0.015077
0.000000
0.000000
0.000000
0.014557
0.000000
0.000000
0.000000
0.016094
0.00000
0.00000
0.00000
Chiu, T.K.
Sohn, C.
Johnson, R.C.
Dickerson, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
66.328
68.693
62.136
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
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
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
O
N
9
N
I
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
N
22
N
H
N
23
N
H
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
N
N
35
S
C
N
36
N
C
N
37
N
O
N
38
N
C
N
39
N
O
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
N
N
48
S
C
N
49
N
C
N
50
N
O
N
51
N
C
N
52
N
C
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
N
N
58
N
O
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
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
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
O
N
81
N
N
N
82
N
O
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
O
N
92
N
P
N
93
N
O
N
94
N
O
N
95
N
O
N
96
N
C
N
97
R
C
N
98
N
O
N
99
S
C
N
100
N
O
N
101
N
C
N
102
R
C
Y
103
N
N
Y
104
N
C
Y
105
N
N
Y
106
N
C
Y
107
N
C
N
108
N
N
Y
109
N
N
Y
110
N
C
Y
111
N
N
Y
112
N
C
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
O
N
128
N
P
N
129
N
O
N
130
N
O
N
131
N
O
N
132
N
C
N
133
R
C
N
134
N
O
N
135
S
C
N
136
N
O
N
137
N
C
N
138
R
C
N
139
N
N
N
140
N
C
N
141
N
O
N
142
N
N
N
143
N
C
N
144
N
N
N
145
N
C
N
146
N
C
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
O
N
162
N
P
N
163
N
O
N
164
N
O
N
165
N
O
N
166
N
C
N
167
R
C
N
168
N
O
N
169
S
C
N
170
N
O
N
171
N
C
N
172
R
C
Y
173
N
N
Y
174
N
C
Y
175
N
N
Y
176
N
C
N
177
N
C
N
178
N
O
N
179
N
N
N
180
N
C
N
181
N
N
N
182
N
N
Y
183
N
C
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
O
N
199
N
P
N
200
N
O
N
201
N
O
N
202
N
O
N
203
N
C
N
204
R
C
N
205
N
O
N
206
S
C
N
207
N
O
N
208
N
C
N
209
R
C
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
N
N
214
N
C
N
215
N
O
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
N
N
235
S
C
N
236
N
C
N
237
N
O
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
O
N
242
N
N
N
243
N
O
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
H
N
254
N
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
N
259
N
C
N
260
N
C
N
261
N
O
N
262
N
O
N
263
N
O
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
N
C
N
275
N
C
N
276
N
O
N
277
N
O
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
Y
288
N
C
Y
289
N
N
Y
290
N
C
Y
291
N
C
Y
292
N
N
N
293
N
O
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
O
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
S
C
N
312
N
C
N
313
N
C
N
314
N
C
N
315
N
O
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
H
N
328
N
H
N
329
N
N
N
330
S
C
N
331
N
C
N
332
N
O
N
333
N
C
N
334
N
C
N
335
N
C
N
336
N
C
N
337
N
O
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
N
356
N
C
N
357
N
C
N
358
N
C
N
359
N
N
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
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
N
381
N
C
N
382
N
S
N
383
N
C
N
384
N
O
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
N
407
N
O
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
N
424
N
C
N
425
N
C
N
426
N
O
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
N
N
437
S
C
N
438
N
C
N
439
N
O
N
440
N
C
N
441
N
O
N
442
N
O
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
R
C
N
455
N
