0.009016
0.000000
0.000000
0.000000
0.009016
0.000000
0.000000
0.000000
0.023180
0.00000
0.00000
0.00000
De Rosa, M.
Zacarias, S.
Athanasiadis, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
110.910
110.910
43.140
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
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
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
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
N
100
N
N
N
101
N
C
N
102
N
O
N
103
N
N
N
104
N
C
N
105
N
N
N
106
N
C
N
107
N
C
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
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
O
N
123
N
P
N
124
N
O
N
125
N
O
N
126
N
O
N
127
N
C
N
128
R
C
N
129
N
O
N
130
S
C
N
131
N
O
N
132
N
C
N
133
R
C
Y
134
N
N
Y
135
N
C
Y
136
N
N
Y
137
N
C
N
138
N
C
N
139
N
O
N
140
N
N
N
141
N
C
N
142
N
N
N
143
N
N
Y
144
N
C
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
H
N
159
N
O
N
160
N
P
N
161
N
O
N
162
N
O
N
163
N
O
N
164
N
C
N
165
R
C
N
166
N
O
N
167
S
C
N
168
N
O
N
169
N
C
N
170
R
C
N
171
N
N
N
172
N
C
N
173
N
O
N
174
N
N
N
175
N
C
N
176
N
O
N
177
N
C
N
178
N
C
N
179
N
C
N
180
N
H
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
N
N
196
S
C
N
197
N
C
N
198
N
O
N
199
N
C
N
200
N
C
N
201
N
C
N
202
N
O
N
203
N
N
N
204
N
O
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
O
N
223
N
O
N
224
N
O
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
N
C
N
236
N
C
N
237
N
O
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
Y
249
N
C
Y
250
N
N
Y
251
N
C
Y
252
N
C
Y
253
N
N
N
254
N
O
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
O
N
266
N
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
S
C
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
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
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
N
N
321
N
O
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
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
N
C
N
343
N
S
N
344
N
C
N
345
N
O
N
346
N
H
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
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
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
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
O
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
N
N
398
S
C
N
399
N
C
N
400
N
O
N
401
N
C
N
402
N
O
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
R
C
N
416
N
O
N
417
N
C
N
418
N
O
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
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
N
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
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
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
N
466
N
O
N
467
N
O
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
N
N
480
S
C
N
481
N
C
N
482
N
O
N
483
N
C
N
484
N
C
N
485
N
C
N
486
N
O
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
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
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
Y
141
N
sing
Y
142
N
sing
Y
143
N
doub
N
144
N
sing
Y
145
N
sing
N
146
N
sing
Y
147
N
doub
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
sing
N
159
N
doub
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
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
doub
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
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
doub
N
209
N
sing
N
210
N
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
doub
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
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
doub
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
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
Y
251
N
sing
Y
252
N
doub
Y
253
N
doub
N
254
N
sing
Y
255
N
sing
N
256
N
sing
Y
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
doub
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
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
N
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
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
doub
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
sing
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
doub
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
doub
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
Y
359
N
doub
Y
360
N
sing
Y
361
N
sing
N
362
N
sing
Y
363
N
doub
N
364
N
sing
Y
365
N
doub
N
366
N
sing
Y
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
doub
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
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
doub
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
sing
N
407
N
doub
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
doub
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
Y
428
N
doub
Y
429
N
sing
Y
430
N
sing
N
431
N
sing
Y
432
N
doub
Y
433
N
sing
Y
434
N
sing
N
435
N
sing
Y
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
439
N
doub
N
440
N
sing
Y
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
Y
456
N
doub
Y
457
N
sing
Y
458
N
sing
N
459
N
sing
Y
460
N
doub
N
461
N
sing
Y
462
N
doub
N
463
N
sing
Y
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
doub
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
41
9924
9933
10.1093/nar/gkt743
23975196
Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ.
