0.022723
0.000000
0.000000
0.000000
0.017861
0.000000
0.000000
0.000000
0.007755
0.00000
0.00000
0.00000
White, M.A.
Zandarashvili, L.
Iwahara, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
44.009
55.989
128.952
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-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
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
Zn 2
65.409
ZINC ION
non-polymer
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
C
N
8
N
O
N
9
N
N
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
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
N
N
112
R
C
N
113
N
C
N
114
N
O
N
115
N
C
N
116
N
S
N
117
N
O
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
O
N
126
N
P
N
127
N
O
N
128
N
O
N
129
N
O
N
130
N
C
N
131
R
C
N
132
N
O
N
133
S
C
N
134
N
O
N
135
N
C
N
136
R
C
Y
137
N
N
Y
138
N
C
Y
139
N
N
Y
140
N
C
Y
141
N
C
N
142
N
N
Y
143
N
N
Y
144
N
C
Y
145
N
N
Y
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
N
173
N
N
N
174
N
C
N
175
N
O
N
176
N
N
N
177
N
C
N
178
N
N
N
179
N
C
N
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
Y
207
N
N
Y
208
N
C
Y
209
N
N
Y
210
N
C
N
211
N
C
N
212
N
O
N
213
N
N
N
214
N
C
N
215
N
N
N
216
N
N
Y
217
N
C
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
H
N
232
N
O
N
233
N
P
N
234
N
O
N
235
N
O
N
236
N
O
N
237
N
C
N
238
R
C
N
239
N
O
N
240
S
C
N
241
N
O
N
242
N
C
N
243
R
C
N
244
N
N
N
245
N
C
N
246
N
O
N
247
N
N
N
248
N
C
N
249
N
O
N
250
N
C
N
251
N
C
N
252
N
C
N
253
N
H
N
254
N
H
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
H
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
N
C
N
273
N
C
N
274
N
C
N
275
N
O
N
276
N
N
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
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
O
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
N
C
N
309
N
C
N
310
N
O
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
N
N
318
S
C
N
319
N
C
N
320
N
O
N
321
N
C
Y
322
N
C
Y
323
N
N
Y
324
N
C
Y
325
N
C
Y
326
N
N
N
327
N
O
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
H
N
338
N
O
N
339
N
H
N
340
N
H
N
341
N
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
S
C
N
346
N
C
N
347
N
C
N
348
N
C
N
349
N
O
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
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
N
368
N
C
N
369
N
C
N
370
N
C
N
371
N
O
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
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
N
C
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
N
N
394
N
O
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
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
N
N
411
S
C
N
412
N
C
N
413
N
O
N
414
N
C
N
415
N
C
N
416
N
S
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
H
N
429
N
H
N
430
N
N
N
431
S
C
N
432
N
C
N
433
N
O
N
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
N
441
N
O
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
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
N
N
454
S
C
N
455
N
C
N
456
N
O
N
457
N
C
N
458
N
C
N
459
N
C
N
460
N
O
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
N
N
471
S
C
N
472
N
C
N
473
N
O
N
474
N
C
N
475
N
O
N
476
N
O
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
N
N
485
S
C
N
486
N
C
N
487
N
O
N
488
R
C
N
489
N
O
N
490
N
C
N
491
N
O
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
498
N
H
N
499
N
H
N
500
N
H
N
501
N
N
N
502
S
C
N
503
N
C
N
504
N
O
N
505
N
C
Y
506
N
C
Y
507
N
C
Y
508
N
C
Y
509
N
C
Y
510
N
C
Y
511
N
C
N
512
N
O
N
513
N
O
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
N
N
526
S
C
N
527
N
C
N
528
N
O
N
529
N
C
N
530
N
C
N
531
N
C
N
532
N
O
N
533
N
H
N
534
N
H
N
535
N
H
N
536
N
H
N
537
N
H
N
538
N
H
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
H
N
544
N
ZN
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
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
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
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
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
doub
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
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
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
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
doub
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
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
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
doub
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
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
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
Y
144
N
sing
Y
145
N
sing
Y
146
N
doub
N
147
N
sing
Y
148
N
sing
Y
149
N
sing
Y
150
N
doub
N
151
N
sing
Y
152
N
doub
N
153
N
sing
N
154
N
sing
Y
155
N
sing
Y
156
N
doub
N
157
N
sing
Y
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
doub
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
sing
N
183
N
sing
N
184
N
doub
N
185
N
sing
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
doub
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
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
Y
217
N
sing
Y
218
N
sing
Y
219
N
doub
N
220
N
sing
Y
221
N
sing
N
222
N
sing
Y
223
N
doub
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
doub
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
sing
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
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
doub
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
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
sing
N
276
N
doub
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
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
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
doub
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
Y
327
N
sing
Y
328
N
doub
Y
329
N
doub
N
330
N
sing
Y
331
N
sing
N
332
N
sing
Y
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
doub
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
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
doub
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
sing
N
386
N
sing
N
387
N
doub
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
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
doub
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
Y
435
N
doub
Y
436
N
sing
Y
437
N
sing
N
438
N
sing
Y
439
N
doub
N
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
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
sing
N
452
N
sing
N
453
N
doub
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
doub
N
471
N
sing
N
472
N
sing
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
doub
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
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
doub
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
Y
504
N
doub
Y
505
N
sing
Y
506
N
sing
N
507
N
sing
Y
508
N
doub
N
509
N
sing
Y
510
N
doub
N
511
N
sing
Y
512
N
sing
N
513
N
sing
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
doub
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
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
sing
NE
Febs Lett.
FEBLAL
0165
0014-5793
589
1748
1753
10.1016/j.febslet.2015.05.022
25999311
Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1.
2015
US
Genes Dev.
