0.015873
0.009164
0.000000
0.000000
0.018329
0.000000
0.000000
0.000000
0.006557
0.00000
0.00000
0.00000
Tsutakawa, S.E.
Jingami, H.
Morikawa, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
63.000
63.000
152.500
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
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
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
O
N
89
N
P
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
C
N
94
R
C
N
95
N
O
N
96
S
C
N
97
N
O
N
98
N
C
N
99
R
C
Y
100
N
N
Y
101
N
C
Y
102
N
N
Y
103
N
C
Y
104
N
C
N
105
N
N
Y
106
N
N
Y
107
N
C
Y
108
N
N
Y
109
N
C
N
110
N
H
N
111
N
H
N
112
N
H
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
O
N
125
N
P
N
126
N
O
N
127
N
O
N
128
N
O
N
129
N
C
N
130
R
C
N
131
N
O
N
132
S
C
N
133
N
O
N
134
N
C
N
135
R
C
N
136
N
N
N
137
N
C
N
138
N
O
N
139
N
N
N
140
N
C
N
141
N
N
N
142
N
C
N
143
N
C
N
144
N
H
N
145
N
H
N
146
N
H
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
O
N
159
N
P
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
C
N
164
R
C
N
165
N
O
N
166
S
C
N
167
N
O
N
168
N
C
N
169
R
C
Y
170
N
N
Y
171
N
C
Y
172
N
N
Y
173
N
C
N
174
N
C
N
175
N
O
N
176
N
N
N
177
N
C
N
178
N
N
N
179
N
N
Y
180
N
C
N
181
N
H
N
182
N
H
N
183
N
H
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
O
N
196
N
P
N
197
N
O
N
198
N
O
N
199
N
O
N
200
N
C
N
201
R
C
N
202
N
O
N
203
S
C
N
204
N
O
N
205
N
C
N
206
R
C
N
207
N
N
N
208
N
C
N
209
N
O
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
C
N
216
N
H
N
217
N
H
N
218
N
H
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
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
O
N
239
N
N
N
240
N
O
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
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
O
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
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
N
N
271
N
C
N
272
N
C
N
273
N
O
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
N
Y
287
N
C
Y
288
N
C
Y
289
N
N
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
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
O
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
S
C
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
O
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
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
O
N
335
N
H
N
336
N
H
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
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
N
N
357
N
O
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
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
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
S
N
380
N
C
N
381
N
O
N
382
N
H
N
383
N
H
N
384
N
H
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
MG
N
394
N
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
N
406
N
H
N
407
N
H
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
N
N
418
S
C
N
419
N
C
N
420
N
O
N
421
N
C
N
422
N
C
N
423
N
C
N
424
N
O
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
N
C
N
439
N
O
N
440
N
O
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
N
N
449
S
C
N
450
N
C
N
451
N
O
N
452
R
C
N
453
N
O
N
454
N
C
N
455
N
O
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
N
N
466
S
C
N
467
N
C
N
468
N
O
N
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
N
Y
474
N
C
Y
475
N
C
Y
476
N
C
Y
477
N
C
Y
478
N
C
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
H
N
492
N
N
N
493
S
C
N
494
N
C
N
495
N
O
N
496
N
C
Y
497
N
C
Y
498
N
C
Y
499
N
C
Y
500
N
C
Y
501
N
C
Y
502
N
C
N
503
N
O
N
504
N
O
N
505
N
H
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
H