2013
10.2210/pdb4lb6/pdb
pdb_00004lb6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
70
1
PIXEL
2012-09-29
PILATUS 6M-F
SINGLE WAVELENGTH
M
x-ray
1
0.97
1.0
ID23-1
ESRF
0.97
SYNCHROTRON
ESRF BEAMLINE ID23-1
8450.583
Protein kinase containing Z-DNA binding domains
2.7.11.1
Zalpha domain, UNP residues 5-70
1
man
polymer
3969.561
5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'
1
syn
polymer
18.015
water
73
nat
water
Uncharacterized protein, Z-DNA binding protein kinase
no
no
GSHMASSAENEIEMRICDYLRRHGRSTVQDIFKELKLEKSTVNRHLYSLQASKQVFKTVEDNKRPVWNLVES
GSHMASSAENEIEMRICDYLRRHGRSTVQDIFKELKLEKSTVNRHLYSLQASKQVFKTVEDNKRPVWNLVES
B
polypeptide(L)
no
no
(DT)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)
TCGCGCGCGCGCG
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
leopard danio,zebra danio,zebra fish
sample
pkz
7955
Danio rerio
469008
Escherichia coli
BL21 (DE3)
pET28b
1
2.67
53.94
VAPOR DIFFUSION, HANGING DROP
5.4
2.0 M ammonium sulfate, 0.1 M sodium acetate, 7.5 % glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-0.648
1
19
C
8
C
11
2.371
C_DC8:DG11_C
1
3.806
-0.298
0.174
-0.179
0.055
1
19
C
9
C
10
-0.820
C_DG9:DC10_C
2
2.111
0.487
0.121
-0.105
-0.055
1
19
C
10
C
9
-0.820
C_DC10:DG9_C
3
2.111
-0.487
0.121
-0.105
0.648
1
19
C
11
C
8
2.371
C_DG11:DC8_C
4
3.806
0.298
0.174
-0.179
2.320
-11.285
C
C
8
9
-11.711
C
C
11
10
3.492
2.282
-0.032
5.364
CC_DC8DG9:DC10DG11_CC
1
1.289
6.614
-10.977
-30.298
1.544
3.311
-55.759
C
C
9
10
5.158
C
C
10
9
3.396
-4.819
0.000
-0.934
CC_DG9DC10:DG9DC10_CC
2
0.000
0.000
-55.567
1.285
0.000
2.320
-11.285
C
C
10
11
-11.711
C
C
9
8
3.492
2.282
0.032
5.364
CC_DC10DG11:DC8DG9_CC
3
-1.289
-6.614
-10.977
-30.298
-1.544
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Database references
Data collection
Database references
Refinement description
1
0
2013-09-18
1
1
2013-12-04
1
2
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2013-06-20
REL
REL
HOH
water
Synthetic oligonucleotide
sample
4LB5
PDB ENTRY 4LB5
PDB
experimental model
HOH
1
3
HOH
HOH
101
B
HOH
2
3
HOH
HOH
102
B
HOH
5
3
HOH
HOH
103
B
HOH
7
3
HOH
HOH
104
B
HOH
10
3
HOH
HOH
105
B
HOH
11
3
HOH
HOH
106
B
HOH
16
3
HOH
HOH
107
B
HOH
17
3
HOH
HOH
108
B
HOH
18
3
HOH
HOH
