0.010823
0.006248
0.000000
0.000000
0.012497
0.000000
0.000000
0.000000
0.004706
0.00000
0.00000
0.00000
Verdine, G.L.
Lee, S.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
92.400
92.400
212.500
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
Ca 2
40.078
CALCIUM ION
non-polymer
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
C10 H13 F N5 O8 P
381.211
n
2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7,9-dihydro-1H-purine-6,8-dione
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
CA
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
O
N
90
N
P
N
91
N
O
N
92
N
O
N
93
N
O
N
94
N
C
N
95
R
C
N
96
N
O
N
97
S
C
N
98
N
O
N
99
N
C
N
100
R
C
Y
101
N
N
Y
102
N
C
Y
103
N
N
Y
104
N
C
Y
105
N
C
N
106
N
N
Y
107
N
N
Y
108
N
C
Y
109
N
N
Y
110
N
C
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
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
N
137
N
N
N
138
N
C
N
139
N
O
N
140
N
N
N
141
N
C
N
142
N
N
N
143
N
C
N
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
Y
171
N
N
Y
172
N
C
Y
173
N
N
Y
174
N
C
N
175
N
C
N
176
N
O
N
177
N
N
N
178
N
C
N
179
N
N
N
180
N
N
Y
181
N
C
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
H
N
196
N
O
N
197
N
P
N
198
N
O
N
199
N
O
N
200
N
O
N
201
N
C
N
202
R
C
N
203
N
O
N
204
S
C
N
205
N
O
N
206
N
C
N
207
R
C
N
208
N
N
N
209
N
C
N
210
N
O
N
211
N
N
N
212
N
C
N
213
N
O
N
214
N
C
N
215
N
C
N
216
N
C
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
H
N
232
N
P
N
233
N
N
N
234
N
C
N
235
N
N
N
236
N
N
N
237
N
C
N
238
N
C
N
239
N
C
N
240
N
O
N
241
N
N
N
242
N
C
N
243
N
O
N
244
N
N
N
245
R
C
N
246
S
C
N
247
N
F
N
248
R
C
N
249
N
O
N
250
R
C
N
251
N
O
N
252
N
C
N
253
N
O
N
254
N
O
N
255
N
O
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
O
N
268
N
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
O
N
278
N
N
N
279
N
O
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
O
N
298
N
O
N
299
N
O
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
N
N
310
N
C
N
311
N
C
N
312
N
O
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
N
N
320
S
C
N
321
N
C
N
322
N
O
N
323
N
C
Y
324
N
C
Y
325
N
N
Y
326
N
C
Y
327
N
C
Y
328
N
N
N
329
N
O
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
H
N
339
N
H
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
N
N
344
S
C
N
345
N
C
N
346
N
O
N
347
S
C
N
348
N
C
N
349
N
C
N
350
N
C
N
351
N
O
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
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
C
N
373
N
O
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
H
N
386
N
H
N
387
N
N
N
388
S
C
N
389
N
C
N
390
N
O
N
391
N
C
N
392
N
C
N
393
N
C
N
394
N
C
N
395
N
N
N
396
N
O
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
H
N
411
N
H
N
412
N
N
N
413
S
C
N
414
N
C
N
415
N
O
N
416
N
C
N
417
N
C
N
418
N
S
N
419
N
C
N
420
N
O
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
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
N
443
N
O
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
N
460
N
C
N
461
N
C
N
462
N
O
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