GEDEEP
2056
1549-5477
28
2304
2313
10.1101/gad.250746.114
25258363
Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
2014
10.2210/pdb4x9j/pdb
pdb_00004x9j
90
1
CCD
2014-11-02
MARMOSAIC 225 mm CCD
Si DCM
SINGLE WAVELENGTH
M
x-ray
1
0.97872
1.0
21-ID-F
APS
0.97872
SYNCHROTRON
APS BEAMLINE 21-ID-F
10722.302
Early growth response protein 1
UNP residues 335-423
1
man
polymer
3458.287
DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')
1
syn
polymer
3307.205
DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3')
1
syn
polymer
65.409
ZINC ION
3
syn
non-polymer
18.015
water
208
nat
water
EGR-1,AT225,Nerve growth factor-induced protein A,NGFI-A,Transcription factor ETR103,Transcription factor Zif268,Zinc finger protein 225,Zinc finger protein Krox-24
no
no
ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRH
TKIHLRQKD
ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRH
TKIHLRQKD
A
polypeptide(L)
no
yes
(DA)(DG)(5CM)(DG)(DT)(DG)(DG)(DG)(5CM)(DG)(DT)
AGCGTGGGCGT
B
polydeoxyribonucleotide
no
yes
(DT)(DA)(5CM)(DG)(DC)(DC)(DC)(DA)(5CM)(DG)(DC)
TACGCCCACGC
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Human
sample
1
89
EGR1, KROX24, ZNF225
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.32
47.00
VAPOR DIFFUSION, SITTING DROP
25mM BisTris pH8, 10% PEG-600, 450mM NaCl
7-8
290
-1.527
1
19
B
2
C
61
0.324
B_DG2:DC61_C
1
-4.195
-0.183
0.064
-0.153
6.455
1
19
B
3
C
60
-0.060
B_5CM3:DG60_C
2
-5.152
0.336
-0.134
-0.123
-1.558
1
19
B
4
C
59
-0.163
B_DG4:5CM59_C
3
-6.006
-0.250
0.014
-0.119
11.664
1
20
B
5
C
58
3.653
B_DT5:DA58_C
4
-2.558
0.015
-0.153
-0.128
2.230
1
19
B
6
C
57
0.481
B_DG6:DC57_C
5
-9.774
-0.265
0.143
-0.299
-8.416
1
19
B
7
C
56
-2.734
B_DG7:DC56_C
6
-9.268
-0.131
-0.055
-0.098
-3.923
1
19
B
8
C
55
-1.612
B_DG8:DC55_C
7
-11.647
0.048
0.125
-0.065
-2.628
1
19
B
9
C
54
-0.958
B_5CM9:DG54_C
8
-6.437
0.194
0.028
-0.094
-0.991
1
19
B
10
C
53
-1.217
B_DG10:5CM53_C
9
-8.688
-0.246
-0.017
-0.155
2.218
1
20
B
11
C
52
2.137
B_DT11:DA52_C
10
-10.151
-0.048
-0.113
-0.185
3.155
24.430
B
B
2
3
5.430
C
C
61
60
3.186
2.291
0.596
-0.656
BB_DG25CM3:DG60DC61_CC
1
2.488
-5.898
24.199
-2.244
-0.652
3.398
33.237
B
B
3
4
12.312
C
C
60
59
3.458
6.975
-1.070
-0.458
BB_5CM3DG4:5CM59DG60_CC
2
-4.247
7.497
32.246
-2.043
1.115
2.943
29.474
B
B
4
5
10.212
C
C
59
58
3.090
5.170
0.796
-0.643
BB_DG4DT5:DA585CM59_CC
3
0.331
-0.653
29.025
-2.289
-1.498
3.611
35.670
B
B
5
6
4.089
C
C
58
57
3.523
2.491
-1.015
-0.347
BB_DT5DG6:DC57DA58_CC
4
-6.097
10.008
35.076
-0.964
0.686
3.430
36.640
B
B
6
7
4.007
C
C
57
56
3.515
2.517
-0.932
-1.452
BB_DG6DG7:DC56DC57_CC
5
-0.815
1.297
36.548
-2.676
1.364
3.164
31.325
B
B
7
8
9.657
C
C
56
55
3.259
5.190
0.316
-0.230
BB_DG7DG8:DC55DC56_CC
6
-1.253
2.332
30.878
-1.394
-0.819
3.356
32.796
B
B
8
9
-0.825
C
C
55
54
3.268
-0.465
0.992
-0.540
BB_DG85CM9:DG54DC55_CC
7
3.235
-5.739
32.637
-0.875
-1.192
3.334
31.255
B
B
9
10
8.969
C
C
54
53
3.277
4.811
-1.237
0.189
BB_5CM9DG10:5CM53DG54_CC
8
-1.845
3.439
30.838
-0.576
1.940
3.170
31.413
B
B
10
11
6.253
C
C
53
52
3.243
3.379
0.764
-0.588
BB_DG10DT11:DA525CM53_CC
9
0.259
-0.480
31.234
-1.708
-1.363
citation
entity_src_gen
pdbx_audit_support
pdbx_entity_src_syn
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_conn_type
struct_ref_seq
repository
Initial release
Database references
Database references
Author supporting evidence
Database references
Derived calculations
Source and taxonomy
Data collection