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
N
N
517
S
C
N
518
N
C
N
519
N
O
N
520
N
C
N
521
N
C
N
522
N
C
N
523
N
O
N
524
N
H
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
H
N
532
N
H
N
533
N
H
N
534
N
H
N
535
N
ZN
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
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
sing
N
31
N
sing
N
32
N
sing
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
doub
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
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
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
Y
106
N
sing
Y
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
110
N
sing
Y
111
N
sing
Y
112
N
doub
N
113
N
sing
Y
114
N
doub
N
115
N
sing
N
116
N
sing
Y
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
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
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
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
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
Y
179
N
sing
Y
180
N
sing
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
doub
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
N
192
N
sing
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
sing
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
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
doub
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
doub
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
doub
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
doub
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
doub
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
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
Y
289
N
sing
Y
290
N
doub
Y
291
N
doub
N
292
N
sing
Y
293
N
sing
N
294
N
sing
Y
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
doub
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
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
doub
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
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
doub
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
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
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
doub
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
doub
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
doub
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
doub
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
Y
466
N
doub
Y
467
N
sing
Y
468
N
sing
N
469
N
sing
Y
470
N
doub
Y
471
N
sing
Y
472
N
sing
N
473
N
sing
Y
474
N
sing
Y
475
N
doub
N
476
N
sing
Y
477
N
doub
N
478
N
sing
Y
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
Y
494
N
doub
Y
495
N
sing
Y
496
N
sing
N
497
N
sing
Y
498
N
doub
N
499
N
sing
Y
500
N
doub
N
501
N
sing
Y
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
doub
N
514
N
sing
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
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
99
615
623
10.1016/S0092-8674(00)81550-0
10612397
Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
1999
10.2210/pdb1cw0/pdb
pdb_00001cw0
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
1999-06-10
RIGAKU RAXIS
SINGLE WAVELENGTH
M
x-ray
1
0.8340
1.0
BL24XU
SPring-8
0.8340
SYNCHROTRON
SPRING-8 BEAMLINE BL24XU
3638.379
DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')
1
syn
polymer
886.637
DNA (5'-D(*AP*GP*C)-3')
1
syn
polymer
2770.834
DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')
1
syn
polymer
17914.473
PROTEIN (DNA MISMATCH ENDONUCLEASE)
3.1.-.-
1
man
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
65.409
ZINC ION
1
syn