N
N
473
S
C
N
474
N
C
N
475
N
O
N
476
N
C
N
477
N
O
N
478
N
O
N
479
N
H
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
N
N
487
S
C
N
488
N
C
N
489
N
O
N
490
R
C
N
491
N
O
N
492
N
C
N
493
N
O
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
H
N
502
N
H
N
503
N
N
N
504
S
C
N
505
N
C
N
506
N
O
N
507
N
C
Y
508
N
C
Y
509
N
C
Y
510
N
C
Y
511
N
N
Y
512
N
C
Y
513
N
C
Y
514
N
C
Y
515
N
C
Y
516
N
C
N
517
N
O
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
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
N
N
531
S
C
N
532
N
C
N
533
N
O
N
534
N
C
Y
535
N
C
Y
536
N
C
Y
537
N
C
Y
538
N
C
Y
539
N
C
Y
540
N
C
N
541
N
O
N
542
N
O
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
N
N
555
S
C
N
556
N
C
N
557
N
O
N
558
N
C
N
559
N
C
N
560
N
C
N
561
N
O
N
562
N
H
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
N
567
N
H
N
568
N
H
N
569
N
H
N
570
N
H
N
571
N
H
N
572
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
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
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
N
248
N
sing
N
249
N
sing
N
250
N
doub
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
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
doub
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
doub
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
sing
N
296
N
sing
N
297
N
doub
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
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
doub
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
doub
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
Y
331
N
doub
N
332
N
sing
Y
333
N
sing
N
334
N
sing
Y
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
doub
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
sing
N
367
N
sing
N
368
N
doub
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
sing
N
388
N
sing
N
389
N
doub
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
sing
N
412
N
sing
N
413
N
doub
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
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
Y
437
N
doub
Y
438
N
sing
Y
439
N
sing
N
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
443
N
doub
N
444
N
sing
Y
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
sing
N
454
N
sing
N
455
N
doub
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
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
doub
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
sing
N
500
N
sing
N
501
N
doub
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
Y
506
N
doub
Y
507
N
sing
Y
508
N
sing
N
509
N
sing
Y
510
N
doub
Y
511
N
sing
Y
512
N
sing
N
513
N
sing
Y
514
N
sing
Y
515
N
doub
N
516
N
sing
Y
517
N
doub
N
518
N
sing
Y
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
doub
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
Y
534
N
doub
Y
535
N
sing
Y
536
N
sing
N
537
N
sing
Y
538
N
doub
N
539
N
sing
Y
540
N
doub
N
541
N
sing
Y
542
N
sing
N
543
N
sing
N
544
N
sing
N
545
N
sing
N
546
N
sing
N
547
N
sing