109
B
HOH
20
3
HOH
HOH
110
B
HOH
23
3
HOH
HOH
111
B
HOH
24
3
HOH
HOH
112
B
HOH
26
3
HOH
HOH
113
B
HOH
27
3
HOH
HOH
114
B
HOH
31
3
HOH
HOH
115
B
HOH
35
3
HOH
HOH
116
B
HOH
39
3
HOH
HOH
117
B
HOH
41
3
HOH
HOH
118
B
HOH
42
3
HOH
HOH
119
B
HOH
43
3
HOH
HOH
120
B
HOH
45
3
HOH
HOH
121
B
HOH
46
3
HOH
HOH
122
B
HOH
47
3
HOH
HOH
123
B
HOH
48
3
HOH
HOH
124
B
HOH
49
3
HOH
HOH
125
B
HOH
50
3
HOH
HOH
126
B
HOH
53
3
HOH
HOH
127
B
HOH
54
3
HOH
HOH
128
B
HOH
55
3
HOH
HOH
129
B
HOH
56
3
HOH
HOH
130
B
HOH
59
3
HOH
HOH
131
B
HOH
61
3
HOH
HOH
132
B
HOH
63
3
HOH
HOH
133
B
HOH
64
3
HOH
HOH
134
B
HOH
67
3
HOH
HOH
135
B
HOH
68
3
HOH
HOH
136
B
HOH
70
3
HOH
HOH
137
B
HOH
71
3
HOH
HOH
138
B
HOH
72
3
HOH
HOH
139
B
HOH
73
3
HOH
HOH
140
B
HOH
74
3
HOH
HOH
141
B
HOH
76
3
HOH
HOH
142
B
HOH
3
3
HOH
HOH
101
C
HOH
4
3
HOH
HOH
102
C
HOH
6
3
HOH
HOH
103
C
HOH
8
3
HOH
HOH
104
C
HOH
9
3
HOH
HOH
105
C
HOH
12
3
HOH
HOH
106
C
HOH
13
3
HOH
HOH
107
C
HOH
14
3
HOH
HOH
108
C
HOH
15
3
HOH
HOH
109
C
HOH
19
3
HOH
HOH
110
C
HOH
21
3
HOH
HOH
111
C
HOH
22
3
HOH
HOH
112
C
HOH
25
3
HOH
HOH
113
C
HOH
28
3
HOH
HOH
114
C
HOH
29
3
HOH
HOH
115
C
HOH
30
3
HOH
HOH
116
C
HOH
32
3
HOH
HOH
117
C
HOH
33
3
HOH
HOH
118
C
HOH
34
3
HOH
HOH
119
C
HOH
36
3
HOH
HOH
120
C
HOH
37
3
HOH
HOH
121
C
HOH
38
3
HOH
HOH
122
C
HOH
40
3
HOH
HOH
123
C
HOH
44
3
HOH
HOH
124
C
HOH
51
3
HOH
HOH
125
C
HOH
52
3
HOH
HOH
126
C
HOH
57
3
HOH
HOH
127
C
HOH
60
3
HOH
HOH
128
C
HOH
62
3
HOH
HOH
129
C
HOH
69
3
HOH
HOH
130
C
HOH
75
3
HOH
HOH
131
C
n
1
-1
B
n
2
0
B
n
3
1
B
n
4
2
B
n
5
3
B
n
6
4
B
n
7
5
B
n
8
6
B
GLU
7
n
9
GLU
7
B
ASN
8
n
10
ASN
8
B
GLU
9
n
11
GLU
9
B
ILE
10
n
12
ILE
10
B
GLU
11
n
13
GLU
11
B
MET
12
n
14
MET
12
B
ARG
13
n
15
ARG
13
B
ILE
14
n
16
ILE
14
B
CYS
15
n
17
CYS
15
B
ASP
16
n
18
ASP
16
B
TYR
17
n
19
TYR
17
B
LEU
18
n
20
LEU
18
B
ARG
19
n
21
ARG
19
B
ARG
20
n
22
ARG
20
B
HIS
21
n
23
HIS
21
B
GLY
22
n
24
GLY
22
B
ARG
23
n
25
ARG
23
B
SER
24
n
26
SER
24
B
THR
25
n
27
THR
25
B
VAL
26
n
28
VAL
26
B
GLN
27
n
29
GLN
27
B
ASP
28
n
30
ASP
28
B
ILE
29
n
31
ILE
29
B
PHE
30
n
32
PHE
30
B
LYS
31
n
33
LYS
31
B
GLU
32
n
34
GLU
32
B
LEU
33
n
35
LEU
33
B
LYS
34
n
36
LYS
34
B
LEU
35
n
37
LEU
35
B
GLU
36
n
38
GLU
36
B
LYS
37
n
39
LYS
37
B
SER
38
n
40
SER
38
B
THR
39