non-polymer
18.015
water
206
nat
water
VSR ENDONUCLEASE, PATCH REPAIR PROTEIN
no
no
(DA)(DC)(DG)(DT)(DA)(DC)(DC)(DT)(DG)(DG)(DC)(DT)
ACGTACCTGGCT
M
polydeoxyribonucleotide
no
no
(DA)(DG)(DC)
AGC
N
polydeoxyribonucleotide
no
no
(DT)(DA)(DG)(DG)(DT)(DA)(DC)(DG)(DT)
TAGGTACGT
O
polydeoxyribonucleotide
no
no
ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPAT
RTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA
ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPAT
RTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA
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
Escherichia
Escherichia
sample
562
Escherichia coli
562
Escherichia coli
1
3.47
64.51
VAPOR DIFFUSION, HANGING DROP
5.60
pH 5.60, VAPOR DIFFUSION, HANGING DROP
6.221
1
20
M
301
O
362
5.396
M_DA301:DT362_O
1
-9.974
-0.079
0.211
-0.111
4.403
1
19
M
302
O
361
1.417
M_DC302:DG361_O
2
-8.266
0.173
-0.231
-0.038
-3.092
1
19
M
303
O
360
0.583
M_DG303:DC360_O
3
-5.571
-0.285
-0.114
-0.025
7.287
1
20
M
304
O
359
-0.358
M_DT304:DA359_O
4
-7.682
-0.042
-0.023
-0.060
-1.217
1
20
M
305
O
358
-0.028
M_DA305:DT358_O
5
-9.655
-0.007
-0.137
-0.165
-0.795
1
19
M
306
O
357
-1.440
M_DC306:DG357_O
6
-9.855
0.186
-0.010
-0.139
-13.001
1
19
M
307
O
356
0.249
M_DC307:DG356_O
7
1.016
0.176
0.352
-0.071
0.139
1
20
M
308
O
355
2.588
M_DT308:DA355_O
8
2.296
0.038
0.052
-0.141
-14.776
28
M
309
O
354
-1.034
M_DG309:DT354_O
9
-11.779
-2.503
-0.221
-0.492
-7.941
1
19
M
310
N
353
-0.526
M_DG310:DC353_N
10
-13.771
-0.130
-0.140
-0.072
-5.292
1
19
M
311
N
352
0.170
M_DC311:DG352_N
11
-3.204
0.078
-0.075
-0.080
-4.366
1
20
M
312
N
351
4.284
M_DT312:DA351_N
12
-12.782
0.013
-0.038
-0.132
3.204
33.347
M
M
301
302
3.652
O
O
362
361
3.275
2.092
-0.229
-0.519
MM_DA301DC302:DG361DT362_OO
1
3.079
-5.376
33.144
-1.249
0.907
3.534
37.103
M
M
302
303
13.716
O
O
361
360
3.476
8.651
-0.200
0.629
MM_DC302DG303:DC360DG361_OO
2
-1.350
2.140
36.090
-0.269
0.118
2.942
31.266
M
M
303
304
7.968
O
O
360
359
3.020
4.281
-0.235
-0.432
MM_DG303DT304:DA359DC360_OO
3
-1.152
2.145
30.957
-1.544
0.237
3.535
41.376
M
M
304
305
8.204
O
O
359
358
3.502
5.779
-0.072
0.487
MM_DT304DA305:DT358DA359_OO
4
0.630
-0.895
40.983
0.021
0.174
3.098
33.631
M
M
305
306
11.161
O
O
358
357
3.195
6.418
-0.087
-0.230
MM_DA305DC306:DG357DT358_OO
5
-1.658
2.884
32.990
-1.415
-0.112
3.712
38.640
M
M
306
307
13.970
O
O
357
356
3.638
9.156
1.489
0.367
MM_DC306DC307:DG356DG357_OO
6
2.507
-3.826
37.499
-0.732
-1.897
2.687
27.055
M
M
307
308
36.716
O
O
356
355
3.090
15.897
-0.162
0.550
MM_DC307DT308:DA355DG356_OO
7
6.486
-14.981
20.988
-2.857
1.992
2.935
39.108
M
M
309
310
20.525
O
N
354
353
3.211
13.418
-0.350
-0.323
MM_DG309DG310:DC353DT354_NO
8
-6.455
9.874
36.266
-2.060
-0.236
3.167
35.926
M
M
310
311
8.892
N
N
353
352
3.209
5.465
0.266
-0.047
MM_DG310DC311:DG352DC353_NN
9
-0.039
0.064
35.521
-0.841
-0.436
3.282
32.485
M
M
311
312
3.476
N
N
352
351
3.312
1.943
0.032
-0.406
MM_DC311DT312:DA351DG352_NN
10
0.837
-1.497
32.418
-1.070
0.090
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
1999-12-12
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-09
_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_asym_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_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-08-25
REL
REL
MG
MAGNESIUM ION
ZN
ZINC ION
HOH
water
1VSR
TRUNCATED VSR MODEL, 1VSR
PDB
experimental model
MG
202
5
MG
MG
202
N
ZN
201
6
ZN
ZN
201
A
MG
203
5
MG
MG
203
A
HOH
402
7
HOH
HOH
402
M
HOH
420
7
HOH
HOH
420
M
HOH
453
7
HOH
HOH
453
M
HOH
459
7
HOH
HOH
459
M
HOH
467
7
HOH
HOH
467
M
HOH
482
7
HOH
HOH
482
M
HOH
485
7
HOH
HOH