O
N
456
N
C
N
457
N
O
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
N
N
468
S
C
N
469
N
C
N
470
N
O
N
471
N
C
Y
472
N
C
Y
473
N
C
Y
474
N
C
Y
475
N
C
Y
476
N
C
Y
477
N
C
N
478
N
O
N
479
N
O
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
N
N
492
S
C
N
493
N
C
N
494
N
O
N
495
N
C
N
496
N
C
N
497
N
C
N
498
N
O
N
499
N
H
N
500
N
H
N
501
N
H
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
N
10
N
doub
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
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
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
doub
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
doub
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
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
sing
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
Y
112
N
sing
Y
113
N
sing
Y
114
N
doub
N
115
N
sing
Y
116
N
sing
Y
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
120
N
doub
N
121
N
sing
N
122
N
sing
Y
123
N
sing
Y
124
N
doub
N
125
N
sing
Y
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
Y
185
N
sing
Y
186
N
sing
Y
187
N
doub
N
188
N
sing
Y
189
N
sing
N
190
N
sing
Y
191
N
doub
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
doub
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
doub
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
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
doub
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
doub
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
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
Y
295
N
sing
Y
296
N
doub
Y
297
N
doub
N
298
N
sing
Y
299
N
sing
N
300
N
sing
Y
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
doub
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
doub
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
doub
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
Y
403
N
doub
Y
404
N
sing
Y
405
N
sing
N
406
N
sing
Y
407
N
doub
N
408
N
sing
Y
409
N
doub
N
410
N
sing
Y
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
doub
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
doub
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
doub
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
Y
472
N
doub
Y
473
N
sing
Y
474
N
sing
N
475
N
sing
Y
476
N
doub
N
477
N
sing
Y
478
N
doub
N
479
N
sing
Y
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
doub
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
UK
EMBO J.
EMJODG
0897
0261-4189
21
801
814
10.1093/emboj/21.4.801
11847127
Testing water-mediated DNA recognition by the Hin recombinase.
2002
Thesis
145
241
How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.
2001
US
Science
SCIEAS
0038
0036-8075
263
348
355
8278807
Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions.
1994
10.2210/pdb1jj8/pdb
pdb_00001jj8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
IMAGE PLATE
1995-09-01
RIGAKU
SINGLE WAVELENGTH
M
x-ray
1
1.543
1.0
1.543
ROTATING ANODE
4436.707
5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
1
syn
polymer
4231.806
5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
1
syn
polymer
6047.051
DNA-INVERTASE HIN
RESIDUES 139 TO 190
1
syn
polymer
18.015
water
12
nat
water
Hin Recombinase
no
yes
(DT)(DG)(5IU)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DA)(DA)(DG)(DA)
TGUTTTTGATAAGA
A
polydeoxyribonucleotide
no
no