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
sing
N
552
N
sing
N
553
N
doub
N
554
N
sing
N
555
N
sing
N
556
N
sing
N
557
N
sing
N
558
N
sing
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
N
563
N
sing
N
564
N
sing
to be published
0353
Structural investigation of hOGG1 bound to a fluorinated oxoG analog
to be published
0353
A Catalytic Checkpoint in Base Excision by the Human 8-Oxoguanine DNA Glycosylase hOGG1
10.2210/pdb3ktu/pdb
pdb_00003ktu
100
1
CCD
2008-02-01
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
24-ID-C
APS
0.979
SYNCHROTRON
APS BEAMLINE 24-ID-C
35727.469
N-glycosylase/DNA lyase
3.2.2.-, 4.2.99.18
sequence database residues 12-325
1
man
polymer
4016.623
DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3')
1
syn
polymer
3672.369
DNA (5'-D(*GP*TP*CP*CP*AP*(FDG)P*GP*TP*CP*TP*AP*C)-3')
1
syn
polymer
40.078
CALCIUM ION
2
syn
non-polymer
18.015
water
72
nat
water
8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
no
no
SEFGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRP
TPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSCNNIARITGMVERLCQAFGP
RLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGT
KVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ
SEFGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRP
TPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSCNNIARITGMVERLCQAFGP
RLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGT
KVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ
A
polypeptide(L)
no
no
(DG)(DG)(DT)(DA)(DG)(DA)(DC)(DC)(DT)(DG)(DG)(DA)(DC)
GGTAGACCTGGAC
B
polydeoxyribonucleotide
no
yes
(DG)(DT)(DC)(DC)(DA)(FDG)(DG)(DT)(DC)(DT)(DA)(DC)
GTCCAXGTCTAC
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
MMH, MUTM, OGG1, OGH1
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)PLYSS
plasmid
pET30a
1
3.03
59.39
6.0
Calcium Chloride, Sodium Cacodylate, pH 6.0, PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
Calcium Chloride
1
Calcium Chloride
2
Sodium Cacodylate
1
Sodium Cacodylate
2
PEG 8000
1
PEG 8000
2
-13.844
B
2
C
29
1.497
B_DG2:DC29_C
1
3.003
-1.835
-0.225
0.107
-10.989
1
20
B
3
C
28
-0.697
B_DT3:DA28_C
2
-11.473
-1.400
0.177
0.197
-13.644
1
20
B
4
C
27
3.442
B_DA4:DT27_C
3
-13.204
-0.795
0.012
0.038
0.493
1
19
B
5
C
26
1.181
B_DG5:DC26_C
4
-14.029
-0.547
-0.236
-0.210
-2.640
1
20
B
6
C
25
-2.338
B_DA6:DT25_C
5
-8.278
-0.418
0.147
0.275
11.364
1
19
B
7
C
24
-4.873
B_DC7:DG24_C
6
-3.181
0.417
-0.119
0.096
-13.878
1
20
B
9
C
22
0.594
B_DT9:DA22_C
7
-0.718
-0.067
0.126
0.136
2.219
1
B
10
C
21
10.362
B_DG10:DC21_C
8
-0.180
1.229
-0.151
0.558
0.710
1
B
11
C
20
9.110
B_DG11:DC20_C
9
-8.922
0.140
-0.143
0.367
0.864
1
20
B
12
C
19
16.140
B_DA12:DT19_C
10
-11.544
0.399
0.299
-0.244
33.953
B
13
C
18
5.492
B_DC13:DG18_C
11
22.452
-1.982
-0.900
0.667
3.369
36.556
B
B
2
3
13.752
C
C
29
28
3.424
8.519
-1.009
-0.347
BB_DG2DT3:DA28DC29_CC
1
-5.662
9.141
35.143
-1.799
0.781
3.509
46.722
B
B
3
4
-8.709
C
C
28
27
3.686
-6.881
-0.028
0.961
BB_DT3DA4:DT27DA28_CC
2
2.749
-3.480
46.163
1.846
0.289
2.950
31.748