485
M
HOH
503
7
HOH
HOH
503
M
HOH
515
7
HOH
HOH
515
M
HOH
518
7
HOH
HOH
518
M
HOH
520
7
HOH
HOH
520
M
HOH
527
7
HOH
HOH
527
M
HOH
533
7
HOH
HOH
533
M
HOH
534
7
HOH
HOH
534
M
HOH
536
7
HOH
HOH
536
M
HOH
539
7
HOH
HOH
539
M
HOH
568
7
HOH
HOH
568
M
HOH
570
7
HOH
HOH
570
M
HOH
577
7
HOH
HOH
577
M
HOH
585
7
HOH
HOH
585
M
HOH
587
7
HOH
HOH
587
M
HOH
591
7
HOH
HOH
591
M
HOH
432
7
HOH
HOH
432
N
HOH
443
7
HOH
HOH
443
N
HOH
450
7
HOH
HOH
450
N
HOH
460
7
HOH
HOH
460
N
HOH
466
7
HOH
HOH
466
N
HOH
478
7
HOH
HOH
478
N
HOH
483
7
HOH
HOH
483
N
HOH
500
7
HOH
HOH
500
N
HOH
509
7
HOH
HOH
509
N
HOH
511
7
HOH
HOH
511
N
HOH
553
7
HOH
HOH
553
N
HOH
436
7
HOH
HOH
436
O
HOH
446
7
HOH
HOH
446
O
HOH
457
7
HOH
HOH
457
O
HOH
472
7
HOH
HOH
472
O
HOH
490
7
HOH
HOH
490
O
HOH
493
7
HOH
HOH
493
O
HOH
495
7
HOH
HOH
495
O
HOH
502
7
HOH
HOH
502
O
HOH
508
7
HOH
HOH
508
O
HOH
522
7
HOH
HOH
522
O
HOH
523
7
HOH
HOH
523
O
HOH
530
7
HOH
HOH
530
O
HOH
547
7
HOH
HOH
547
O
HOH
552
7
HOH
HOH
552
O
HOH
567
7
HOH
HOH
567
O
HOH
589
7
HOH
HOH
589
O
HOH
592
7
HOH
HOH
592
O
HOH
602
7
HOH
HOH
602
O
HOH
401
7
HOH
HOH
401
A
HOH
403
7
HOH
HOH
403
A
HOH
404
7
HOH
HOH
404
A
HOH
405
7
HOH
HOH
405
A
HOH
406
7
HOH
HOH
406
A
HOH
407
7
HOH
HOH
407
A
HOH
408
7
HOH
HOH
408
A
HOH
409
7
HOH
HOH
409
A
HOH
410
7
HOH
HOH
410
A
HOH
411
7
HOH
HOH
411
A
HOH
412
7
HOH
HOH
412
A
HOH
413
7
HOH
HOH
413
A
HOH
414
7
HOH
HOH
414
A
HOH
415
7
HOH
HOH
415
A
HOH
416
7
HOH
HOH
416
A
HOH
417
7
HOH
HOH
417
A
HOH
418
7
HOH
HOH
418
A
HOH
419
7
HOH
HOH
419
A
HOH
421
7
HOH
HOH
421
A
HOH
422
7
HOH
HOH
422
A
HOH
423
7
HOH
HOH
423
A
HOH
424
7
HOH
HOH
424
A
HOH
425
7
HOH
HOH
425
A
HOH
426
7
HOH
HOH
426
A
HOH
427
7
HOH
HOH
427
A
HOH
428
7
HOH
HOH
428
A
HOH
429
7
HOH
HOH
429
A
HOH
430
7
HOH
HOH
430
A
HOH
431
7
HOH
HOH
431
A
HOH
433
7
HOH
HOH
433
A
HOH
434
7
HOH
HOH
434
A
HOH
435
7
HOH
HOH
435
A
HOH
437
7
HOH
HOH
437
A
HOH
438
7
HOH
HOH
438
A
HOH
439
7
HOH
HOH
439
A
HOH
440
7
HOH
HOH
440
A
HOH
441
7
HOH
HOH
441
A
HOH
442
7
HOH
HOH
442
A
HOH
444
7
HOH
HOH
444
A
HOH
445
7
HOH
HOH
445
A
HOH
447
7
HOH
HOH
447
A
HOH
448
7
HOH
HOH
448
A
HOH
449
7
HOH
HOH
449
A
HOH
451
7
HOH
HOH
451
A
HOH
452
7
HOH
HOH
452
A
HOH
454
7
HOH
HOH
454
A
HOH
455
7
HOH
HOH
455
A
HOH
456
7
HOH
HOH
456
A
HOH
458
7
HOH
HOH
458
A
HOH
461
7
HOH
HOH
461
A
HOH
462
7
HOH
HOH
462
A
HOH
463
7
HOH
HOH
463
A
HOH
464
7
HOH
HOH
464
A
HOH
465
7
HOH
HOH
465
A
HOH
468
7
HOH
HOH
468
A
HOH
469
7
HOH
HOH
469
A
HOH
470
7
HOH
HOH
470
A
HOH
471
7
HOH
HOH
471
A
HOH
473
7
HOH
HOH
473
A
HOH
474
7
HOH
HOH
474
A
HOH
475
7
HOH
HOH
475
A
HOH
476
7
HOH
HOH
476
A
HOH
477
7
HOH
HOH
477
A
HOH
479
7
HOH
HOH
479
A
HOH
480
7
HOH
HOH
480
A
HOH
481
7
HOH
HOH
481
A
HOH
484
7
HOH
HOH
484
A
HOH
486
7
HOH
HOH
486
A
HOH
487
7
HOH
HOH
487
A
HOH
488
7
HOH
HOH
488
A
HOH
489
7
HOH
HOH
489
A
HOH
491
7
HOH
HOH
491
A
HOH
492
7
HOH
HOH
492
A
HOH
494
7
HOH
HOH
494
A
HOH
496
7
HOH
HOH
496
A
HOH
497
7
HOH
HOH
497
A
HOH
498
7
HOH
HOH
498
A
HOH
499
7
HOH
HOH
499
A
HOH
501
7
HOH
HOH
501
A
HOH
504
7
HOH
HOH
504
A
HOH
505
7
HOH
HOH
505
A
HOH
506
7
HOH
HOH
506
A
HOH
507
7
HOH
HOH
507
A
HOH
510
7
HOH
HOH
510
A
HOH
512
7
HOH
HOH
512
A
HOH
513
7
HOH
HOH
513
A
HOH
514
7
HOH
HOH
514
A
HOH
516
7
HOH
HOH
516
A
HOH
517
7
HOH
HOH
517
A
HOH
519
7
HOH
HOH
519
A
HOH
521
7
HOH
HOH
521
A
HOH
524
7
HOH
HOH
524
A
HOH
525
7
HOH
HOH
525
A
HOH
526
7
HOH
HOH
526
A
HOH
528
7
HOH
HOH
528
A
HOH
529
7
HOH
HOH
529
A
HOH
531
7
HOH
HOH
531
A
HOH
532
7
HOH
HOH
532
A
HOH
535
7
HOH
HOH
535
A
HOH
537
7
HOH
HOH
537
A
HOH
538
7
HOH
HOH
538
A
HOH
540
7
HOH
HOH
540
A
HOH
541
7
HOH
HOH
541
A
HOH
542
7
HOH
HOH
542
A
HOH
543
7
HOH
HOH
543
A
HOH
544
7
HOH
HOH
544