(DA)(DT)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DA)(DC)
ATCTTATCAAAAAC
B
polydeoxyribonucleotide
no
no
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
C
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
1
2.423
47.27
VAPOR DIFFUSION, HANGING DROP
4.60
0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6),
25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE.
RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2,
AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS
INCREASED IN 5% INCREMENTS TO 35%. CONDITIONS FOR NATIVE ARE THE SAME
EXCEPT THE CONCENTRATION OF MGCL2 IS 5 TIMES SMALLER., pH 4.60, VAPOR DIFFUSION, HANGING DROP
DNA
1
HIN
1
sodium acetate
1
MgCl2
1
NaCl
1
PEG 400
1
sodium cacodylate
1
sodium acetate
2
MgCl2
2
PEG 400
2
-14.683
1
19
A
3
B
29
2.557
A_DG3:DC29_B
1
-9.559
0.297
-0.500
-0.109
-3.727
1
20
A
4
B
28
-6.744
A_5IU4:DA28_B
2
-0.701
0.725
-0.128
0.123
-7.007
1
20
A
5
B
27
1.218
A_DT5:DA27_B
3
-11.966
-0.175
-0.010
-0.278
-2.100
1
20
A
6
B
26
0.544
A_DT6:DA26_B
4
-23.330
-0.062
-0.130
-0.085
-11.183
1
20
A
7
B
25
-9.120
A_DT7:DA25_B
5
-14.275
-0.139
-0.057
-0.298
-7.404
1
20
A
8
B
24
-5.587
A_DT8:DA24_B
6
-17.312
0.217
-0.137
-0.070
-6.581
1
19
A
9
B
23
0.284
A_DG9:DC23_B
7
-5.072
-0.359
-0.486
-0.354
5.705
1
20
A
10
B
22
-2.913
A_DA10:DT22_B
8
-14.048
0.118
-0.050
-0.262
7.273
1
20
A
11
B
21
0.573
A_DT11:DA21_B
9
-11.070
0.238
-0.067
-0.209
-3.703
1
20
A
12
B
20
-2.907
A_DA12:DT20_B
10
-15.375
0.097
-0.223
-0.227
5.019
1
20
A
13
B
19
6.340
A_DA13:DT19_B
11
-12.572
0.018
0.272
0.001
5.209
1
19
A
14
B
18
5.982
A_DG14:DC18_B
12
-19.653
0.122
-0.019
0.271
3.156
35.498
A
A
3
4
-2.262
B
B
29
28
3.123
-1.379
-0.626
-1.007
AA_DG35IU4:DA28DC29_BB
1
0.186
-0.306
35.471
-1.458
1.053
3.167
30.280
A
A
4
5
2.528
B
B
28
27
3.231
1.318
-0.258
-0.567
AA_5IU4DT5:DA27DA28_BB
2
2.811
-5.390
30.124
-1.346
1.051
3.126
34.351
A
A
5
6
6.759
B
B
27
26
3.159
3.979
-0.054
0.010
AA_DT5DT6:DA26DA27_BB
3
2.762
-4.692
34.018
-0.585
0.509
3.518
37.419
A
A
6
7
-1.093
B
B
26
25
3.515
-0.701
0.177
-0.015
AA_DT6DT7:DA25DA26_BB
4
0.643
-1.002
37.408
0.076
-0.185
3.145
34.828
A
A
7
8
0.698
B
B
25
24
3.127
0.418
-0.686
-0.484
AA_DT7DT8:DA24DA25_BB
5
-1.362
2.276
34.800
-0.870
0.948
3.563
34.235
A
A
8
9
6.156
B
B
24
23
3.391
3.613
0.976
1.173
AA_DT8DG9:DC23DA24_BB
6
2.954
-5.034
33.925
1.386
-1.161
3.270
39.144
A
A
9
10
1.196
B
B
23
22
3.089
0.796
-1.116
0.992
AA_DG9DA10:DT22DC23_BB
7
-8.281
12.448
38.284
1.387
0.689
3.202
29.793
A
A
10
11
5.503
B
B
22
21
3.277
2.824
0.254
-0.752
AA_DA10DT11:DA21DT22_BB
8
1.619
-3.155
29.619
-2.049
-0.159
3.742
39.654
A
A
11
12
7.382
B
B
21
20
3.654
4.993
-0.564
0.763
AA_DT11DA12:DT20DA21_BB
9
-1.928
2.850
39.305
0.463
0.576
2.909
34.883
A
A
12
13
-3.885
B
B
20
19
2.936
-2.326
0.371
-0.062
AA_DA12DA13:DT19DT20_BB
10
-1.957
3.269
34.754
0.212
-0.884
3.210
34.194
A
A
13
14
11.455
B
B
19
18
3.346
6.691
-0.117
-0.332
AA_DA13DG14:DC18DT19_BB
11
1.887
-3.231
33.501
-1.635
0.500
chem_comp_atom
chem_comp_bond
database_2
struct_conn
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Database references
Other
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-02-22
1
1
2008-04-27
1
2
2011-07-13
1
3
2015-02-04
1
4
2024-02-07
1
5
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
Native wild-type Hin recombinase DNA-binding domain bound to underivatized
hixL half-site.