B
B
4
5
14.638
C
C
27
26
3.000
7.927
-0.439
0.175
BB_DA4DG5:DC26DT27_CC
3
0.197
-0.364
30.766
-1.025
0.836
3.345
38.357
B
B
5
6
8.578
C
C
26
25
3.306
5.591
-0.602
0.135
BB_DG5DA6:DT25DC26_CC
4
-6.554
10.055
37.412
-0.514
0.072
3.042
36.037
B
B
6
7
-1.804
C
C
25
24
3.033
-1.115
0.095
-0.327
BB_DA6DC7:DG24DT25_CC
5
2.295
-3.713
35.949
-0.381
0.148
2.993
42.055
B
B
9
10
-3.953
C
C
22
21
3.126
-2.834
0.520
1.671
BB_DT9DG10:DC21DA22_CC
6
-1.449
2.022
41.940
2.604
-0.865
3.310
32.770
B
B
10
11
13.699
C
C
21
20
3.289
7.661
-0.465
0.445
BB_DG10DG11:DC20DC21_CC
7
-0.464
0.830
31.883
-0.561
0.743
3.114
39.892
B
B
11
12
3.686
C
C
20
19
3.200
2.508
0.232
-0.511
BB_DG11DA12:DT19DC20_CC
8
-4.860
7.143
39.530
-1.029
-0.884
3.073
35.756
B
B
12
13
-31.574
C
C
19
18
3.384
-18.423
0.529
-0.225
BB_DA12DC13:DG18DT19_CC
9
5.439
-9.322
30.301
2.491
-0.017
pdbx_entity_src_syn
software
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Refinement description
Source and taxonomy
Database references
Derived calculations
Data collection
Refinement description
1
0
2010-07-14
1
1
2011-07-13
1
2
2017-11-01
1
3
2021-10-13
1
4
2023-09-06
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
_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.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.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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HOGG1 disulphide cross-linked to undamaged DNA
HOGG1 COMPLEXED WITH OXOG CONTAINING DNA
RCSB
Y
RCSB
2009-11-26
REL
REL
CA
CALCIUM ION
HOH
water
SYNTHETIC DNA
32630
synthetic construct
sample
SYNTHETIC DNA
32630
synthetic construct
sample
1EBM
PDB ENTRY 1EBM
PDB
experimental model
CA
2
4
CA
CA
2
A
CA
1
4
CA
CA
1
C
HOH
1
5
HOH
HOH
1
A
HOH
3
5
HOH
HOH
3
A
HOH
4
5
HOH
HOH
4
A
HOH
5
5
HOH
HOH
5
A
HOH
6
5
HOH
HOH
6
A
HOH
7
5
HOH
HOH
7
A
HOH
326
5
HOH
HOH
326
A
HOH
327
5
HOH
HOH
327
A
HOH
328
5
HOH
HOH
328
A
HOH
329
5
HOH
HOH
329
A
HOH
330
5
HOH
HOH
330
A
HOH
331
5
HOH
HOH
331
A
HOH
332
5
HOH
HOH
332
A
HOH
333
5
HOH
HOH
333
A
HOH
334
5
HOH
HOH
334
A
HOH
335
5
HOH
HOH
335
A
HOH
336
5
HOH
HOH
336
A
HOH
337
5
HOH
HOH
337
A
HOH
338
5
HOH
HOH
338
A
HOH
339
5
HOH
HOH
339
A
HOH
340
5
HOH
HOH
340
A
HOH
341
5
HOH
HOH
341
A
HOH
342
5
HOH
HOH
342
A
HOH
343
5
HOH
HOH
343
A
HOH
344
5
HOH
HOH
344
A
HOH
345
5
HOH
HOH
345
A
HOH
346
5
HOH
HOH
346
A
HOH
347
5
HOH
HOH
347
A
HOH
348
5
HOH
HOH
348
A
HOH
349
5
HOH
HOH
349
A
HOH
350
5
HOH
HOH
350
A
HOH
351
5
HOH
HOH
351
A
HOH
352
5
HOH
HOH
352
A
HOH
353
5
HOH
HOH
353
A
HOH
354
5
HOH
HOH
354
A
HOH
355
5
HOH
HOH
355
A
HOH
356
5
HOH
HOH
356
A
HOH
357
5
HOH
HOH
357
A
HOH
358
5
HOH
HOH
358
A
HOH
359
5
HOH
HOH
359
A
HOH
360
5
HOH
HOH
360
A
HOH
361
5
HOH
HOH
361
A
HOH
362
5
HOH
HOH
362
A
HOH
363
5
HOH
HOH
363
A
HOH
364
5
HOH
HOH
364
A
HOH
365
5
HOH
HOH
365
A
HOH
366
5
HOH
HOH
366
A
HOH
367
5
HOH
HOH
367
A
HOH
368
5
HOH
HOH
368
A
HOH
369
5
HOH
HOH
369
A
HOH
370
5
HOH
HOH
370
A
HOH
371
5
HOH
HOH
371
A
HOH
372
5
HOH
HOH
372
A
HOH
373
5
HOH
HOH
373
A
HOH
374
5
HOH
HOH
374
A
HOH
375
5