Database references
Derived calculations
Refinement description
1
0
2015-05-13
1
1
2015-06-03
1
2
2015-07-15
1
3
2017-09-27
1
4
2023-09-27
_citation.journal_id_CSD
_entity_src_gen.pdbx_alt_source_flag
_pdbx_entity_src_syn.pdbx_alt_source_flag
_pdbx_struct_oper_list.symmetry_operation
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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_ref_seq.db_align_beg
_struct_ref_seq.db_align_end
Same protein with singly methylated DNA
N
RCSB
Y
RCSB
2014-12-11
REL
REL
ZN
ZINC ION
HOH
water
32630
synthetic construct
sample
1
11
32630
synthetic construct
sample
1
11
4R2A
PDb entry 4R2A
PDB
experimental model
ZN
1
4
ZN
ZN
501
A
ZN
2
4
ZN
ZN
502
A
ZN
3
4
ZN
ZN
503
A
HOH
118
5
HOH
HOH
601
A
HOH
75
5
HOH
HOH
602
A
HOH
123
5
HOH
HOH
603
A
HOH
116
5
HOH
HOH
604
A
HOH
96
5
HOH
HOH
605
A
HOH
126
5
HOH
HOH
606
A
HOH
180
5
HOH
HOH
607
A
HOH
92
5
HOH
HOH
608
A
HOH
57
5
HOH
HOH
609
A
HOH
195
5
HOH
HOH
610
A
HOH
80
5
HOH
HOH
611
A
HOH
52
5
HOH
HOH
612
A
HOH
28
5
HOH
HOH
613
A
HOH
200
5
HOH
HOH
614
A
HOH
66
5
HOH
HOH
615
A
HOH
101
5
HOH
HOH
616
A
HOH
98
5
HOH
HOH
617
A
HOH
114
5
HOH
HOH
618
A
HOH
82
5
HOH
HOH
619
A
HOH
14
5
HOH
HOH
620
A
HOH
43
5
HOH
HOH
621
A
HOH
39
5
HOH
HOH
622
A
HOH
49
5
HOH
HOH
623
A
HOH
178
5
HOH
HOH
624
A
HOH
102
5
HOH
HOH
625
A
HOH
8
5
HOH
HOH
626
A
HOH
121
5
HOH
HOH
627
A
HOH
105
5
HOH
HOH
628
A
HOH
204
5
HOH
HOH
629
A
HOH
107
5
HOH
HOH
630
A
HOH
89
5
HOH
HOH
631
A
HOH
42
5
HOH
HOH
632
A
HOH
144
5
HOH
HOH
633
A
HOH
152
5
HOH
HOH
634
A
HOH
194
5
HOH
HOH
635
A
HOH
81
5
HOH
HOH
636
A
HOH
172
5
HOH
HOH
637
A
HOH
201
5
HOH
HOH
638
A
HOH
189
5
HOH
HOH
639
A
HOH
185
5
HOH
HOH
640
A
HOH
191
5
HOH
HOH
641
A
HOH
95
5
HOH
HOH
642
A
HOH
164
5
HOH
HOH
643
A
HOH
183
5
HOH
HOH
644
A
HOH
167
5
HOH
HOH
645
A
HOH
155
5
HOH
HOH
646
A
HOH
184
5
HOH
HOH
647
A
HOH
79
5
HOH
HOH
648
A
HOH
4
5
HOH
HOH
649
A
HOH
110
5
HOH
HOH
650
A
HOH
140
5
HOH
HOH
651
A
HOH
111
5
HOH
HOH
652
A
HOH
131
5
HOH
HOH
653
A
HOH
2
5
HOH
HOH
654
A
HOH
6
5
HOH
HOH
655
A
HOH
9
5
HOH
HOH
656
A
HOH
11
5
HOH
HOH
657
A
HOH
12
5
HOH
HOH
658
A
HOH
13
5
HOH
HOH
659
A
HOH
15
5
HOH
HOH
660
A
HOH
17
5
HOH
HOH
661
A
HOH
18
5
HOH
HOH
662
A
HOH
19
5
HOH
HOH
663
A
HOH
20
5
HOH
HOH
664
A
HOH
23
5
HOH
HOH
665
A
HOH
25
5
HOH
HOH
666
A
HOH
29
5
HOH
HOH
667
A
HOH
30
5
HOH
HOH
668
A
HOH
32
5
HOH
HOH
669
A
HOH
36
5
HOH
HOH
670
A
HOH
37
5
HOH
HOH
671
A
HOH
38
5
HOH
HOH
672
A
HOH
41
5
HOH
HOH
673
A
HOH
54
5
HOH
HOH
674
A
HOH
63
5
HOH
HOH
675
A
HOH
65
5
HOH
HOH
676
A
HOH
67
5
HOH
HOH
677
A
HOH
71
5
HOH
HOH
678
A
HOH
74
5
HOH
HOH
679
A
HOH
87
5
HOH
HOH
680
A
HOH
97
5
HOH
HOH
681
A
HOH
100
5
HOH
HOH
682
A
HOH
103
5
HOH
HOH
683
A
HOH
106
5
HOH
HOH
684
A
HOH
117
5
HOH
HOH
685
A
HOH
119
5
HOH
HOH
686
A
HOH
120
5
HOH
HOH
687
A
HOH
128
5
HOH
HOH
688
A
HOH
129
5
HOH
HOH
689
A
HOH
133
5
HOH
HOH
690
A
HOH
139
5
HOH
HOH
691
A
HOH
141
5
HOH
HOH
692
A
HOH
142
5
HOH
HOH
693
A
HOH
143
5
HOH
HOH
694
A
HOH
147
5
HOH
HOH
695
A
HOH
148
5
HOH
HOH
696
A
HOH
153
5
HOH
HOH
697
A
HOH
159
5
HOH
HOH
698
A
HOH
160
5
HOH
HOH
699
A
HOH
162
5
HOH
HOH
700
A
HOH
175
5
HOH
HOH
701
A
HOH
179
5
HOH
HOH
702
A
HOH
193
5
HOH
HOH
703
A
HOH
197
5
HOH
HOH
704
A
HOH
208
5
HOH
HOH
705
A
HOH
58
5
HOH
HOH
101
B
HOH
40
5
HOH
HOH
102
B
HOH
1
5
HOH
HOH
103
B
HOH
108
5
HOH
HOH
104
B
HOH
45
5
HOH
HOH
105
B
HOH
27
5
HOH
HOH
106
B
HOH
151
5
HOH
HOH
107
B
HOH
90
5
HOH
HOH
108
B
HOH
31
5
HOH
HOH
109
B
HOH
72
5
HOH
HOH
110
B
HOH