A
HOH
545
7
HOH
HOH
545
A
HOH
546
7
HOH
HOH
546
A
HOH
548
7
HOH
HOH
548
A
HOH
549
7
HOH
HOH
549
A
HOH
550
7
HOH
HOH
550
A
HOH
551
7
HOH
HOH
551
A
HOH
554
7
HOH
HOH
554
A
HOH
555
7
HOH
HOH
555
A
HOH
556
7
HOH
HOH
556
A
HOH
557
7
HOH
HOH
557
A
HOH
558
7
HOH
HOH
558
A
HOH
559
7
HOH
HOH
559
A
HOH
560
7
HOH
HOH
560
A
HOH
561
7
HOH
HOH
561
A
HOH
562
7
HOH
HOH
562
A
HOH
563
7
HOH
HOH
563
A
HOH
564
7
HOH
HOH
564
A
HOH
565
7
HOH
HOH
565
A
HOH
566
7
HOH
HOH
566
A
HOH
569
7
HOH
HOH
569
A
HOH
571
7
HOH
HOH
571
A
HOH
572
7
HOH
HOH
572
A
HOH
573
7
HOH
HOH
573
A
HOH
574
7
HOH
HOH
574
A
HOH
575
7
HOH
HOH
575
A
HOH
576
7
HOH
HOH
576
A
HOH
578
7
HOH
HOH
578
A
HOH
579
7
HOH
HOH
579
A
HOH
580
7
HOH
HOH
580
A
HOH
581
7
HOH
HOH
581
A
HOH
582
7
HOH
HOH
582
A
HOH
583
7
HOH
HOH
583
A
HOH
584
7
HOH
HOH
584
A
HOH
586
7
HOH
HOH
586
A
HOH
588
7
HOH
HOH
588
A
HOH
590
7
HOH
HOH
590
A
HOH
593
7
HOH
HOH
593
A
HOH
594
7
HOH
HOH
594
A
HOH
595
7
HOH
HOH
595
A
HOH
596
7
HOH
HOH
596
A
HOH
597
7
HOH
HOH
597
A
HOH
598
7
HOH
HOH
598
A
HOH
599
7
HOH
HOH
599
A
HOH
600
7
HOH
HOH
600
A
HOH
601
7
HOH
HOH
601
A
HOH
603
7
HOH
HOH
603
A
HOH
604
7
HOH
HOH
604
A
HOH
605
7
HOH
HOH
605
A
HOH
606
7
HOH
HOH
606
A
A
301
n
1
DA
301
M
C
302
n
2
DC
302
M
G
303
n
3
DG
303
M
T
304
n
4
DT
304
M
A
305
n
5
DA
305
M
C
306
n
6
DC
306
M
C
307
n
7
DC
307
M
T
308
n
8
DT
308
M
G
309
n
9
DG
309
M
G
310
n
10
DG
310
M
C
311
n
11
DC
311
M
T
312
n
12
DT
312
M
A
351
n
1
DA
351
N
G
352
n
2
DG
352
N
C
353
n
3
DC
353
N
T
354
n
1
DT
354
O
A
355
n
2
DA
355
O
G
356
n
3
DG
356
O
G
357
n
4
DG
357
O
T
358
n
5
DT
358
O
A
359
n
6
DA
359
O
C
360
n
7
DC
360
O
G
361
n
8
DG
361
O
T
362
n
9
DT
362
O
ALA
2
n
1
ALA
2
A
ASP
3
n
2
ASP
3
A
VAL
4
n
3
VAL
4
A
HIS
5
n
4
HIS
5
A
ASP
6
n
5
ASP
6
A
LYS
7
n
6
LYS
7
A
ALA
8
n
7
ALA
8
A
THR
9
n
8
THR
9
A
ARG
10
n
9
ARG
10
A
SER
11
n
10
SER
11
A
LYS
12
n
11
LYS
12
A
ASN
13
n
12
ASN
13
A
MET
14
n
13
MET
14
A
ARG
15
n
14
ARG
15
A
ALA
16
n
15
ALA
16
A
ILE
17
n
16
ILE
17
A
ALA
18
n
17
ALA
18
A
THR
19
n
18
THR
19
A
ARG
20
n
19
ARG
20
A
ASP
21
n
20
ASP
21
A
THR
22
n
21
THR
22
A
ALA
23
n
22
ALA
23
A
ILE
24
n
23
ILE
24
A
GLU
25
n
24
GLU
25
A
LYS
26
n
25
LYS
26
A
ARG
27
n
26
ARG
27
A
LEU
28
n
27
LEU
28
A
ALA
29
n
28
ALA
29
A
SER
30
n
29
SER
30
A
LEU
31
n
30
LEU
31
A
LEU
32
n
31
LEU
32
A
THR
33
n
32
THR
33
A
GLY
34
n
33
GLY
34
A
GLN
35
n
34
GLN
35
A
GLY
36
n
35
GLY
36
A
LEU
37
n
36
LEU
37
A
ALA
38
n
37
ALA
38
A
PHE
39
n
38
PHE
39
A
ARG
40
n
39
ARG
40
A
VAL
41
n
40
VAL
41
A
GLN
42
n
41
GLN
42
A
ASP
43
n
42
ASP
43
A
ALA
44
n
43
ALA
44
A
SER
45
n
44
SER
45
A
LEU
46
n
45
LEU
46
A
PRO
47
n
46
PRO
47
A
GLY
48
n
47
GLY
48
A
ARG
49
n
48
ARG
49
A
PRO
50
n
49
PRO
50
A
ASP
51
n
50
ASP
51
A
PHE
52
n
51
PHE
52
A
VAL
53
n
52
VAL
53
A
VAL
54
n
53
VAL
54
A
ASP
55
n
54
ASP
55
A
GLU
56
n
55
GLU
56
A
TYR
57
n
56
TYR
57
A
ARG
58
n
57
ARG
58
A
CYS
59
n
58
CYS
59
A
VAL
60
n
59
VAL
60
A
ILE
61
n
60
ILE
61
A
PHE
62
n
61
PHE
62
A
THR
63
n
62
THR
63
A
HIS
64
n
63
HIS
64
A
GLY
65
n
64
GLY
65
A
CYS
66
n
65
CYS
66
A
PHE
67
n
66
PHE
67
A
TRP
68
n
67
TRP
68
A
HIS
69
n
68
HIS
69
A
HIS
70
n
69
HIS
70
A
HIS
71
n
70
HIS
71
A
HIS
72
n
71
HIS
72
A
CYS
73
n
72
CYS
73
A
TYR
74
n
73
TYR
74
A
LEU
75
n
74
LEU
75
A
PHE
76
n
75
PHE
76
A
LYS
77
n
76
LYS
77
A
VAL
78
n
77
VAL
78
A
PRO
79
n
78
PRO
79
A
ALA
80
n
79
ALA
80
A
THR
81
n
80
THR
81
A
ARG
82
n
81
ARG
82
A
THR
83
n
82
THR
83
A
GLU
84
n
83
GLU
84
A
PHE
85
n
84
PHE
85
A
TRP
86
n
85
TRP
86
A
LEU
87
n
86
LEU
87
A
GLU
88
n
87
GLU
88
A
LYS
89
n
88
LYS
89
A
ILE
90
n
89
ILE
90
A
GLY
91
n
90
GLY
91
A
LYS
92
n
91
LYS
92
A
ASN
93
n
92
ASN
93
A
VAL
94
n
93
VAL
94
A
GLU
95
n
94
GLU
95
A
ARG
96
n
95
ARG