HOH
HOH
375
A
HOH
376
5
HOH
HOH
376
A
HOH
377
5
HOH
HOH
377
A
HOH
378
5
HOH
HOH
378
A
HOH
379
5
HOH
HOH
379
A
HOH
380
5
HOH
HOH
380
A
HOH
381
5
HOH
HOH
381
A
HOH
382
5
HOH
HOH
382
A
HOH
383
5
HOH
HOH
383
A
HOH
384
5
HOH
HOH
384
A
HOH
385
5
HOH
HOH
385
A
HOH
386
5
HOH
HOH
386
A
HOH
387
5
HOH
HOH
387
A
HOH
388
5
HOH
HOH
388
A
HOH
389
5
HOH
HOH
389
A
HOH
55
5
HOH
HOH
55
C
HOH
109
5
HOH
HOH
109
C
SER
9
n
1
SER
9
A
GLU
10
n
2
GLU
10
A
PHE
11
n
3
PHE
11
A
GLY
12
n
4
GLY
12
A
HIS
13
n
5
HIS
13
A
ARG
14
n
6
ARG
14
A
THR
15
n
7
THR
15
A
LEU
16
n
8
LEU
16
A
ALA
17
n
9
ALA
17
A
SER
18
n
10
SER
18
A
THR
19
n
11
THR
19
A
PRO
20
n
12
PRO
20
A
ALA
21
n
13
ALA
21
A
LEU
22
n
14
LEU
22
A
TRP
23
n
15
TRP
23
A
ALA
24
n
16
ALA
24
A
SER
25
n
17
SER
25
A
ILE
26
n
18
ILE
26
A
PRO
27
n
19
PRO
27
A
CYS
28
n
20
CYS
28
A
PRO
29
n
21
PRO
29
A
ARG
30
n
22
ARG
30
A
SER
31
n
23
SER
31
A
GLU
32
n
24
GLU
32
A
LEU
33
n
25
LEU
33
A
ARG
34
n
26
ARG
34
A
LEU
35
n
27
LEU
35
A
ASP
36
n
28
ASP
36
A
LEU
37
n
29
LEU
37
A
VAL
38
n
30
VAL
38
A
LEU
39
n
31
LEU
39
A
PRO
40
n
32
PRO
40
A
SER
41
n
33
SER
41
A
GLY
42
n
34
GLY
42
A
GLN
43
n
35
GLN
43
A
SER
44
n
36
SER
44
A
PHE
45
n
37
PHE
45
A
ARG
46
n
38
ARG
46
A
TRP
47
n
39
TRP
47
A
ARG
48
n
40
ARG
48
A
GLU
49
n
41
GLU
49
A
GLN
50
n
42
GLN
50
A
SER
51
n
43
SER
51
A
PRO
52
n
44
PRO
52
A
ALA
53
n
45
ALA
53
A
HIS
54
n
46
HIS
54
A
TRP
55
n
47
TRP
55
A
SER
56
n
48
SER
56
A
GLY
57
n
49
GLY
57
A
VAL
58
n
50
VAL
58
A
LEU
59
n
51
LEU
59
A
ALA
60
n
52
ALA
60
A
ASP
61
n
53
ASP
61
A
GLN
62
n
54
GLN
62
A
VAL
63
n
55
VAL
63
A
TRP
64
n
56
TRP
64
A
THR
65
n
57
THR
65
A
LEU
66
n
58
LEU
66
A
THR
67
n
59
THR
67
A
GLN
68
n
60
GLN
68
A
THR
69
n
61
THR
69
A
GLU
70
n
62
GLU
70
A
GLU
71
n
63
GLU
71
A
GLN
72
n
64
GLN
72
A
LEU
73
n
65
LEU
73
A
HIS
74
n
66
HIS
74
A
CYS
75
n
67
CYS
75
A
THR
76
n
68
THR
76
A
VAL
77
n
69
VAL
77
A
TYR
78
n
70
TYR
78
A
ARG
79
n
71
ARG
79
A
n
72
80
A
n
73
81
A
n
74
82
A
SER
83
n
75
SER
83
A
GLN
84
n
76
GLN
84
A
ALA
85
n
77
ALA
85
A
SER
86
n
78
SER
86
A
ARG
87
n
79
ARG
87
A
PRO
88
n
80
PRO
88
A
THR
89
n
81
THR
89
A
PRO
90
n
82
PRO
90
A
ASP
91
n
83
ASP
91
A
GLU
92
n
84
GLU
92
A
LEU
93
n
85
LEU
93
A
GLU
94
n
86
GLU
94
A
ALA
95
n
87
ALA
95
A
VAL
96
n
88
VAL
96
A
ARG
97
n
89
ARG
97
A
LYS
98
n
90
LYS
98
A
TYR
99
n
91
TYR
99
A
PHE
100
n
92
PHE
100
A
GLN
101
n
93
GLN
101
A
LEU
102
n
94
LEU
102
A
ASP
103
n
95
ASP
103
A
VAL
104
n
96
VAL
104
A
THR
105
n
97
THR
105
A
LEU
106
n
98
LEU
106
A
ALA
107
n
99
ALA
107
A
GLN
108
n
100
GLN
108
A
LEU
109
n
101
LEU
109
A
TYR
110
n
102
TYR
110
A
HIS
111
n
103
HIS
111
A
HIS
112
n
104
HIS
112
A
TRP
113
n
105
TRP
113
A
GLY
114
n
106
GLY
114
A
SER
115
n
107
SER
115
A
VAL
116
n
108
VAL
116
A
ASP
117
n
109
ASP
117
A
SER
118
n
110
SER
118
A
HIS
119
n
111
HIS
119
A
PHE
120
n
112
PHE
120
A
GLN
121
n
113
GLN
121
A
GLU
122
n
114
GLU
122
A
VAL
123
n
115
VAL
123
A
ALA
124
n
116
ALA
124
A
GLN
125
n
117
GLN
125
A
LYS
126
n
118
LYS
126
A
PHE
127
n
119
PHE
127
A
GLN
128
n
120
GLN
128
A
GLY
129
n
121
GLY
129
A
VAL
130
n
122
VAL
130
A
ARG
131
n
123
ARG