FORM1 BR18 DERIVATIVE
FORM1 I5 DERIVATIVE
FORM1 A10G MUTANT
FORM1 T11G MUTANT
FORM1 G9T MUTANT
FORM1 T11C MUTANT
RCSB
Y
RCSB
2001-07-03
REL
REL
HOH
water
SYNTHETIC PEPTIDE
sample
SIRAS PHASES
Other
experimental model
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
204
4
HOH
HOH
204
B
HOH
207
4
HOH
HOH
207
B
HOH
208
4
HOH
HOH
208
B
HOH
210
4
HOH
HOH
210
B
HOH
211
4
HOH
HOH
211
B
HOH
212
4
HOH
HOH
212
B
HOH
201
4
HOH
HOH
201
C
HOH
202
4
HOH
HOH
202
C
HOH
203
4
HOH
HOH
203
C
HOH
209
4
HOH
HOH
209
C
T
2
n
1
DT
2
A
G
3
n
2
DG
3
A
U
4
n
3
5IU
4
A
T
5
n
4
DT
5
A
T
6
n
5
DT
6
A
T
7
n
6
DT
7
A
T
8
n
7
DT
8
A
G
9
n
8
DG
9
A
A
10
n
9
DA
10
A
T
11
n
10
DT
11
A
A
12
n
11
DA
12
A
A
13
n
12
DA
13
A
G
14
n
13
DG
14
A
A
15
n
14
DA
15
A
A
16
n
1
DA
16
B
T
17
n
2
DT
17
B
C
18
n
3
DC
18
B
T
19
n
4
DT
19
B
T
20
n
5
DT
20
B
A
21
n
6
DA
21
B
T
22
n
7
DT
22
B
C
23
n
8
DC
23
B
A
24
n
9
DA
24
B
A
25
n
10
DA
25
B
A
26
n
11
DA
26
B
A
27
n
12
DA
27
B
A
28
n
13
DA
28
B
C
29
n
14
DC
29
B
GLY
139
n
1
GLY
139
C
ARG
140
n
2
ARG
140
C
PRO
141
n
3
PRO
141
C
ARG
142
n
4
ARG
142
C
ALA
143
n
5
ALA
143
C
ILE
144
n
6
ILE
144
C
ASN
145
n
7
ASN
145
C
LYS
146
n
8
LYS
146
C
HIS
147
n
9
HIS
147
C
GLU
148
n
10
GLU
148
C
GLN
149
n
11
GLN
149
C
GLU
150
n
12
GLU
150
C
GLN
151
n
13
GLN
151
C
ILE
152
n
14
ILE
152
C
SER
153
n
15
SER
153
C
ARG
154
n
16
ARG
154
C
LEU
155
n
17
LEU
155
C
LEU
156
n
18
LEU
156
C
GLU
157
n
19
GLU
157
C
LYS
158
n
20
LYS
158
C
GLY
159
n
21
GLY
159
C
HIS
160
n
22
HIS
160
C
PRO
161
n
23
PRO
161
C
ARG
162
n
24
ARG
162
C
GLN
163
n
25
GLN
163
C
GLN
164
n
26
GLN
164
C
LEU
165
n
27
LEU
165
C
ALA
166
n
28
ALA
166
C
ILE
167
n
29
ILE
167
C
ILE
168
n
30
ILE
168
C
PHE
169
n
31
PHE
169
C
GLY
170
n
32
GLY
170
C
ILE
171
n
33
ILE
171
C
GLY
172
n
34
GLY
172
C
VAL
173
n
35
VAL
173
C
SER
174
n
36
SER
174
C
THR
175
n
37
THR
175
C
LEU
176
n
38
LEU
176
C
TYR
177
n
39
TYR
177
C
ARG
178
n
40
ARG
178
C
TYR
179
n
41
TYR
179
C
PHE
180
n
42
PHE
180
C
PRO
181
n
43
PRO
181
C
ALA
182
n
44
ALA
182
C
SER
183
n
45
SER
183
C
SER
184
n
46
SER
184
C
ILE
185
n
47
ILE
185
C
LYS
186
n
48
LYS
186
C
LYS
187
n
49
LYS
187
C
n
50
188
C
n
51
189
C
n
52
190
C
author_defined_assembly
3
trimeric
A
5IU
4
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
A
5IU
3
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
B
HOH
212
E
HOH
1
A
C4'
DA
15
A
C4'
DA
14
1
Y
1
A
O4'
DA
15
A
O4'
DA
14
1
Y
1
A
C3'
DA
15
A
C3'
DA
14
1
Y
1