96
A
ASP
97
n
96
ASP
97
A
ARG
98
n
97
ARG
98
A
ARG
99
n
98
ARG
99
A
ASP
100
n
99
ASP
100
A
ILE
101
n
100
ILE
101
A
SER
102
n
101
SER
102
A
ARG
103
n
102
ARG
103
A
LEU
104
n
103
LEU
104
A
GLN
105
n
104
GLN
105
A
GLU
106
n
105
GLU
106
A
LEU
107
n
106
LEU
107
A
GLY
108
n
107
GLY
108
A
TRP
109
n
108
TRP
109
A
ARG
110
n
109
ARG
110
A
VAL
111
n
110
VAL
111
A
LEU
112
n
111
LEU
112
A
ILE
113
n
112
ILE
113
A
VAL
114
n
113
VAL
114
A
TRP
115
n
114
TRP
115
A
GLU
116
n
115
GLU
116
A
CYS
117
n
116
CYS
117
A
ALA
118
n
117
ALA
118
A
LEU
119
n
118
LEU
119
A
ARG
120
n
119
ARG
120
A
GLY
121
n
120
GLY
121
A
ARG
122
n
121
ARG
122
A
GLU
123
n
122
GLU
123
A
LYS
124
n
123
LYS
124
A
LEU
125
n
124
LEU
125
A
THR
126
n
125
THR
126
A
ASP
127
n
126
ASP
127
A
GLU
128
n
127
GLU
128
A
ALA
129
n
128
ALA
129
A
LEU
130
n
129
LEU
130
A
THR
131
n
130
THR
131
A
GLU
132
n
131
GLU
132
A
ARG
133
n
132
ARG
133
A
LEU
134
n
133
LEU
134
A
GLU
135
n
134
GLU
135
A
GLU
136
n
135
GLU
136
A
TRP
137
n
136
TRP
137
A
ILE
138
n
137
ILE
138
A
CYS
139
n
138
CYS
139
A
GLY
140
n
139
GLY
140
A
GLU
141
n
140
GLU
141
A
GLY
142
n
141
GLY
142
A
ALA
143
n
142
ALA
143
A
SER
144
n
143
SER
144
A
ALA
145
n
144
ALA
145
A
GLN
146
n
145
GLN
146
A
ILE
147
n
146
ILE
147
A
ASP
148
n
147
ASP
148
A
THR
149
n
148
THR
149
A
GLN
150
n
149
GLN
150
A
GLY
151
n
150
GLY
151
A
ILE
152
n
151
ILE
152
A
HIS
153
n
152
HIS
153
A
LEU
154
n
153
LEU
154
A
LEU
155
n
154
LEU
155
A
ALA
156
n
155
ALA
156
A
author_defined_assembly
4
tetrameric
N
DC
353
B
O3'
DC
3
1_555
N
MG
202
E
MG
MG
1_555
O
DT
354
C
OP3
DT
1
1_555
77.0
N
DC
353
B
O3'
DC
3
1_555
N
MG
202
E
MG
MG
1_555
A
ASP
51
D
OD1
ASP
50
1_555
154.7
O
DT
354
C
OP3
DT
1
1_555
N
MG
202
E
MG
MG
1_555
A
ASP
51
D
OD1
ASP
50
1_555
85.4
N
DC
353
B
O3'
DC
3
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
496
K
O
HOH
1_555
85.8
O
DT
354
C
OP3
DT
1
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
496
K
O
HOH
1_555
86.5
A
ASP
51
D
OD1
ASP
50
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
496
K
O
HOH
1_555
75.0
N
DC
353
B
O3'
DC
3
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
498
K
O
HOH
1_555
95.0
O
DT
354
C
OP3
DT
1
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
498
K
O
HOH
1_555
170.6
A
ASP
51
D
OD1
ASP
50
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
498
K
O
HOH
1_555
100.5
A
HOH
496
K
O
HOH
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
498
K
O
HOH
1_555
87.9
N
DC
353
B
O3'
DC
3
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
100.6
O
DT
354
C
OP3
DT
1
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
87.3
A
ASP
51
D
OD1
ASP
50
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
96.5
A
HOH
496
K
O
HOH
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
169.9
A
HOH
498
K
O
HOH
1_555
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
99.2
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
O
DT
354
C
OP3
DT
1
1_555
65.8
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
O
HOH
495
J
O
HOH
1_555
92.6
O
DT
354
C
OP3
DT
1
1_555
A
MG
203
G
MG
MG
1_555
O
HOH
495
J
O
HOH
1_555
98.0
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
ASP
51
D
OD2
ASP
50
1_555
170.3
O
DT
354
C
OP3
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
ASP
51
D
OD2
ASP
50
1_555
104.5
O
HOH
495
J
O
HOH
1_555
A
MG
203
G
MG
MG
1_555
A
ASP
51
D
OD2
ASP
50
1_555
90.0
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
THR
63
D
O
THR
62
1_555
98.1
O
DT
354
C
OP3
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
THR
63
D
O
THR
62
1_555
163.9
O
HOH
495
J
O
HOH
1_555
A
MG
203
G
MG
MG
1_555
A
THR
63
D
O
THR
62
1_555
81.7
A
ASP
51
D
OD2
ASP
50
1_555
A