131
A
LEU
132
n
124
LEU
132
A
LEU
133
n
125
LEU
133
A
ARG
134
n
126
ARG
134
A
GLN
135
n
127
GLN
135
A
ASP
136
n
128
ASP
136
A
PRO
137
n
129
PRO
137
A
ILE
138
n
130
ILE
138
A
GLU
139
n
131
GLU
139
A
CYS
140
n
132
CYS
140
A
LEU
141
n
133
LEU
141
A
PHE
142
n
134
PHE
142
A
SER
143
n
135
SER
143
A
PHE
144
n
136
PHE
144
A
ILE
145
n
137
ILE
145
A
CYS
146
n
138
CYS
146
A
SER
147
n
139
SER
147
A
SER
148
n
140
SER
148
A
CYS
149
n
141
CYS
149
A
ASN
150
n
142
ASN
150
A
ASN
151
n
143
ASN
151
A
ILE
152
n
144
ILE
152
A
ALA
153
n
145
ALA
153
A
ARG
154
n
146
ARG
154
A
ILE
155
n
147
ILE
155
A
THR
156
n
148
THR
156
A
GLY
157
n
149
GLY
157
A
MET
158
n
150
MET
158
A
VAL
159
n
151
VAL
159
A
GLU
160
n
152
GLU
160
A
ARG
161
n
153
ARG
161
A
LEU
162
n
154
LEU
162
A
CYS
163
n
155
CYS
163
A
GLN
164
n
156
GLN
164
A
ALA
165
n
157
ALA
165
A
PHE
166
n
158
PHE
166
A
GLY
167
n
159
GLY
167
A
PRO
168
n
160
PRO
168
A
ARG
169
n
161
ARG
169
A
LEU
170
n
162
LEU
170
A
ILE
171
n
163
ILE
171
A
GLN
172
n
164
GLN
172
A
LEU
173
n
165
LEU
173
A
ASP
174
n
166
ASP
174
A
ASP
175
n
167
ASP
175
A
VAL
176
n
168
VAL
176
A
THR
177
n
169
THR
177
A
TYR
178
n
170
TYR
178
A
HIS
179
n
171
HIS
179
A
GLY
180
n
172
GLY
180
A
PHE
181
n
173
PHE
181
A
PRO
182
n
174
PRO
182
A
SER
183
n
175
SER
183
A
LEU
184
n
176
LEU
184
A
GLN
185
n
177
GLN
185
A
ALA
186
n
178
ALA
186
A
LEU
187
n
179
LEU
187
A
ALA
188
n
180
ALA
188
A
GLY
189
n
181
GLY
189
A
PRO
190
n
182
PRO
190
A
GLU
191
n
183
GLU
191
A
VAL
192
n
184
VAL
192
A
GLU
193
n
185
GLU
193
A
ALA
194
n
186
ALA
194
A
HIS
195
n
187
HIS
195
A
LEU
196
n
188
LEU
196
A
ARG
197
n
189
ARG
197
A
LYS
198
n
190
LYS
198
A
LEU
199
n
191
LEU
199
A
GLY
200
n
192
GLY
200
A
LEU
201
n
193
LEU
201
A
GLY
202
n
194
GLY
202
A
TYR
203
n
195
TYR
203
A
ARG
204
n
196
ARG
204
A
ALA
205
n
197
ALA
205
A
ARG
206
n
198
ARG
206
A
TYR
207
n
199
TYR
207
A
VAL
208
n
200
VAL
208
A
SER
209
n
201
SER
209
A
ALA
210
n
202
ALA
210
A
SER
211
n
203
SER
211
A
ALA
212
n
204
ALA
212
A
ARG
213
n
205
ARG
213
A
ALA
214
n
206
ALA
214
A
ILE
215
n
207
ILE
215
A
LEU
216
n
208
LEU
216
A
GLU
217
n
209
GLU
217
A
GLU
218
n
210
GLU
218
A
GLN
219
n
211
GLN
219
A
GLY
220
n
212
GLY
220
A
GLY
221
n
213
GLY
221
A
LEU
222
n
214
LEU
222
A
ALA
223
n
215
ALA
223
A
TRP
224
n
216
TRP
224
A
LEU
225
n
217
LEU
225
A
GLN
226
n
218
GLN
226
A
GLN
227
n
219
GLN
227
A
LEU
228
n
220
LEU
228
A
ARG
229
n
221
ARG
229
A
GLU
230
n
222
GLU
230
A
SER
231
n
223
SER
231
A
SER
232
n
224
SER
232
A
TYR
233
n
225
TYR
233
A
GLU
234
n
226
GLU
234
A
GLU
235
n
227
GLU
235
A
ALA
236
n
228
ALA
236
A
HIS
237
n
229
HIS
237
A
LYS
238
n
230
LYS
238
A
ALA
239
n
231
ALA
239
A
LEU
240
n
232
LEU
240
A
CYS
241
n
233
CYS
241
A
ILE
242
n
234
ILE
242
A
LEU
243
n
235
LEU
243
A
PRO
244
n
236
PRO
244
A
GLY
245
n
237
GLY
245
A
VAL
246
n
238
VAL
246
A
GLY
247
n
239
GLY
247
A
THR
248
n
240
THR
248
A
LYS
249
n
241
LYS
249
A
VAL
250
n
242
VAL
250
A
ALA
251
n
243
ALA
251
A
ASP
252
n
244
ASP
252
A
CYS
253
n
245
CYS
253
A
ILE
254
n
246
ILE
254
A
CYS
255
n
247
CYS
255
A
LEU
256
n
248
LEU
256
A
MET
257
n