n
41
THR
39
B
VAL
40
n
42
VAL
40
B
ASN
41
n
43
ASN
41
B
ARG
42
n
44
ARG
42
B
HIS
43
n
45
HIS
43
B
LEU
44
n
46
LEU
44
B
TYR
45
n
47
TYR
45
B
SER
46
n
48
SER
46
B
LEU
47
n
49
LEU
47
B
GLN
48
n
50
GLN
48
B
ALA
49
n
51
ALA
49
B
SER
50
n
52
SER
50
B
LYS
51
n
53
LYS
51
B
GLN
52
n
54
GLN
52
B
VAL
53
n
55
VAL
53
B
PHE
54
n
56
PHE
54
B
LYS
55
n
57
LYS
55
B
THR
56
n
58
THR
56
B
VAL
57
n
59
VAL
57
B
GLU
58
n
60
GLU
58
B
ASP
59
n
61
ASP
59
B
ASN
60
n
62
ASN
60
B
LYS
61
n
63
LYS
61
B
ARG
62
n
64
ARG
62
B
PRO
63
n
65
PRO
63
B
VAL
64
n
66
VAL
64
B
TRP
65
n
67
TRP
65
B
ASN
66
n
68
ASN
66
B
LEU
67
n
69
LEU
67
B
VAL
68
n
70
VAL
68
B
GLU
69
n
71
GLU
69
B
n
72
70
B
n
1
7
C
DC
8
n
2
DC
8
C
DG
9
n
3
DG
9
C
DC
10
n
4
DC
10
C
DG
11
n
5
DG
11
C
DC
12
n
6
DC
12
C
DG
13
n
7
DG
13
C
n
8
14
C
n
9
15
C
n
10
16
C
n
11
17
C
n
12
18
C
n
13
19
C
2.6131
1.8549
-0.3418
5.9651
-0.0347
2.0744
-0.0160
0.2205
-0.1579
-0.3529
-0.3420
-0.5563
0.1730
1.0005
0.2932
0.1615
0.0215
-0.0458
0.5634
0.0690
0.3920
refined
-4.6410
27.9134
20.4601
X-RAY DIFFRACTION
6.1764
2.5436
0.4755
7.4409
-0.1937
5.3858
-0.6224
1.7057
0.4543
-0.7020
0.8746
-0.2335
-0.0756
0.5530
-0.1489
0.1870
-0.0467
-0.0318
0.4917
0.0455
0.2409
refined
-13.0537
28.1087
14.8579
X-RAY DIFFRACTION
9.7803
0.8630
2.2742
9.1128
4.6871
2.8301
0.1051
-0.5851
0.3494
0.3995
0.0212
-0.2850
0.0687
0.0973
-0.0938
0.1332
-0.0046
0.0120
0.2462
0.0267
0.1799
refined
-15.1365
28.8271
25.6203
X-RAY DIFFRACTION
9.0410
-6.1577
2.0030
6.0914
-1.5014
5.7413
-0.0751
-0.7726
1.5113
-0.0479
0.6892
0.3140
-0.3547
0.6560
-0.4742
0.2292
-0.0585
-0.0125
0.4531
-0.1431
0.8008
refined
-10.6694
38.2505
26.6675
X-RAY DIFFRACTION
1.8823
0.5101
-0.9253
0.4033
0.9697
6.6748
-0.4020
0.0861
1.9318
-0.2186
-0.1638
0.3378
-1.1181
-0.0405
0.5734
0.2992
-0.0648
-0.0773
0.2587
0.0761
0.8813
refined
-16.2159
39.6957
19.5571
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'B' and (resid 7 through 21 )
X-RAY DIFFRACTION
2
chain 'B' and (resid 22 through 36 )
X-RAY DIFFRACTION
3
chain 'B' and (resid 37 through 49 )
X-RAY DIFFRACTION
4
chain 'B' and (resid 50 through 56 )
X-RAY DIFFRACTION
5
chain 'B' and (resid 57 through 69 )
author_defined_assembly
8
octameric
2800
-25
9050