A
O3'
DA
15
A
O3'
DA
14
1
Y
1
A
C2'
DA
15
A
C2'
DA
14
1
Y
1
A
C1'
DA
15
A
C1'
DA
14
1
Y
1
A
N9
DA
15
A
N9
DA
14
1
Y
1
A
C8
DA
15
A
C8
DA
14
1
Y
1
A
N7
DA
15
A
N7
DA
14
1
Y
1
A
C5
DA
15
A
C5
DA
14
1
Y
1
A
C6
DA
15
A
C6
DA
14
1
Y
1
A
N6
DA
15
A
N6
DA
14
1
Y
1
A
N1
DA
15
A
N1
DA
14
1
Y
1
A
C2
DA
15
A
C2
DA
14
1
Y
1
A
N3
DA
15
A
N3
DA
14
1
Y
1
A
C4
DA
15
A
C4
DA
14
1
Y
1
C
CB
LYS
146
C
CB
LYS
8
1
Y
1
C
CG
LYS
146
C
CG
LYS
8
1
Y
1
C
CD
LYS
146
C
CD
LYS
8
1
Y
1
C
CE
LYS
146
C
CE
LYS
8
1
Y
1
C
NZ
LYS
146
C
NZ
LYS
8
1
Y
1
C
CG
GLU
150
C
CG
GLU
12
1
Y
1
C
CD
GLU
150
C
CD
GLU
12
1
Y
1
C
OE1
GLU
150
C
OE1
GLU
12
1
Y
1
C
OE2
GLU
150
C
OE2
GLU
12
1
Y
1
C
CD
ARG
154
C
CD
ARG
16
1
Y
1
C
NE
ARG
154
C
NE
ARG
16
1
Y
1
C
CZ
ARG
154
C
CZ
ARG
16
1
Y
1
C
NH1
ARG
154
C
NH1
ARG
16
1
Y
1
C
NH2
ARG
154
C
NH2
ARG
16
1
Y
1
C
CG
LYS
158
C
CG
LYS
20
1
Y
1
C
CD
LYS
158
C
CD
LYS
20
1
Y
1
C
CE
LYS
158
C
CE
LYS
20
1
Y
1
C
NZ
LYS
158
C
NZ
LYS
20
1
Y
1
C
CB
LYS
187
C
CB
LYS
49
1
Y
1
C
CG
LYS
187
C
CG
LYS
49
1
Y
1
C
CD
LYS
187
C
CD
LYS
49
1
Y
1
C
CE
LYS
187
C
CE
LYS
49
1
Y
1
C
NZ
LYS
187
C
NZ
LYS
49
1
Y
1
C
ARG
188
C
ARG
50
1
Y
1
C
MET
189
C
MET
51
1
Y
1
C
ASN
190
C
ASN
52
1
Y
1
B
DA
25
0.064
SIDE CHAIN
1
B
DA
28
0.075
SIDE CHAIN
1
A
A
O3'
P
5IU
DT
4
5
1.81
1
-12.67
1.90
104.00
91.33
A
A
A
O3'
P
O5'
5IU
DT
DT
4
5
5
Y
1
9.57
1.20
110.70
120.27
A
A
A
O5'
P
OP2
DT
DT
DT
5
5
5
N
1
1.86
0.30
108.30
110.16
B
B
B
O4'
C1'
N9
DA
DA
DA
28
28
28
N
1
A
A
O3'
P
5IU
DT
4
5
0.202
0.012
1.607
1.809
Y
1
C
GLU
157
-103.47
63.58
1
C
LYS
158
-169.06
-1.92
1
C
LYS
186
-53.33
-5.15
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
WATER_REP.PARAM
WATER.TOP
45.00
9.450
0.00000
0.00000
-5.107
0.00000
-4.343
0.2771
0.2134
0.2134
2.75
25.00
369
3765
9.46
96.49
RANDOM
10000.00
1
ANISOTROPIC_FIXED_ISOTROPIC
0.000
SIRAS
SIRAS PHASES
MLF
18.88
0.28
0.46
0.36
5.00
0.60
0.53
2.75
25.00
12
939
0
552
375
0.009
1.30
19.41
1.45
1.49
1.50
2.45
2.00
2.32
2.00
3.63
2.05
0.5136
0.3529
2.87
45
394
8
9.39
91.64
44.00
2.75
25.0
1JJ8
3765
1.000
0.081
1
19.6
15.000
96.49
2.75
2.87
4.5
0.267
1
4.2
91.64
phasing
SOLVE
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
C
ASN
145
C
ASN
7
HELX_P
C
GLU
157
C
GLU
19
1
1
13
C
PRO
161
C
PRO
23
HELX_P
C
GLY
170
C
GLY
32
1
2
10
C
GLY
172
C
GLY
34
HELX_P
C
PHE
180
C
PHE
42
1
3
9
C
PRO
181
C
PRO
43
HELX_P
C
ILE
185
C
ILE
47
5
4
5
covale
1.616
both
A
DG
3
A
O3'
DG
2
1_555
A
5IU
4
A
P
5IU
3
