GLY
193
n
196
SER
193
A
PRO
194
n
197
PRO
194
A
ALA
195
n
198
GLN
195
A
CYS
196
n
199
CYS
196
A
PRO
197
n
200
PRO
197
A
SER
198
n
201
SER
198
A
CYS
199
n
202
CYS
199
A
PRO
200
n
203
PRO
200
A
LEU
201
n
204
LEU
201
A
LEU
202
n
205
LEU
202
A
HIS
203
n
206
HIS
203
A
LEU
204
n
207
LEU
204
A
CYS
205
n
208
CYS
205
A
ALA
206
n
209
ARG
206
A
GLU
207
n
210
GLU
207
A
GLY
208
n
211
GLY
208
A
LYS
209
n
212
LYS
209
A
LYS
210
n
213
LYS
210
A
ARG
211
n
214
ARG
211
A
MET
212
n
215
MET
212
A
ALA
213
n
216
ARG
213
A
GLY
214
n
217
LYS
214
A
n
218
215
A
n
219
216
A
n
220
217
A
n
221
218
A
n
222
219
A
n
223
220
A
n
224
221
A
n
225
222
A
n
226
223
A
author_defined_assembly
3
trimeric
C
DC
21
B
OP1
DC
10
1_555
A
NA
224
D
NA
NA
1_555
A
MET
113
C
O
MET
116
1_555
162.5
C
DC
21
B
OP1
DC
10
1_555
A
NA
224
D
NA
NA
1_555
A
LEU
115
C
O
LEU
118
1_555
94.6
A
MET
113
C
O
MET
116
1_555
A
NA
224
D
NA
NA
1_555
A
LEU
115
C
O
LEU
118
1_555
102.5
C
DC
21
B
OP1
DC
10
1_555
A
NA
224
D
NA
NA
1_555
A
VAL
118
C
O
VAL
121
1_555
91.7
A
MET
113
C
O
MET
116
1_555
A
NA
224
D
NA
NA
1_555
A
VAL
118
C
O
VAL
121
1_555
87.4
A
LEU
115
C
O
LEU
118
1_555
A
NA
224
D
NA
NA
1_555
A
VAL
118
C
O
VAL
121
1_555
82.4
A
CYS
189
C
SG
CYS
192
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S1
SF4
1_555
110.7
A
CYS
189
C
SG
CYS
192
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
109.0
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
113.6
A
CYS
189
C
SG
CYS
192
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
119.4
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
101.1
A
SF4
300
E
S3
SF4
1_555
A
SF4
300
E
FE2
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
103.0
A
CYS
196
C
SG
CYS
199
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S1
SF4
1_555
102.0
A
CYS
196
C
SG
CYS
199
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S2
SF4
1_555
125.1
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S2
SF4
1_555
101.7
A
CYS
196
C
SG
CYS
199
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
112.0
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
107.1
A
SF4
300
E
S2
SF4
1_555
A
SF4
300
E
FE3
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
107.0
A
CYS
199
C
SG
CYS
202
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S2
SF4
1_555
121.1
A
CYS
199
C
SG
CYS
202
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
112.5
A
SF4