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_556
-y,-x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
43.1400000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
10_454
-x-1/2,-y+1/2,z-1/2
crystal symmetry operation
-55.4550000000
55.4550000000
-21.5700000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
15_455
y-1/2,x+1/2,-z+1/2
crystal symmetry operation
-55.4550000000
55.4550000000
21.5700000000
B
N
PHE
54
A
N
PHE
56
B
O
ASN
66
A
O
ASN
68
1
B
HOH
117
C
HOH
1
C
HOH
108
D
HOH
1
C
HOH
119
D
HOH
1
C
HOH
120
D
HOH
1
C
HOH
121
D
HOH
1
B
GLY
-1
A
GLY
1
1
Y
1
B
SER
0
A
SER
2
1
Y
1
B
HIS
1
A
HIS
3
1
Y
1
B
MET
2
A
MET
4
1
Y
1
B
ALA
3
A
ALA
5
1
Y
1
B
SER
4
A
SER
6
1
Y
1
B
SER
5
A
SER
7
1
Y
1
B
ALA
6
A
ALA
8
1
Y
1
B
SER
70
A
SER
72
1
Y
1
C
DT
7
B
DT
1
1
Y
1
C
DC
14
B
DC
8
1
Y
1
C
DG
15
B
DG
9
1
Y
1
C
DC
16
B
DC
10
1
Y
1
C
DG
17
B
DG
11
1
Y
1
C
DC
18
B
DC
12
1
Y
1
C
DG
19
B
DG
13
1
Y
1
C
C
OP1
O
DG
HOH
9
112
2.07
1
B
B
OD2
NH1
ASP
ARG
16
20
2.11
1
B
B
O
O
HOH
HOH
126
133
2.13
1
3.01
0.40
120.30
123.31
C
C
C
C6
N1
C2
DC
DC
DC
8
8
8
N
1
2.54
0.40
121.90
124.44
C
C
C
N3
C4
C5
DC
DC
DC
8
8
8
N
1
-7.54
0.90
105.70
98.16
C
C
C
O5'
P
OP1
DG
DG
DG
9
9
9
N
1
3.94
0.60
106.00
109.94
C
C
C
O4'
C4'
C3'
DG
DG
DG
9
9
9
N
1
-4.57
0.60
125.10
120.53
C
C
C
C6
N1
C2
DG
DG
DG
9
9
9
N
1
9.60
1.50
119.60
129.20
C
C
C
OP1
P
OP2
DG
DG
DG
13
13
13
N
1
-5.53
0.40
104.50
98.97
C
C
C
O4'
C4'
C3'
DG
DG
DG
13
13
13
N
1
-11.40
1.80
114.10
102.70
C
C
C
C5'
C4'
C3'
DG
DG
DG
13
13
13
N
1
-16.98
2.50
109.70
92.72
C
C
C
C4'
C3'
O3'
DG
DG
DG
13
13
13
N
1
-6.14
0.70
108.00
101.86
C
C
C
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
-3.75
0.60
125.10
121.35
C
C
C
C6
N1
C2
DG
DG
DG
13
13
13
N
1
C
C
C5'
C4'
DC
DC
12
12
0.049
0.007
1.512
1.561
N
1
C
C
O4'
C4'
DG
DG
13
13
-0.062
0.010
1.446
1.384
N
1
C
C
O3'
C3'
DG
DG
13
13
-0.064
0.006
1.419
1.355
N
1
B
B
O
O
HOH
HOH
104
141
1.80
1_555
15_455
1
C
C
O
O
HOH
HOH
124
131
1.85
1_555
8_556
1
B
ASP
59
49.01
-130.94
0.2116
0.1809
0.1841
1.800
28.072
1216
12155
10.00
94.99
0.17
lattice symmetry 10%
1
1.35
MOLECULAR REPLACEMENT
21.00
0.90
1.11
PDB ENTRY 4LB5
ML
FLAT BULK SOLVENT MODEL
1.800
28.072
73
731
0
123
535
0.019
684
2.062
944
19.133
274
0.138
105
0.009