169
5
HOH
HOH
111
B
HOH
26
5
HOH
HOH
112
B
HOH
69
5
HOH
HOH
113
B
HOH
3
5
HOH
HOH
114
B
HOH
5
5
HOH
HOH
115
B
HOH
7
5
HOH
HOH
116
B
HOH
10
5
HOH
HOH
117
B
HOH
24
5
HOH
HOH
118
B
HOH
33
5
HOH
HOH
119
B
HOH
34
5
HOH
HOH
120
B
HOH
44
5
HOH
HOH
121
B
HOH
46
5
HOH
HOH
122
B
HOH
53
5
HOH
HOH
123
B
HOH
55
5
HOH
HOH
124
B
HOH
59
5
HOH
HOH
125
B
HOH
64
5
HOH
HOH
126
B
HOH
73
5
HOH
HOH
127
B
HOH
76
5
HOH
HOH
128
B
HOH
83
5
HOH
HOH
129
B
HOH
85
5
HOH
HOH
130
B
HOH
86
5
HOH
HOH
131
B
HOH
88
5
HOH
HOH
132
B
HOH
104
5
HOH
HOH
133
B
HOH
112
5
HOH
HOH
134
B
HOH
113
5
HOH
HOH
135
B
HOH
124
5
HOH
HOH
136
B
HOH
125
5
HOH
HOH
137
B
HOH
127
5
HOH
HOH
138
B
HOH
130
5
HOH
HOH
139
B
HOH
138
5
HOH
HOH
140
B
HOH
149
5
HOH
HOH
141
B
HOH
150
5
HOH
HOH
142
B
HOH
154
5
HOH
HOH
143
B
HOH
156
5
HOH
HOH
144
B
HOH
161
5
HOH
HOH
145
B
HOH
165
5
HOH
HOH
146
B
HOH
168
5
HOH
HOH
147
B
HOH
171
5
HOH
HOH
148
B
HOH
186
5
HOH
HOH
149
B
HOH
188
5
HOH
HOH
150
B
HOH
196
5
HOH
HOH
151
B
HOH
198
5
HOH
HOH
152
B
HOH
199
5
HOH
HOH
153
B
HOH
202
5
HOH
HOH
154
B
HOH
206
5
HOH
HOH
155
B
HOH
109
5
HOH
HOH
101
C
HOH
78
5
HOH
HOH
102
C
HOH
205
5
HOH
HOH
103
C
HOH
166
5
HOH
HOH
104
C
HOH
137
5
HOH
HOH
105
C
HOH
91
5
HOH
HOH
106
C
HOH
84
5
HOH
HOH
107
C
HOH
132
5
HOH
HOH
108
C
HOH
173
5
HOH
HOH
109
C
HOH
51
5
HOH
HOH
110
C
HOH
190
5
HOH
HOH
111
C
HOH
170
5
HOH
HOH
112
C
HOH
136
5
HOH
HOH
113
C
HOH
16
5
HOH
HOH
114
C
HOH
21
5
HOH
HOH
115
C
HOH
22
5
HOH
HOH
116
C
HOH
35
5
HOH
HOH
117
C
HOH
47
5
HOH
HOH
118
C
HOH
48
5
HOH
HOH
119
C
HOH
50
5
HOH
HOH
120
C
HOH
56
5
HOH
HOH
121
C
HOH
60
5
HOH
HOH
122
C
HOH
61
5
HOH
HOH
123
C
HOH
62
5
HOH
HOH
124
C
HOH
68
5
HOH
HOH
125
C
HOH
70
5
HOH
HOH
126
C
HOH
77
5
HOH
HOH
127
C
HOH
93
5
HOH
HOH
128
C
HOH
94
5
HOH
HOH
129
C
HOH
99
5
HOH
HOH
130
C
HOH
115
5
HOH
HOH
131
C
HOH
122
5
HOH
HOH
132
C
HOH
134
5
HOH
HOH
133
C
HOH
135
5
HOH
HOH
134
C
HOH
145
5
HOH
HOH
135
C
HOH
146
5
HOH
HOH
136
C
HOH
157
5
HOH
HOH
137
C
HOH
158
5
HOH
HOH
138
C
HOH
163
5
HOH
HOH
139
C
HOH
174
5
HOH
HOH
140
C
HOH
176
5
HOH
HOH
141
C
HOH
177
5
HOH
HOH
142
C
HOH
181
5
HOH
HOH
143
C
HOH
182
5
HOH
HOH
144
C
HOH
187
5
HOH
HOH
145
C
HOH
192
5
HOH
HOH
146
C
HOH
203
5
HOH
HOH
147
C
HOH
207
5
HOH
HOH
148
C
GLU
335
n
1
GLU
102
A
ARG
336
n
2
ARG
103
A
PRO
337
n
3
PRO
104
A
TYR
338
n
4
TYR
105
A
ALA
339
n
5
ALA
106
A
CYS
340
n
6
CYS
107
A
PRO
341
n
7
PRO
108
A
VAL
342
n
8
VAL
109
A
GLU
343
n
9
GLU
110
A
SER
344
n
10
SER
111
A
CYS
345
n
11
CYS
112
A
ASP
346
n
12
ASP
113
A
ARG
347
n
13
ARG
114
A
ARG
348
n
14
ARG
115
A
PHE
349
n
15
PHE
116
A
SER
350
n
16
SER
117
A
ARG
351
n
17
ARG
118
A
SER
352
n
18
SER
119
A
ASP
353
n
19
ASP
120
A
GLU
354
n
20
GLU
121
A
LEU
355
n
21
LEU
122
A
THR
356
n
22
THR
123
A
ARG
357
n
23
ARG
124
A
HIS
358
n
24
HIS
125
A
ILE
359
n
25
ILE
126
A
ARG
360
n
26
ARG
127
A
ILE
361
n
27
ILE
128
A
HIS
362
n
28
HIS
129
A
THR
363
n
29
THR
130
A
GLY
364
n
30
GLY
131
A
GLN
365
n
31
GLN
132
A
LYS
366
n
32
LYS
133
A
PRO
367
n
33
PRO
134
A
PHE
368
n
34
PHE
135
A
GLN
369
n
35
GLN
136
A
CYS
370
n
36
CYS
137
A
ARG
371
n
37
ARG
138
A
ILE
372
n
38
ILE
139
A
CYS
373
n
39
CYS
140
A
MET
374
n
40
MET
141
A
ARG
375
n
41
ARG
142
A
ASN
376
n
42
ASN
143
A
PHE
377
n
43
PHE
144
A
SER
378
n
44
SER
145
A
ARG
379
n
45
ARG
146
A
SER
380
n
46
SER
147
A
ASP
381
n
47
ASP
148
A
HIS
382
n
48
HIS
149
A
LEU
383
n
49
LEU
150
A
THR
384
n
50
THR
151
A
THR
385
n
51
THR
152
A
HIS
386
n
52
HIS
153
A
ILE
387
n
53
ILE
154
A
ARG
388
n
54
ARG
155
A
THR