249
MET
257
A
ALA
258
n
250
ALA
258
A
LEU
259
n
251
LEU
259
A
ASP
260
n
252
ASP
260
A
LYS
261
n
253
LYS
261
A
PRO
262
n
254
PRO
262
A
GLN
263
n
255
GLN
263
A
ALA
264
n
256
ALA
264
A
VAL
265
n
257
VAL
265
A
PRO
266
n
258
PRO
266
A
VAL
267
n
259
VAL
267
A
ASP
268
n
260
ASP
268
A
VAL
269
n
261
VAL
269
A
HIS
270
n
262
HIS
270
A
MET
271
n
263
MET
271
A
TRP
272
n
264
TRP
272
A
HIS
273
n
265
HIS
273
A
ILE
274
n
266
ILE
274
A
ALA
275
n
267
ALA
275
A
GLN
276
n
268
GLN
276
A
ARG
277
n
269
ARG
277
A
ASP
278
n
270
ASP
278
A
TYR
279
n
271
TYR
279
A
SER
280
n
272
SER
280
A
TRP
281
n
273
TRP
281
A
HIS
282
n
274
HIS
282
A
PRO
283
n
275
PRO
283
A
THR
284
n
276
THR
284
A
THR
285
n
277
THR
285
A
SER
286
n
278
SER
286
A
GLN
287
n
279
GLN
287
A
ALA
288
n
280
ALA
288
A
LYS
289
n
281
LYS
289
A
GLY
290
n
282
GLY
290
A
PRO
291
n
283
PRO
291
A
SER
292
n
284
SER
292
A
PRO
293
n
285
PRO
293
A
GLN
294
n
286
GLN
294
A
THR
295
n
287
THR
295
A
ASN
296
n
288
ASN
296
A
LYS
297
n
289
LYS
297
A
GLU
298
n
290
GLU
298
A
LEU
299
n
291
LEU
299
A
GLY
300
n
292
GLY
300
A
ASN
301
n
293
ASN
301
A
PHE
302
n
294
PHE
302
A
PHE
303
n
295
PHE
303
A
ARG
304
n
296
ARG
304
A
SER
305
n
297
SER
305
A
LEU
306
n
298
LEU
306
A
TRP
307
n
299
TRP
307
A
GLY
308
n
300
GLY
308
A
PRO
309
n
301
PRO
309
A
TYR
310
n
302
TYR
310
A
ALA
311
n
303
ALA
311
A
GLY
312
n
304
GLY
312
A
TRP
313
n
305
TRP
313
A
ALA
314
n
306
ALA
314
A
GLN
315
n
307
GLN
315
A
ALA
316
n
308
ALA
316
A
VAL
317
n
309
VAL
317
A
LEU
318
n
310
LEU
318
A
PHE
319
n
311
PHE
319
A
SER
320
n
312
SER
320
A
ALA
321
n
313
ALA
321
A
ASP
322
n
314
ASP
322
A
LEU
323
n
315
LEU
323
A
ARG
324
n
316
ARG
324
A
GLN
325
n
317
GLN
325
A
DG
1
n
1
DG
1
B
DG
2
n
2
DG
2
B
DT
3
n
3
DT
3
B
DA
4
n
4
DA
4
B
DG
5
n
5
DG
5
B
DA
6
n
6
DA
6
B
DC
7
n
7
DC
7
B
DC
8
n
8
DC
8
B
DT
9
n
9
DT
9
B
DG
10
n
10
DG
10
B
DG
11
n
11
DG
11
B
DA
12
n
12
DA
12
B
DC
13
n
13
DC
13
B
DG
18
n
1
DG
18
C
DT
19
n
2
DT
19
C
DC
20
n
3
DC
20
C
DC
21
n
4
DC
21
C
DA
22
n
5
DA
22
C
FDG
23
n
6
FDG
23
C
DG
24
n
7
DG
24
C
DT
25
n
8
DT
25
C
DC
26
n
9
DC
26
C
DT
27
n
10
DT
27
C
DA
28
n
11
DA
28
C
DC
29
n
12
DC
29
C
author_and_software_defined_assembly
PISA
3
trimeric
3950
-44
17130
A
CYS
241
A
O
CYS
233
1_555
A
CA
2
D
CA
CA
1_555
A
LEU
243
A
O
LEU
235
1_555
95.8
A
CYS
241
A
O
CYS
233
1_555
A
CA
2
D
CA
CA
1_555
A
VAL
246
A
O
VAL
238
1_555
88.8
A
LEU
243
A
O
LEU
235
1_555
A
CA
2
D
CA
CA
1_555
A
VAL
246
A
O
VAL
238
1_555
82.4
A
CYS
241
A
O
CYS
233
1_555
A
CA
2
D
CA
CA
1_555
C
DC
26
C
OP1
DC
9
1_555
173.7
A
LEU
243
A
O
LEU
235
1_555
A
CA
2
D
CA
CA
1_555
C
DC
26
C
OP1
DC
9
1_555
77.9
A
VAL
246
A
O
VAL
238
1_555
A
CA
2
D
CA
CA
1_555
C
DC
26
C
OP1
DC
9
1_555
91.4
C
FDG
23
C
FDG
6
DG
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
ALA
24
A
N
ALA
16
A
O
CYS
75
A
O
CYS
67
A
O
HIS
74
A
O
HIS
66
A
N
THR
67
A
N
THR
59
A
O
GLN
62
A
O
GLN
54
A
N
LEU
59
A
N
LEU
51
A
O
SER
56
A
O
SER
48
A
N
ARG
48
A
N
ARG
40
A
N
LEU
170
A
N
LEU
162
A
O
TYR
178
A
O
TYR
170
1
A
CG
GLN
125
A
CG
GLN
117
1
Y
1
A
CD
GLN
125
A
CD
GLN
117
1
Y
1
A
OE1
GLN
125
A