100
0.2574
0.2328
1.8721
131
1188
95.00
0.2510
0.2237
1.9573
133
1188
95.00
0.2436
0.2019
2.0604
131
1178
95.00
0.2300
0.1877
2.1895
135
1213
96.00
0.2112
0.1793
2.3584
135
1211
96.00
0.2229
0.1893
2.5956
136
1231
97.00
0.2175
0.1948
2.9709
138
1241
97.00
0.2000
0.1662
3.7416
139
1244
96.00
0.1939
0.1667
28.0754
138
1245
90.00
27.1
1.8
32.55
4LB6
12161
2.0
0.074
1
11.3
4.6
96.4
0.679
1.8
1.9
2.2
1
4.7
96.0
data collection
DNA
phasing
PHASER
refinement
PHENIX
(phenix.refine: 1.8.2_1309)
data reduction
MOSFLM
data scaling
SCALA
Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)
1
N
N
2
N
N
3
N
N
3
N
N
B
GLU
7
A
GLU
9
HELX_P
B
GLY
22
A
GLY
24
1
1
16
B
THR
25
A
THR
27
HELX_P
B
LYS
34
A
LYS
36
1
2
10
B
GLU
36
A
GLU
38
HELX_P
B
SER
50
A
SER
52
1
3
15
hydrog
WATSON-CRICK
C
DC
8
B
N3
DC
2
1_555
C
DG
11
B
N1
DG
5
8_556
hydrog
WATSON-CRICK
C
DC
8
B
N4
DC
2
1_555
C
DG
11
B
O6
DG
5
8_556
hydrog
WATSON-CRICK
C
DC
8
B
O2
DC
2
1_555
C
DG
11
B
N2
DG
5
8_556
hydrog
WATSON-CRICK
C
DG
9
B
N1
DG
3
1_555
C
DC
10
B
N3
DC
4
8_556
hydrog
WATSON-CRICK
C
DG
9
B
N2
DG
3
1_555
C
DC
10
B
O2
DC
4
8_556
hydrog
WATSON-CRICK
C
DG
9
B
O6
DG
3
1_555
C
DC
10
B
N4
DC
4
8_556
hydrog
WATSON-CRICK
C
DC
10
B
N3
DC
4
1_555
C
DG
9
B
N1
DG
3
8_556
hydrog
WATSON-CRICK
C
DC
10
B
N4
DC
4
1_555
C
DG
9
B
O6
DG
3
8_556
hydrog
WATSON-CRICK
C
DC
10
B
O2
DC
4
1_555
C
DG
9
B
N2
DG
3
8_556
hydrog
WATSON-CRICK
C
DG
11
B
N1
DG
5
1_555
C
DC
8
B
N3
DC
2
8_556
hydrog
WATSON-CRICK
C
DG
11
B
N2
DG
5
1_555
C
DC
8
B
O2
DC
2
8_556
hydrog
WATSON-CRICK
C
DG
11
B
O6
DG
5
1_555
C
DC
8
B
N4
DC
2
8_556
TRANSFERASE/DNA
wHTH, Zalpha, ZBD, Kinase, innate immunity, Z-DNA, Z-RNA, eIF2a, TRANSFERASE-DNA complex
Q5NE14_DANRE
UNP
1
5
Q5NE14
SAENEIEMRICDYLRRHGRSTVQDIFKELKLEKSTVNRHLYSLQASKQVFKTVEDNKRPVWNLVES
4LB6
PDB
2
4LB6
TCGCGCGCGCGCG
5
70
4LB6
5
70
Q5NE14
B
1
7
72
7
19
4LB6
7
19
4LB6
C
2
1
13
1
expression tag
GLY
-1
4LB6
B
Q5NE14
UNP
1
1
expression tag
SER
0
4LB6
B
Q5NE14
UNP
2
1
expression tag
HIS
1
4LB6
B
Q5NE14
UNP
3
1
expression tag
MET
2
4LB6
B
Q5NE14
UNP
4
1
expression tag
ALA
3
4LB6
B
Q5NE14
UNP
5
1
expression tag
SER
4
4LB6
B
Q5NE14
UNP
6
2
anti-parallel
B
VAL
53
A
VAL
55
B
THR
56
A
THR
58
B
VAL
64
A
VAL
66
B
LEU
67
A
LEU
69
97
I 4 2 2