389
n
55
THR
156
A
HIS
390
n
56
HIS
157
A
THR
391
n
57
THR
158
A
GLY
392
n
58
GLY
159
A
GLU
393
n
59
GLU
160
A
LYS
394
n
60
LYS
161
A
PRO
395
n
61
PRO
162
A
PHE
396
n
62
PHE
163
A
ALA
397
n
63
ALA
164
A
CYS
398
n
64
CYS
165
A
ASP
399
n
65
ASP
166
A
ILE
400
n
66
ILE
167
A
CYS
401
n
67
CYS
168
A
GLY
402
n
68
GLY
169
A
ARG
403
n
69
ARG
170
A
LYS
404
n
70
LYS
171
A
PHE
405
n
71
PHE
172
A
ALA
406
n
72
ALA
173
A
ARG
407
n
73
ARG
174
A
SER
408
n
74
SER
175
A
ASP
409
n
75
ASP
176
A
GLU
410
n
76
GLU
177
A
ARG
411
n
77
ARG
178
A
LYS
412
n
78
LYS
179
A
ARG
413
n
79
ARG
180
A
HIS
414
n
80
HIS
181
A
THR
415
n
81
THR
182
A
LYS
416
n
82
LYS
183
A
ILE
417
n
83
ILE
184
A
HIS
418
n
84
HIS
185
A
LEU
419
n
85
LEU
186
A
ARG
420
n
86
ARG
187
A
n
87
188
A
n
88
189
A
n
89
190
A
DA
1
n
1
DA
1
B
DG
2
n
2
DG
2
B
5CM
3
n
3
5CM
3
B
DG
4
n
4
DG
4
B
DT
5
n
5
DT
5
B
DG
6
n
6
DG
6
B
DG
7
n
7
DG
7
B
DG
8
n
8
DG
8
B
5CM
9
n
9
5CM
9
B
DG
10
n
10
DG
10
B
DT
11
n
11
DT
11
B
DT
1
n
1
DT
51
C
DA
2
n
2
DA
52
C
5CM
3
n
3
5CM
53
C
DG
4
n
4
DG
54
C
DC
5
n
5
DC
55
C
DC
6
n
6
DC
56
C
DC
7
n
7
DC
57
C
DA
8
n
8
DA
58
C
5CM
9
n
9
5CM
59
C
DG
10
n
10
DG
60
C
DC
11
n
11
DC
61
C
0.0059
-0.0068
0.0063
0.0089
-0.0086
0.0101
-0.0244
-0.0201
0.0094
0.0315
0.0029
-0.0002
0.0382
0.0191
-0.0107
0.2102
-0.0224
-0.0399
0.1615
-0.0193
0.0661
refined
6.4181
-6.2665
-3.4961
X-RAY DIFFRACTION
0.0011
-0.0003
0.0013
0.0007
0.0000
0.0018
-0.0025
-0.0024
0.0014
-0.0037
-0.0129
0.0056
-0.0044
-0.0047
-0.0000
0.2525
-0.0512
-0.0103
0.2810
-0.0827
0.1470
refined
-5.5280
-2.5466
-5.0991
X-RAY DIFFRACTION
0.0003
-0.0005
-0.0001
0.0011
0.0002
0.0005
-0.0098
0.0066
0.0108
0.0104
-0.0106
-0.0052
-0.0156
-0.0056
0.0000
0.1381
-0.0398
-0.0064
0.1949
-0.0740
0.1460
refined
-15.7982
-1.6767
-17.0065
X-RAY DIFFRACTION
0.0018
-0.0001
-0.0012
0.0089
-0.0022
0.0029
0.0134
-0.0205
0.0415
-0.0069
-0.0562
-0.0088
-0.0440
0.0681
-0.0097
0.0907
-0.0293
0.0013
0.1131
-0.0048
0.0845
refined
-9.8020
-10.5535
-24.3116
X-RAY DIFFRACTION
0.0004
-0.0003
-0.0000
0.0009
-0.0001
0.0008
-0.0091
0.0117
-0.0049
0.0114
-0.0188
-0.0110
-0.0152
0.0097
-0.0019
0.0635
-0.0113
-0.0000
0.1171
-0.0006
0.0730
refined
-7.3987
-20.7040
-29.4115
X-RAY DIFFRACTION
0.0095
-0.0020
-0.0069
0.0112
-0.0002
0.0062
-0.0033
-0.0084
-0.0105
0.0046
-0.0137
-0.0073
0.0111
0.0106
0.0012
0.0556
0.0035
0.0332
0.0904
0.0110
0.0800
refined
-3.5278
-30.2563
-27.6462
X-RAY DIFFRACTION
0.0130
0.0035
-0.0008
0.0016
-0.0014
0.0018
-0.0014
-0.0100
-0.0115
-0.0035
-0.0056
0.0196
0.0037
0.0003
-0.0110
0.1367
-0.1482
-0.0015
0.1164
0.0047
0.0960
refined
-12.0992
-17.7784
-17.8239
X-RAY DIFFRACTION
0.0002
0.0000
0.0019
0.0011
-0.0018
0.0060
0.0079
-0.0278
-0.0256
-0.0108
-0.0013
-0.0227
0.0149
-0.0111
0.0254
0.1461
-0.1292
0.0199
0.1111
0.0372
0.1365
refined
5.8325
-9.5535
-16.1096
X-RAY DIFFRACTION
0.0034
0.0036
0.0011
0.0083
-0.0036
0.0075
-0.0112
-0.0029
0.0118
-0.0030
-0.0139
0.0020
-0.0086
0.0056
-0.0337
0.1443
-0.1285
0.0084
0.1010
-0.0215
0.1127
refined
1.9398
-5.6107
-21.0824
X-RAY DIFFRACTION
0.0167
0.0107
0.0004
0.0121
-0.0004
0.0004
0.0020
-0.0158
-0.0018
0.0055
-0.0056
-0.0160
0.0039
0.0001
-0.0048
0.1344
-0.1056
-0.0128
0.1201
0.0360
0.0946
refined
-3.4961
-20.8602
-13.7105
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(chain A and resid 102:125)
X-RAY DIFFRACTION
2
(chain A and resid 126:133)
X-RAY DIFFRACTION
3
(chain A and resid 134:143)
X-RAY DIFFRACTION
4
(chain A and resid 144:166)