MG
203
G
MG
MG
1_555
A
THR
63
D
O
THR
62
1_555
91.6
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
88.3
O
DT
354
C
OP3
DT
1
1_555
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
89.1
O
HOH
495
J
O
HOH
1_555
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
172.6
A
ASP
51
D
OD2
ASP
50
1_555
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
90.3
A
THR
63
D
O
THR
62
1_555
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
90.9
A
CYS
66
D
SG
CYS
65
1_555
A
ZN
201
F
ZN
ZN
1_555
A
HIS
71
D
ND1
HIS
70
1_555
109.9
A
CYS
66
D
SG
CYS
65
1_555
A
ZN
201
F
ZN
ZN
1_555
A
CYS
73
D
SG
CYS
72
1_555
114.9
A
HIS
71
D
ND1
HIS
70
1_555
A
ZN
201
F
ZN
ZN
1_555
A
CYS
73
D
SG
CYS
72
1_555
107.1
A
CYS
66
D
SG
CYS
65
1_555
A
ZN
201
F
ZN
ZN
1_555
A
CYS
117
D
SG
CYS
116
1_555
106.6
A
HIS
71
D
ND1
HIS
70
1_555
A
ZN
201
F
ZN
ZN
1_555
A
CYS
117
D
SG
CYS
116
1_555
100.2
A
CYS
73
D
SG
CYS
72
1_555
A
ZN
201
F
ZN
ZN
1_555
A
CYS
117
D
SG
CYS
116
1_555
117.1
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
N
ARG
40
D
N
ARG
39
A
O
VAL
53
D
O
VAL
52
A
N
VAL
54
D
N
VAL
53
A
O
CYS
59
D
O
CYS
58
A
N
VAL
60
D
N
VAL
59
A
O
ARG
110
D
O
ARG
109
A
N
ILE
113
D
N
ILE
112
A
O
ALA
145
D
O
ALA
144
A
N
ASP
148
D
N
ASP
147
A
O
GLY
151
D
O
GLY
150
1
A
CB
LYS
77
D
CB
LYS
76
0
Y
1
A
CG
LYS
77
D
CG
LYS
76
0
Y
1
A
CD
LYS
77
D
CD
LYS
76
0
Y
1
A
CE
LYS
77
D
CE
LYS
76
0
Y
1
A
NZ
LYS
77
D
NZ
LYS
76
0
Y
1
A
CB
GLU
106
D
CB
GLU
105
0
Y
1
A
CG
GLU
106
D
CG
GLU
105
0
Y
1
A
CD
GLU
106
D
CD
GLU
105
0
Y
1
A
OE1
GLU
106
D
OE1
GLU
105
0
Y
1
A
OE2
GLU
106
D
OE2
GLU
105
0
Y
1
A
ARG
27
0.103
SIDE CHAIN
1
A
ARG
49
0.281
SIDE CHAIN
1
A
ARG
58
0.153
SIDE CHAIN
1
A
ARG
82
0.124
SIDE CHAIN
1
A
ARG
98
0.112
SIDE CHAIN
1
A
ARG
103
0.119
SIDE CHAIN
1
A
ARG
120
0.113
SIDE CHAIN
1
A
ARG
49
43.59
71.37
1
A
ARG
58
38.95
54.41
1
A
HIS
70
48.63
70.75
1
A
ASP
148
-123.44
-162.53
PROTEIN-ALLHDG.PARAM
PROTEIN-ALLHDG.TOP
DNA-RNA-ALLATOM.PARAM
DNA-RNA-ALLATOM.TOP
31.8
2.87
5.97
0.00
2.87
0.00
-5.74
0.2300000
0.008
0.2040000
0.2040000
2.30
22.0
753
14332
5.000
94.3
RANDOM
1
RESTRAINED
THROUGHOUT
2.000
TRUNCATED VSR MODEL, 1VSR
ENGH & HUBER
FLAT MODEL
50.36
0.322
0.30
0.26
5.00
0.23
0.23
2.30
22.0
206
1957
3
488
1260
0.011
1.1
24.3
0.86
1.18
1.50
1.85
2.00
1.82
2.00
2.64
2.50
0.2800000
0.026
0.2430000
2.44
116
2384
6
4.6
98.7
28.5
2.300
24.254
1CW0
15166
-3.000
0.0590000
1
14.4000
4.600
99.8
0.3160000
2.30
2.38
4.60
100.0
phasing
AMoRE
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
5
N
N
7
N
N
7
N
N
7
N
N
7
N
N
A
ASP
6
D
ASP
5
HELX_P
A
ILE
17
D
ILE
16
1
1
12
A
THR
22
D
THR
21
HELX_P
A
GLN
35
D
GLN
34
1
2
14
A
ASP
55
D
ASP
54
HELX_P
A
TYR
57
D
TYR
56
5
3
3
A
ARG
82
D
ARG
81
HELX_P
A
LEU
107
D
LEU
106
1
4
26
A
GLU
116
D
GLU
115
HELX_P
A
ARG
120
D
ARG
119
1
5
5
A
THR
126
D
THR
125
HELX_P
A
GLY
140
D
GLY
139
1
6
15
metalc
2.272
N
MG
202
E
MG
MG
1_555
N
DC
353
B
O3'
DC
3
1_555
metalc
2.206
N
MG
202
E
MG
MG
1_555
O
DT
354
C
OP3
DT
1
1_555
metalc
2.372
N
MG
202
E
MG
MG
1_555
A
ASP
51
D
OD1
ASP
50
1_555
metalc
2.333
N
MG
202
E
MG
MG
1_555
A
HOH
496
K
O
HOH
1_555
metalc
2.007
N
MG
202
E
MG
MG
1_555
A
HOH
498
K
O
HOH
1_555
metalc
1.931
N
MG
202
E
MG
MG
1_555
A
HOH
596
K
O
HOH
1_555
metalc
2.314
O
DT
354
C
OP2
DT
1
1_555
A
MG
203
G
MG
MG
1_555
metalc
2.287
O
DT
354
C
OP3
DT
1
1_555
A
MG
203
G
MG
MG
1_555
metalc
2.059
O
HOH
495
J
O
HOH
1_555
A
MG
203
G
MG
MG
1_555
metalc
2.376
A
ASP
51
D
OD2
ASP
50
1_555
A
MG
203
G
MG
MG
1_555
metalc
2.282
A
THR
63
D
O
THR
62
1_555
A
MG
203
G
MG
MG
1_555
metalc
2.295
A
CYS
66
D
SG
CYS
65
1_555
A
ZN
201
F
ZN
ZN
1_555
metalc
1.942
A
HIS
71
D
ND1
HIS
70
1_555
A
ZN
201
F
ZN
ZN