300
E
S2
SF4
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
100.4
A
CYS
199
C
SG
CYS
202
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
118.8
A
SF4
300
E
S2
SF4
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
101.1
A
SF4
300
E
S3
SF4
1_555
A
SF4
300
E
FE1
SF4
1_555
A
SF4
300
E
S4
SF4
1_555
99.5
A
CYS
205
C
SG
CYS
208
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S1
SF4
1_555
118.1
A
CYS
205
C
SG
CYS
208
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S2
SF4
1_555
106.6
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S2
SF4
1_555
100.2
A
CYS
205
C
SG
CYS
208
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
118.9
A
SF4
300
E
S1
SF4
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
105.4
A
SF4
300
E
S2
SF4
1_555
A
SF4
300
E
FE4
SF4
1_555
A
SF4
300
E
S3
SF4
1_555
105.4
B
5IU
7
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
A
5IU
7
DU
C
5IU
14
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
B
5IU
3
DU
C
5IU
20
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
B
5IU
9
DU
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
1
C
P
DG
13
B
P
DG
2
1
Y
1
C
OP1
DG
13
B
OP1
DG
2
1
Y
1
C
OP2
DG
13
B
OP2
DG
2
1
Y
1
A
CG
MET
1
C
CG
MET
4
1
Y
1
A
SD
MET
1
C
SD
MET
4
1
Y
1
A
CE
MET
1
C
CE
MET
4
1
Y
1
A
CG
LYS
4
C
CG
LYS
7
1
Y
1
A
CD
LYS
4
C
CD
LYS
7
1
Y
1
A
CE
LYS
4
C
CE
LYS
7
1
Y
1
A
NZ
LYS
4
C
NZ
LYS
7
1
Y
1
A
NE
ARG
8
C
NE
ARG
11
1
Y
1
A
CZ
ARG
8
C
CZ
ARG
11
1
Y
1
A
NH1
ARG
8
C
NH1
ARG
11
1
Y
1
A
NH2
ARG
8
C
NH2
ARG
11
1
Y
1
A
CG
ASP
12
C
CG
ASP
15
1
Y
1
A
OD1
ASP
12
C
OD1
ASP
15
1
Y
1
A
OD2
ASP
12
C
OD2
ASP
15
1
Y
1
A
CE
LYS
16
C
CE
LYS
19
1
Y
1
A
NZ
LYS
16
C
NZ
LYS
19
1
Y
1
A
CB
ASP
20
C
CB
ASP
23
1
Y
1
A
CG
ASP
20
C
CG
ASP
23
1
Y
1
A
OD1
ASP
20
C
OD1
ASP
23
1
Y
1
A
OD2
ASP
20
C
OD2
ASP
23
1
Y
1
A
CD
LYS
50
C
CD
LYS
53
1
Y
1
A
CE
LYS
50
C
CE
LYS
53
1
Y
1
A
NZ
LYS
50
C
NZ
LYS
53
1
Y
1
A
CD
LYS
53
C
CD
LYS
56
1
Y
1
A
CE
LYS
53
C
CE
LYS
56
1
Y
1
A
NZ
LYS
53
C
NZ
LYS
56
1
Y
1
A
CG
ARG
88
C
CG
ARG
91
1
Y
1
A
CD
ARG
88
C
CD
ARG
91
1
Y
1
A
NE
ARG
88
C
NE
ARG
91
1
Y
1
A
CZ
ARG
88
C
CZ
ARG
91
1
Y
1
A
NH1
ARG
88
C
NH1
ARG
91
1
Y
1
A
NH2
ARG
88
C
NH2
ARG
91
1
Y
1
A
CD
LYS
92
C
CD
LYS
95
1
Y
1
A
CE
LYS
92
C
CE
LYS
95
1
Y
1
A
NZ
LYS
92
C
NZ
LYS
95
1
Y
1
A
CD
LYS
100
C
CD
LYS
103
1
Y
1
A
CE
LYS
100
C
CE
LYS
103
1
Y
1
A
NZ
LYS
100
C
NZ
LYS
103
1
Y
1
A
NE
ARG
153
C
NE
ARG