X-RAY DIFFRACTION
5
(chain A and resid 167:178)
X-RAY DIFFRACTION
6
(chain A and resid 179:187)
X-RAY DIFFRACTION
7
(chain B and resid 1:5)
X-RAY DIFFRACTION
8
(chain B and resid 6:11)
X-RAY DIFFRACTION
9
(chain C and resid 51:56)
X-RAY DIFFRACTION
10
(chain C and resid 57:61)
author_defined_assembly
3
trimeric
A
CYS
107
A
SG
CYS
6
1_555
A
ZN
501
D
ZN
ZN
1_555
A
CYS
112
A
SG
CYS
11
1_555
112.7
A
CYS
107
A
SG
CYS
6
1_555
A
ZN
501
D
ZN
ZN
1_555
A
HIS
125
A
NE2
HIS
24
1_555
109.0
A
CYS
112
A
SG
CYS
11
1_555
A
ZN
501
D
ZN
ZN
1_555
A
HIS
125
A
NE2
HIS
24
1_555
109.9
A
CYS
107
A
SG
CYS
6
1_555
A
ZN
501
D
ZN
ZN
1_555
A
HIS
129
A
NE2
HIS
28
1_555
105.2
A
CYS
112
A
SG
CYS
11
1_555
A
ZN
501
D
ZN
ZN
1_555
A
HIS
129
A
NE2
HIS
28
1_555
121.4
A
HIS
125
A
NE2
HIS
24
1_555
A
ZN
501
D
ZN
ZN
1_555
A
HIS
129
A
NE2
HIS
28
1_555
97.1
A
CYS
137
A
SG
CYS
36
1_555
A
ZN
502
E
ZN
ZN
1_555
A
CYS
140
A
SG
CYS
39
1_555
114.9
A
CYS
137
A
SG
CYS
36
1_555
A
ZN
502
E
ZN
ZN
1_555
A
HIS
153
A
NE2
HIS
52
1_555
108.7
A
CYS
140
A
SG
CYS
39
1_555
A
ZN
502
E
ZN
ZN
1_555
A
HIS
153
A
NE2
HIS
52
1_555
108.4
A
CYS
137
A
SG
CYS
36
1_555
A
ZN
502
E
ZN
ZN
1_555
A
HIS
157
A
NE2
HIS
56
1_555
111.5
A
CYS
140
A
SG
CYS
39
1_555
A
ZN
502
E
ZN
ZN
1_555
A
HIS
157
A
NE2
HIS
56
1_555
111.1
A
HIS
153
A
NE2
HIS
52
1_555
A
ZN
502
E
ZN
ZN
1_555
A
HIS
157
A
NE2
HIS
56
1_555
101.2
A
CYS
165
A
SG
CYS
64
1_555
A
ZN
503
F
ZN
ZN
1_555
A
CYS
168
A
SG
CYS
67
1_555
113.4
A
CYS
165
A
SG
CYS
64
1_555
A
ZN
503
F
ZN
ZN
1_555
A
HIS
181
A
NE2
HIS
80
1_555
106.5
A
CYS
168
A
SG
CYS
67
1_555
A
ZN
503
F
ZN
ZN
1_555
A
HIS
181
A
NE2
HIS
80
1_555
107.0
A
CYS
165
A
SG
CYS
64
1_555
A
ZN
503
F
ZN
ZN
1_555
A
HIS
185
A
NE2
HIS
84
1_555
108.2
A
CYS
168
A
SG
CYS
67
1_555
A
ZN
503
F
ZN
ZN
1_555
A
HIS
185
A
NE2
HIS
84
1_555
115.2
A
HIS
181
A
NE2
HIS
80
1_555
A
ZN
503
F
ZN
ZN
1_555
A
HIS
185
A
NE2
HIS
84
1_555
105.9
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
TYR
105
A
N
TYR
4
A
O
PHE
116
A
O
PHE
15
A
N
PHE
135
A
N
PHE
34
A
O
PHE
144
A
O
PHE
43
A
N
PHE
163
A
N
PHE
62
A
O
PHE
172
A
O
PHE
71
1
A
HOH
642
G
HOH
1
A
GLN
188
A
GLN
87
1
Y
1
A
LYS
189
A
LYS
88
1
Y
1
A
ASP
190
A
ASP
89
1
Y
1
B
B
OP2
O
5CM
HOH
3
132
1.99
1
A
A
NH1
O
ARG
HOH
178
601
2.13
1
C
C
OP2
O
DC
HOH
57
101
2.13
1
C
C
OP2
O
DA
HOH
58
146
2.15
1
A
A
OE2
O
GLU
HOH
177
691
2.16
1
C
C
O
O
HOH
HOH
129
139
2.18
1
C
C
OP1
O
DC
HOH
56
102
2.18
B
1
B
B
OP2
O
DG
HOH
7
143
2.19
1
2.96
0.30
108.30
111.26
B
B
B
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.25
0.30
108.30
110.55
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
3.32
0.30
108.30
111.62
C
C
C
O4'
C1'
N9
DG
DG
DG
54
54
54
N
1
C
C
O3'
C3'
DG
DG
54
54
-0.062
0.006
1.419
1.357
N
0.2002
0.1717
0.1738
1.412
27.357
3489
46626
7.48
78.83
0.13
Random
1
FREE R-VALUE
1.37
MOLECULAR REPLACEMENT
21.46
0.90
1.11
PDb entry 4R2A
ML
FLAT BULK SOLVENT MODEL
1.412
27.357
208
1382
3
449
722
0.013
1283
1.338
1827
22.003
505
0.071
190
0.032
163
0.3441
0.3055
1.4312
3
33
1.00
0.3119
0.2704
1.4517
17
219
10.00
0.2572
0.2539
1.4733
37
464
21.00
0.2765
0.2466
1.4963
54
663
30.00
0.2356
0.2350
1.5209
66
816
37.00
0.2560
0.2256
1.5471
84
1091
50.00
0.2346
0.1966
1.5752
118
1457
67.00
0.2235
0.1904
1.6055
132
1750
79.00
0.2020
0.1921
1.6383
163
1979
90.00
0.2228
0.1847
1.6739
169
2094
96.00
0.1808
0.1871
1.7128
172
2098
96.00
0.2672
0.1749
1.7557
171
2145
98.00
0.1998
0.1801
1.8031
176
2191
100.00
0.2310
0.1766
1.8562
175
2172
100.00