1_555
covale
1.809
both
A
5IU
4
A
O3'
5IU
3
1_555
A
DT
5
A
P
DT
4
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
2
1_555
B
DC
29
B
N3
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
2
1_555
B
DC
29
B
O2
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
2
1_555
B
DC
29
B
N4
DC
14
1_555
hydrog
WATSON-CRICK
A
5IU
4
A
N3
5IU
3
1_555
B
DA
28
B
N1
DA
13
1_555
hydrog
WATSON-CRICK
A
5IU
4
A
O4
5IU
3
1_555
B
DA
28
B
N6
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
4
1_555
B
DA
27
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
4
1_555
B
DA
27
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
5
1_555
B
DA
26
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
5
1_555
B
DA
26
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
6
1_555
B
DA
25
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
6
1_555
B
DA
25
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
7
1_555
B
DA
24
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
7
1_555
B
DA
24
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
8
1_555
B
DC
23
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
8
1_555
B
DC
23
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
8
1_555
B
DC
23
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
9
1_555
B
DT
22
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
9
1_555
B
DT
22
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
11
A
N3
DT
10
1_555
B
DA
21
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
11
A
O4
DT
10
1_555
B
DA
21
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N1
DA
11
1_555
B
DT
20
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
11
1_555
B
DT
20
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
12
1_555
B
DT
19
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
12
1_555
B
DT
19
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N1
DG
13
1_555
B
DC
18
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N2
DG
13
1_555
B
DC
18
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
14
A
O6
DG
13
1_555
B
DC
18
B
N4
DC
3
1_555
DNA BINDING PROTEIN/DNA
WATER-MEDIATED RECOGNITION, PROTEIN-DNA COMPLEX, HIN RECOMBINASE, I4 FORM 2, DNA BINDING PROTEIN-DNA COMPLEX
HIN_SALTY
UNP
3
139
P03013
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
1JJ8
PDB
1
1JJ8
1JJ8
PDB
2
1JJ8
139
190
1JJ8
139
190
P03013
C
1
1
52
2
15
1JJ8
2
15
1JJ8
A
2
1
14
16
29
1JJ8
16
29
1JJ8
B
3
1
14
20
C 2 2 21