156
1
Y
1
A
CZ
ARG
153
C
CZ
ARG
156
1
Y
1
A
NH1
ARG
153
C
NH1
ARG
156
1
Y
1
A
NH2
ARG
153
C
NH2
ARG
156
1
Y
1
A
OD1
ASP
155
C
OD1
ASP
158
1
Y
1
A
OD2
ASP
155
C
OD2
ASP
158
1
Y
1
A
CG
GLU
160
C
CG
GLU
163
1
Y
1
A
CD
GLU
160
C
CD
GLU
163
1
Y
1
A
OE1
GLU
160
C
OE1
GLU
163
1
Y
1
A
OE2
GLU
160
C
OE2
GLU
163
1
Y
1
A
CE
LYS
190
C
CE
LYS
193
1
Y
1
A
NZ
LYS
190
C
NZ
LYS
193
1
Y
1
A
CB
GLN
192
C
CB
GLN
195
1
Y
1
A
CG
GLN
192
C
CG
GLN
195
1
Y
1
A
CD
GLN
192
C
CD
GLN
195
1
Y
1
A
OE1
GLN
192
C
OE1
GLN
195
1
Y
1
A
NE2
GLN
192
C
NE2
GLN
195
1
Y
1
A
CB
SER
193
C
CB
SER
196
1
Y
1
A
OG
SER
193
C
OG
SER
196
1
Y
1
A
CG
GLN
195
C
CG
GLN
198
1
Y
1
A
CD
GLN
195
C
CD
GLN
198
1
Y
1
A
OE1
GLN
195
C
OE1
GLN
198
1
Y
1
A
NE2
GLN
195
C
NE2
GLN
198
1
Y
1
A
CG
ARG
206
C
CG
ARG
209
1
Y
1
A
CD
ARG
206
C
CD
ARG
209
1
Y
1
A
NE
ARG
206
C
NE
ARG
209
1
Y
1
A
CZ
ARG
206
C
CZ
ARG
209
1
Y
1
A
NH1
ARG
206
C
NH1
ARG
209
1
Y
1
A
NH2
ARG
206
C
NH2
ARG
209
1
Y
1
A
CE
LYS
210
C
CE
LYS
213
1
Y
1
A
NZ
LYS
210
C
NZ
LYS
213
1
Y
1
A
CG
ARG
213
C
CG
ARG
216
1
Y
1
A
CD
ARG
213
C
CD
ARG
216
1
Y
1
A
NE
ARG
213
C
NE
ARG
216
1
Y
1
A
CZ
ARG
213
C
CZ
ARG
216
1
Y
1
A
NH1
ARG
213
C
NH1
ARG
216
1
Y
1
A
NH2
ARG
213
C
NH2
ARG
216
1
Y
1
A
CB
LYS
214
C
CB
LYS
217
1
Y
1
A
CG
LYS
214
C
CG
LYS
217
1
Y
1
A
CD
LYS
214
C
CD
LYS
217
1
Y
1
A
CE
LYS
214
C
CE
LYS
217
1
Y
1
A
NZ
LYS
214
C
NZ
LYS
217
1
Y
1
C
DT
12
B
DT
1
1
Y
1
A
GLY
-2
C
GLY
1
1
Y
1
A
SER
-1
C
SER
2
1
Y
1
A
HIS
0
C
HIS
3
1
Y
1
A
ARG
215
C
ARG
218
1
Y
1
A
GLU
216
C
GLU
219
1
Y
1
A
GLU
217
C
GLU
220
1
Y
1
A
LYS
218
C
LYS
221
1
Y
1
A
ALA
219
C
ALA
222
1
Y
1
A
ALA
220
C
ALA
223
1
Y
1
A
ASN
221
C
ASN
224
1
Y
1
A
GLN
222
C
GLN
225
1
Y
1
A
LYS
223
C
LYS
226
1
Y
1
A
ASP
20
-100.33
45.30
1
A
ALA
41
-36.68
120.19
1
A
ALA
135
-172.73
148.68
1
A
ILE
168
-89.83
-77.03
1
A
HIS
188
-130.33
-71.21
1
A
GLN
192
-56.94
-70.48
1
A
PRO
200
-57.35
-7.04
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
ION.PARAM
ION.TOP
WATER_REP.PARAM
WATER.TOP
FS4.PARAM
FS4.TOP
38.3
4.27
0.00
0.00
-6.18
0.00
1.91
0.269
0.007
0.214
0.214
2.50
29.31
1599
17052
9.4
87.2
RANDOM
854279.88
854279.88
0
1
RESTRAINED
THROUGHOUT
0
FOURIER SYNTHESIS
PDB ENTRY 1ORN
Engh & Huber
FLAT MODEL
28.0823
0.317717
0.43
0.33
5.0
0.38
0.28
2.50
29.31
31
2114
9
417
1657
0.008
1.2
19.1
0.95
1.12
1.50
1.81
2.00
3.98
2.00
4.62
2.50
0.341
0.030
0.295
2.59
130
1432
10
8.3