0.2033
0.1824
1.9161
182
2173
100.00
0.2108
0.1905
1.9845
179
2206
100.00
0.1908
0.1752
2.0640
177
2180
100.00
0.2006
0.1755
2.1579
179
2175
100.00
0.1861
0.1646
2.2716
178
2200
100.00
0.1760
0.1626
2.4138
177
2181
100.00
0.2143
0.1775
2.6001
175
2183
100.00
0.2199
0.1842
2.8615
176
2183
100.00
0.2207
0.1756
3.2749
181
2213
100.00
0.1785
0.1467
4.1238
171
2145
99.00
0.1643
0.1453
27.3624
177
2126
97.00
10.750
1.400
43.000
4X9J
29071
0.127
0.036
0.131
1.321
1
30.828
10.700
447598
15.400
90.600
0.653
1.400
1.420
743
0.671
0.292
0.719
0.392
1
5.700
0
46.000
0.522
1.420
1.450
847
0.795
0.227
0.571
0.413
1
6.000
0
54.400
0.421
1.450
1.480
969
0.853
0.181
0.460
0.430
1
6.100
0
60.500
0.332
1.480
1.510
1095
0.904
0.141
0.362
0.419
1
6.300
0
70.500
0.300
1.510
1.540
1318
0.938
0.126
0.327
0.451
1
6.500
0
82.800
1.540
1.580
1570
0.543
0.484
0.475
1
13.500
0
98.600
1.580
1.620
1578
0.901
0.359
0.503
1
15.600
0
100.000
0.913
1.620
1.660
1569
0.970
0.239
0.944
0.621
1
15.900
0
100.000
0.613
1.660
1.710
1617
0.980
0.162
0.634
0.868
1
16.300
0
100.000
0.538
1.710
1.760
1583
0.985
0.139
0.556
0.906
1
17.000
0
100.000
0.455
1.760
1.830
1576
0.988
0.112
0.469
0.999
1
18.100
0
100.000
0.363
1.830
1.900
1609
0.969
0.089
0.374
1.094
1
18.300
0
100.000
0.287
1.900
1.990
1596
0.992
0.070
0.295
1.249
1
18.300
0
100.000
0.215
1.990
2.090
1603
0.990
0.052
0.221
1.456
1
18.400
0
100.000
0.177
2.090
2.220
1603
0.967
0.043
0.182
1.743
1
18.300
0
100.000
0.144
2.220
2.390
1603
0.989
0.035
0.148
1.914
1
18.400
0
100.000
0.122
2.390
2.630
1611
0.987
0.029
0.126
2.101
1
18.400
0
100.000
0.110
2.630
3.020
1635
0.988
0.026
0.113
2.396
1
18.100
0
100.000
0.086
3.020
3.800
1649
0.988
0.022
0.089
2.217
1
18.000
0
100.000
0.061
3.800
43.000
1697
0.995
0.015
0.063
1.497
1
16.700
0
97.200
refinement
PHENIX
(phenix.refine: dev_1810)
data reduction
HKL-2000
data extraction
PDB_EXTRACT
3.15
data scaling
HKL-2000
phasing
PHENIX
EGR-1 with Doubly Methylated DNA
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
ARG
118
A
ARG
17
HELX_P
A
GLY
131
A
GLY
30
1
AA1
14
A
ARG
146
A
ARG
45
HELX_P
A
GLY
159
A
GLY
58
1
AA2
14
A
ARG
174
A
ARG
73
HELX_P
A
LYS
183
A
LYS
82
1
AA3
10
A
ILE
184
A
ILE
83
HELX_P
A
LEU
186
A
LEU
85
5
AA4
3
covale
1.597
both
B
DG
2
B
O3'
DG
2
1_555
B
5CM
3
B
P
5CM
3
1_555
covale
1.592
both
B
5CM
3
B
O3'
5CM
3
1_555
B
DG
4
B
P
DG
4
1_555
covale
1.603
both
B
DG
8
B
O3'
DG
8
1_555
B
5CM
9
B
P
5CM
9
1_555
covale
1.589
both
B
5CM
9
B
O3'
5CM
9
1_555
B
DG
10
B
P
DG
10
1_555
covale
1.612
both
C
DA
52
C
O3'
DA
2
1_555
C
5CM
53
C
P
5CM
3
1_555
covale
1.578
both
C
5CM
53
C
O3'
5CM
3
1_555
C
DG
54
C
P
DG
4
1_555
covale
1.604
both
C
DA
58
C
O3'
DA
8
1_555
C
5CM
59
C
P
5CM
9
1_555
covale
1.597
both
C
5CM
59
C
O3'
5CM
9
1_555
C
DG
60
C
P
DG
10
1_555
metalc
2.279
A
CYS
107
A
SG
CYS
6
1_555
A
ZN
501
D
ZN
ZN
1_555
metalc
2.303
A
CYS
112
A
SG
CYS
11
1_555
A
ZN
501
D
ZN
ZN
1_555
metalc
2.034
A
HIS
125
A
NE2
HIS
24
1_555
A
ZN
501
D
ZN
ZN
1_555
metalc
1.910
A
HIS
129
A
NE2
HIS
28
1_555
A
ZN
501
D
ZN
ZN
1_555
metalc
2.338
A
CYS
137
A
SG
CYS
36
1_555
A
ZN
502
E
ZN
ZN
1_555
metalc
2.293
A
CYS
140
A
SG
CYS
39
1_555
A
ZN
502
E
ZN
ZN
1_555
metalc
2.072
A
HIS
153
A
NE2
HIS
52
1_555
A
ZN
502
E
ZN
ZN
1_555
metalc
2.036
A
HIS
157
A
NE2
HIS
56
1_555
A
ZN
502
E
ZN
ZN
1_555
metalc
2.354
A
CYS
165
A
SG
CYS
64
1_555
A
ZN
503
F
ZN
ZN
1_555
metalc
2.294
A
CYS
168
A
SG
CYS
67
1_555
A
ZN
503
F
ZN
ZN
1_555
metalc
2.025
A
HIS