1_555
metalc
2.350
A
CYS
73
D
SG
CYS
72
1_555
A
ZN
201
F
ZN
ZN
1_555
metalc
2.430
A
CYS
117
D
SG
CYS
116
1_555
A
ZN
201
F
ZN
ZN
1_555
metalc
2.059
A
MG
203
G
MG
MG
1_555
A
HOH
494
K
O
HOH
1_555
hydrog
WATSON-CRICK
M
DA
301
A
N1
DA
1
1_555
O
DT
362
C
N3
DT
9
1_555
hydrog
WATSON-CRICK
M
DA
301
A
N6
DA
1
1_555
O
DT
362
C
O4
DT
9
1_555
hydrog
WATSON-CRICK
M
DC
302
A
N3
DC
2
1_555
O
DG
361
C
N1
DG
8
1_555
hydrog
WATSON-CRICK
M
DC
302
A
N4
DC
2
1_555
O
DG
361
C
O6
DG
8
1_555
hydrog
WATSON-CRICK
M
DC
302
A
O2
DC
2
1_555
O
DG
361
C
N2
DG
8
1_555
hydrog
WATSON-CRICK
M
DG
303
A
N1
DG
3
1_555
O
DC
360
C
N3
DC
7
1_555
hydrog
WATSON-CRICK
M
DG
303
A
N2
DG
3
1_555
O
DC
360
C
O2
DC
7
1_555
hydrog
WATSON-CRICK
M
DG
303
A
O6
DG
3
1_555
O
DC
360
C
N4
DC
7
1_555
hydrog
WATSON-CRICK
M
DT
304
A
N3
DT
4
1_555
O
DA
359
C
N1
DA
6
1_555
hydrog
WATSON-CRICK
M
DT
304
A
O4
DT
4
1_555
O
DA
359
C
N6
DA
6
1_555
hydrog
WATSON-CRICK
M
DA
305
A
N1
DA
5
1_555
O
DT
358
C
N3
DT
5
1_555
hydrog
WATSON-CRICK
M
DA
305
A
N6
DA
5
1_555
O
DT
358
C
O4
DT
5
1_555
hydrog
WATSON-CRICK
M
DC
306
A
N3
DC
6
1_555
O
DG
357
C
N1
DG
4
1_555
hydrog
WATSON-CRICK
M
DC
306
A
N4
DC
6
1_555
O
DG
357
C
O6
DG
4
1_555
hydrog
WATSON-CRICK
M
DC
306
A
O2
DC
6
1_555
O
DG
357
C
N2
DG
4
1_555
hydrog
WATSON-CRICK
M
DC
307
A
N3
DC
7
1_555
O
DG
356
C
N1
DG
3
1_555
hydrog
WATSON-CRICK
M
DC
307
A
N4
DC
7
1_555
O
DG
356
C
O6
DG
3
1_555
hydrog
WATSON-CRICK
M
DC
307
A
O2
DC
7
1_555
O
DG
356
C
N2
DG
3
1_555
hydrog
WATSON-CRICK
M
DT
308
A
N3
DT
8
1_555
O
DA
355
C
N1
DA
2
1_555
hydrog
WATSON-CRICK
M
DT
308
A
O4
DT
8
1_555
O
DA
355
C
N6
DA
2
1_555
hydrog
TYPE_28_PAIR
M
DG
309
A
N1
DG
9
1_555
O
DT
354
C
O2
DT
1
1_555
hydrog
TYPE_28_PAIR
M
DG
309
A
O6
DG
9
1_555
O
DT
354
C
N3
DT
1
1_555
hydrog
WATSON-CRICK
M
DG
310
A
N1
DG
10
1_555
N
DC
353
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
M
DG
310
A
N2
DG
10
1_555
N
DC
353
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
M
DG
310
A
O6
DG
10
1_555
N
DC
353
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
M
DC
311
A
N3
DC
11
1_555
N
DG
352
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
M
DC
311
A
N4
DC
11
1_555
N
DG
352
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
M
DC
311
A
O2
DC
11
1_555
N
DG
352
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
M
DT
312
A
N3
DT
12
1_555
N
DA
351
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
M
DT
312
A
O4
DT
12
1_555
N
DA
351
B
N6
DA
1
1_555
HYDROLASE/DNA
PROTEIN-DNA COMPLEX, MISMATCH, INTERCALATION, ZINC, HYDROLASE/DNA, HYDROLASE-DNA complex
VSR_ECOLI
UNP
4
P09184
1CW0
PDB
1
1CW0
1CW0
PDB
2
1CW0
1CW0
PDB
3
1CW0
1
155
1CW0
2
156
P09184
A
1
1
155
301
312
1CW0
301
312
1CW0
M
2
1
12
351
353
1CW0
351
353
1CW0
N
3
1
3
354
362
1CW0
354
362
1CW0
O
4
1
9
6
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
A
ARG
40
D
ARG
39
A
VAL
41
D
VAL
40
A
PHE
52
D
PHE
51
A
VAL
54
D
VAL
53
A
CYS
59
D
CYS
58
A
HIS
64
D
HIS
63
A
ARG
110
D
ARG
109
A
TRP
115
D
TRP
114
A
ALA
145
D
ALA
144
A
ASP
148
D
ASP
147
A
GLY
151
D
GLY
150
A
LEU
154
D
LEU
153
BINDING SITE FOR RESIDUE ZN A 201
A
ZN
201
Software
4
BINDING SITE FOR RESIDUE MG N 202
N
MG
202
Software
7
BINDING SITE FOR RESIDUE MG A 203
A
MG
203
Software
5
A
CYS
66
D
CYS
65
4
1_555
A
HIS
71
D
HIS
70
4
1_555
A
CYS
73
D
CYS
72
4
1_555
A
CYS
117
D
CYS
116
4
1_555
A
ARG
49
D
ARG
48
7
1_555
A
ASP
51
D
ASP
50
7
1_555
A
HOH
496
K
HOH
7
1_555
A
HOH
498
K
HOH
7
1_555
A
HOH
596
K
HOH
7
1_555
N
DC
353
B
DC
3
7
1_555
O
DT
354
C
DT
1
7
1_555
A
ASP
51
D
ASP
50
5
1_555
A
THR
63
D
THR
62
5
1_555
A
HOH
494
K
HOH
5
1_555
O
DT
354
C
DT
1
5
1_555
O
HOH
495
J
HOH
5
1_555
170
hexagonal
P 65