78.5
36.7
2.5
50
1P59
19576
17421
-3
0.056
1
19.6
3.0
89.0
0.271
2.50
2.59
3.7
1997
2.7
83.1
refinement
CNS
1.0
data scaling
SCALEPACK
phasing
CNS
Structure of a non-covalent Endonuclease III-DNA Complex
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
6
N
N
6
N
N
A
THR
3
C
THR
6
HELX_P
A
PHE
18
C
PHE
21
1
1
16
A
ASN
29
C
ASN
32
HELX_P
A
ALA
41
C
ALA
44
1
2
13
A
THR
44
C
THR
47
HELX_P
A
TYR
59
C
TYR
62
1
3
16
A
THR
61
C
THR
64
HELX_P
A
ALA
67
C
ALA
70
1
4
7
A
PRO
69
C
PRO
72
HELX_P
A
ILE
77
C
ILE
80
1
5
9
A
LEU
82
C
LEU
85
HELX_P
A
TYR
101
C
TYR
104
1
6
20
A
ASP
108
C
ASP
111
HELX_P
A
LYS
114
C
LYS
117
1
7
7
A
GLY
119
C
GLY
122
HELX_P
A
GLY
132
C
GLY
135
1
8
14
A
ASP
139
C
ASP
142
HELX_P
A
GLY
150
C
GLY
153
1
9
12
A
SER
157
C
SER
160
HELX_P
A
ILE
169
C
ILE
172
1
10
13
A
PRO
170
C
PRO
173
HELX_P
A
GLU
172
C
GLU
175
5
11
3
A
GLU
173
C
GLU
176
HELX_P
A
HIS
188
C
HIS
191
1
12
16
A
GLN
195
C
GLN
198
HELX_P
A
CYS
199
C
CYS
202
5
13
5
A
LEU
201
C
LEU
204
HELX_P
A
LEU
204
C
LEU
207
5
14
4
A
CYS
205
C
CYS
208
HELX_P
A
LYS
214
C
LYS
217
1
15
10
covale
1.607
both
B
DG
6
A
O3'
DG
6
1_555
B
5IU
7
A
P
5IU
7
1_555
covale
1.600
both
B
5IU
7
A
O3'
5IU
7
1_555
B
DG
8
A
P
DG
8
1_555
covale
1.613
both
C
DG
13
B
O3'
DG
2
1_555
C
5IU
14
B
P
5IU
3
1_555
covale
1.608
both
C
5IU
14
B
O3'
5IU
3
1_555
C
DC
15
B
P
DC
4
1_555
covale
1.619
both
C
DA
17
B
O3'
DA
6
1_555
C
3DR
18
B
P
3DR
7
1_555
covale
1.602
both
C
3DR
18
B
O3'
3DR
7
1_555
C
DG
19
B
P
DG
8
1_555
covale
1.605
both
C
DG
19
B
O3'
DG
8
1_555
C
5IU
20
B
P
5IU
9
1_555
covale
1.606
both
C
5IU
20
B
O3'
5IU
9
1_555
C
DC
21
B
P
DC
10
1_555
metalc
2.370
C
DC
21
B
OP1
DC
10
1_555
A
NA
224
D
NA
NA
1_555
metalc
2.255
A
MET
113
C
O
MET
116
1_555
A
NA
224
D
NA
NA
1_555
metalc
2.376
A
LEU
115
C
O
LEU
118
1_555
A
NA
224
D
NA
NA
1_555
metalc
2.568
A
VAL
118
C
O
VAL
121
1_555
A
NA
224
D
NA
NA
1_555
metalc
2.634
A
CYS
189
C
SG
CYS
192
1_555
A
SF4
300
E
FE2
SF4
1_555
metalc
2.462
A
CYS
196
C
SG
CYS
199
1_555
A
SF4
300
E
FE3
SF4
1_555
metalc
2.339
A
CYS
199
C
SG
CYS
202
1_555
A
SF4
300
E
FE1
SF4
1_555
metalc
2.423
A
CYS
205
C
SG
CYS
208
1_555
A
SF4
300
E
FE4
SF4
1_555
hydrog
WATSON-CRICK
B
DA
2
A
N1
DA
2
1_555
C
DT
22
B
N3
DT
11
1_555
hydrog
WATSON-CRICK
B
DA
2
A
N6
DA
2
1_555
C
DT
22
B
O4
DT
11
1_555
hydrog
WATSON-CRICK
B
DG
3
A
N1
DG
3
1_555
C
DC
21
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