181
A
NE2
HIS
80
1_555
A
ZN
503
F
ZN
ZN
1_555
metalc
2.007
A
HIS
185
A
NE2
HIS
84
1_555
A
ZN
503
F
ZN
ZN
1_555
hydrog
WATSON-CRICK
B
DG
2
B
N1
DG
2
1_555
C
DC
61
C
N3
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
2
B
N2
DG
2
1_555
C
DC
61
C
O2
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
2
B
O6
DG
2
1_555
C
DC
61
C
N4
DC
11
1_555
hydrog
WATSON-CRICK
B
5CM
3
B
N3
5CM
3
1_555
C
DG
60
C
N1
DG
10
1_555
hydrog
WATSON-CRICK
B
5CM
3
B
N4
5CM
3
1_555
C
DG
60
C
O6
DG
10
1_555
hydrog
WATSON-CRICK
B
5CM
3
B
O2
5CM
3
1_555
C
DG
60
C
N2
DG
10
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N1
DG
4
1_555
C
5CM
59
C
N3
5CM
9
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N2
DG
4
1_555
C
5CM
59
C
O2
5CM
9
1_555
hydrog
WATSON-CRICK
B
DG
4
B
O6
DG
4
1_555
C
5CM
59
C
N4
5CM
9
1_555
hydrog
WATSON-CRICK
B
DT
5
B
N3
DT
5
1_555
C
DA
58
C
N1
DA
8
1_555
hydrog
WATSON-CRICK
B
DT
5
B
O4
DT
5
1_555
C
DA
58
C
N6
DA
8
1_555
hydrog
WATSON-CRICK
B
DG
6
B
N1
DG
6
1_555
C
DC
57
C
N3
DC
7
1_555
hydrog
WATSON-CRICK
B
DG
6
B
N2
DG
6
1_555
C
DC
57
C
O2
DC
7
1_555
hydrog
WATSON-CRICK
B
DG
6
B
O6
DG
6
1_555
C
DC
57
C
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
B
DG
7
B
N1
DG
7
1_555
C
DC
56
C
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
B
DG
7
B
N2
DG
7
1_555
C
DC
56
C
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
B
DG
7
B
O6
DG
7
1_555
C
DC
56
C
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
B
DG
8
B
N1
DG
8
1_555
C
DC
55
C
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
B
DG
8
B
N2
DG
8
1_555
C
DC
55
C
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
B
DG
8
B
O6
DG
8
1_555
C
DC
55
C
N4
DC
5
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N3
5CM
9
1_555
C
DG
54
C
N1
DG
4
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N4
5CM
9
1_555
C
DG
54
C
O6
DG
4
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
O2
5CM
9
1_555
C
DG
54
C
N2
DG
4
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N1
DG
10
1_555
C
5CM
53
C
N3
5CM
3
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N2
DG
10
1_555
C
5CM
53
C
O2
5CM
3
1_555
hydrog
WATSON-CRICK
B
DG
10
B
O6
DG
10
1_555
C
5CM
53
C
N4
5CM
3
1_555
hydrog
WATSON-CRICK
B
DT
11
B
N3
DT
11
1_555
C
DA
52
C
N1
DA
2
1_555
hydrog
WATSON-CRICK
B
DT
11
B
O4
DT
11
1_555
C
DA
52
C
N6
DA
2
1_555
Transcription Regulator/DNA
DNA Binding, Methylated DNA, ZINC FINGER, TRANSCRIPTION, Transcription Regulator-DNA complex
EGR1_HUMAN
UNP
1
335
P18146
ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRH
TKIHLRQKD
4X9J
PDB
2
1
4X9J
4X9J
PDB
3
1
4X9J
335
423
4X9J
102
190
P18146
A
1
1
89
1
11
4X9J
1
11
4X9J
B
2
1
11
51
61
4X9J
51
61
4X9J
C
3
1
11
2
2
2
anti-parallel
anti-parallel
anti-parallel
A
TYR
105
A
TYR
4
A
ALA
106
A
ALA
5
A
ARG
115
A
ARG
14
A
PHE
116
A
PHE
15
A
PHE
135
A
PHE
34
A
GLN
136
A
GLN
35
A
ASN
143
A
ASN
42
A
PHE
144
A
PHE
43
A
PHE
163
A
PHE
62
A
ALA
164
A
ALA
63
A
LYS
171
A
LYS
70
A
PHE
172
A
PHE
71
binding site for residue ZN A 501
A
ZN
501
Software
4
binding site for residue ZN A 502
A
ZN
502
Software
4
binding site for residue ZN A 503
A
ZN
503
Software
4
A
CYS
107
A
CYS
6
4
1_555
A
CYS
112
A
CYS
11
4
1_555
A
HIS
125
A
HIS
24
4
1_555
A
HIS
129
A
HIS
28
4
1_555
A
CYS
137
A
CYS
36
4
1_555
A
CYS
140
A
CYS
39
4
1_555
A
HIS
153
A
HIS
52
4
1_555
A
HIS
157
A
HIS
56
4
1_555
A
CYS
165
A
CYS
64
4
1_555
A
CYS
168
A
CYS
67
4
1_555
A
HIS
181
A
HIS
80
4
1_555
A
HIS
185
A
HIS
84
4
1_555
20
C 2 2 21