B
DG
3
A
N2
DG
3
1_555
C
DC
21
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
B
DG
3
A
O6
DG
3
1_555
C
DC
21
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
B
DA
4
A
N1
DA
4
1_555
C
5IU
20
B
N3
5IU
9
1_555
hydrog
WATSON-CRICK
B
DA
4
A
N6
DA
4
1_555
C
5IU
20
B
O4
5IU
9
1_555
hydrog
WATSON-CRICK
B
DC
5
A
N3
DC
5
1_555
C
DG
19
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
B
DC
5
A
N4
DC
5
1_555
C
DG
19
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
B
DC
5
A
O2
DC
5
1_555
C
DG
19
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
B
5IU
7
A
N3
5IU
7
1_555
C
DA
17
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
B
5IU
7
A
O4
5IU
7
1_555
C
DA
17
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
B
DG
8
A
N1
DG
8
1_555
C
DC
16
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
B
DG
8
A
N2
DG
8
1_555
C
DC
16
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
B
DG
8
A
O6
DG
8
1_555
C
DC
16
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
B
DG
9
A
N1
DG
9
1_555
C
DC
15
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
B
DG
9
A
N2
DG
9
1_555
C
DC
15
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
B
DG
9
A
O6
DG
9
1_555
C
DC
15
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
B
DA
10
A
N1
DA
10
1_555
C
5IU
14
B
N3
5IU
3
1_555
hydrog
WATSON-CRICK
B
DA
10
A
N6
DA
10
1_555
C
5IU
14
B
O4
5IU
3
1_555
hydrog
WATSON-CRICK
B
DC
11
A
N3
DC
11
1_555
C
DG
13
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
B
DC
11
A
N4
DC
11
1_555
C
DG
13
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
B
DC
11
A
O2
DC
11
1_555
C
DG
13
B
N2
DG
2
1_555
HYDROLASE/DNA
DNA REPAIR, DNA GLYCOSYLASE, [4FE-4S] CLUSTER, IRON-SULFUR CLUSTER, HYDROLASE-DNA COMPLEX
1P59
PDB
1
1P59
1P59
PDB
2
1P59
1P59
PDB
3
1P59
1
11
1P59
1
11
1P59
B
1
1
11
12
22
1P59
12
22
1P59
C
2
1
11
-2
223
1P59
-2
223
1P59
A
3
1
226
BINDING SITE FOR RESIDUE NA A 224
A
NA
224
Software
4
BINDING SITE FOR RESIDUE SF4 A 300
A
SF4
300
Software
7
A
MET
113
C
MET
116
4
1_555
A
LEU
115
C
LEU
118
4
1_555
A
VAL
118
C
VAL
121
4
1_555
C
DC
21
B
DC
10
4
1_555
A
LEU
149
C
LEU
152
7
1_555
A
PHE
184
C
PHE
187
7
1_555
A
CYS
189
C
CYS
192
7
1_555
A
CYS
196
C
CYS
199
7
1_555
A
CYS
199
C
CYS
202
7
1_555
A
CYS
205
C
CYS
208
7
1_555
A
GLY
208
C
GLY
211
7
1_555
18
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