OE1
GLN
117
1
Y
1
A
NE2
GLN
125
A
NE2
GLN
117
1
Y
1
A
CG
LYS
126
A
CG
LYS
118
1
Y
1
A
CD
LYS
126
A
CD
LYS
118
1
Y
1
A
CE
LYS
126
A
CE
LYS
118
1
Y
1
A
NZ
LYS
126
A
NZ
LYS
118
1
Y
1
A
CG
GLN
325
A
CG
GLN
317
1
Y
1
A
CD
GLN
325
A
CD
GLN
317
1
Y
1
A
OE1
GLN
325
A
OE1
GLN
317
1
Y
1
A
NE2
GLN
325
A
NE2
GLN
317
1
Y
1
A
GLY
80
A
GLY
72
1
Y
1
A
ASP
81
A
ASP
73
1
Y
1
A
LYS
82
A
LYS
74
1
Y
1
9.29
1.50
119.30
128.59
A
A
A
C
N
CA
GLY
PRO
PRO
308
309
309
Y
1
A
CYS
28
-171.46
108.96
1
A
CYS
149
33.38
53.56
1
A
LEU
170
-103.56
-144.30
1
A
ASP
174
55.05
-131.57
1
A
GLU
218
-143.68
-31.99
1
A
ALA
258
-140.42
-10.79
1
A
THR
284
-105.74
-70.10
1
A
ALA
288
-45.96
151.73
PROTEIN_REP.PARAM
DNA-RNA_REP.PARAM
WATER_REP.PARAM
ION.PARAM
FOG_PAR.TXT
58.94
4.66600
0.00000
0.00000
4.66600
0.00000
-9.3330
0.257
0.225
0.225
2.30
25.21
2316
23379
9.400
94.7
1.00
1.00
1
0.000
MOLECULAR REPLACEMENT
PDB ENTRY 1EBM
42.65
2.30
25.21
72
3069
2
510
2485
1.351
1.500
2.198
2.000
2.012
2.000
3.028
2.500
2.300
50.000
3KTU
24522
0.11200
1
14.3000
9.200
99.6
0.39700
2.30
2.38
9.50
100.0
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns-online.org/
CNS
package
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
phasing
CNS
Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
A
THR
19
A
THR
11
HELX_P
A
TRP
23
A
TRP
15
5
1
5
A
ARG
34
A
ARG
26
HELX_P
A
LEU
39
A
LEU
31
1
2
6
A
THR
89
A
THR
81
HELX_P
A
PHE
100
A
PHE
92
1
3
12
A
THR
105
A
THR
97
HELX_P
A
ASP
117
A
ASP
109
1
4
13
A
ASP
136
A
ASP
128
HELX_P
A
CYS
146
A
CYS
138
1
6
11
A
ASN
151
A
ASN
143
HELX_P
A
GLY
167
A
GLY
159
1
7
17
A
SER
183
A
SER
175
HELX_P
A
ALA
188
A
ALA
180
1
8
6
A
GLU
191
A
GLU
183
HELX_P
A
LEU
199
A
LEU
191
1
9
9
A
TYR
203
A
TYR
195
HELX_P
A
GLU
218
A
GLU
210
1
10
16
A
GLY
221
A
GLY
213
HELX_P
A
GLN
227
A
GLN
219
1
11
7
A
LEU
228
A
LEU
220
HELX_P
A
SER
231
A
SER
223
5
12
4
A
SER
232
A
SER
224
HELX_P
A
CYS
241
A
CYS
233
1
13
10
A
GLY
247
A
GLY
239
HELX_P
A
LEU
259
A
LEU
251
1
14
13
A
ASP
268
A
ASP
260
HELX_P
A
SER
280
A
SER
272
1
15
13
A
SER
292
A
SER
284
HELX_P
A
GLY
308
A
GLY
300
1
16
17
A
TYR
310
A
TYR
302
HELX_P
A
ARG
324
A
ARG
316
1
17
15
covale
1.626
both
C
DA
22
C
O3'
DA
5
1_555
C
FDG
23
C
P
FDG
6
1_555
covale
1.615
both
C
FDG
23
C
O3'
FDG
6
1_555
C
DG
24
C
P
DG
7
1_555
metalc
2.580
A
CA
2
D
CA
CA
1_555
A
CYS
241
A
O
CYS
233
1_555
metalc
2.830
A
CA
2
D
CA
CA
1_555
A
LEU
243
A
O
LEU
235
1_555
metalc
2.839
A
CA
2
D
CA
CA
1_555
A
VAL
246
A
O
VAL
238
1_555
metalc
2.644
A
CA
2
D
CA
CA
1_555
C
DC
26
C
OP1
DC
9
1_555
metalc
2.907
C
CA
1
E
CA
CA
1_555
C
DG
24
C
OP1
DG
7
1_555
hydrog
DG-DC PAIR
B
DG
2
B
N1
DG
2
1_555
C
DC
29
C
O2
DC
12
1_555
hydrog
WATSON-CRICK
B
DT
3
B
N3
DT
3
1_555
C
DA
28
C
N1
DA
11
1_555
hydrog
WATSON-CRICK
B
DT
3
B
O4
DT
3
1_555
C
DA
28
C
N6
DA
11
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N1
DA
4
1_555
C
DT
27
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N6
DA
4
1_555
C
DT
27
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DG
5
B
N1
DG
5
1_555
C
DC
26
C
N3
DC
9
1_555
hydrog
WATSON-CRICK
B
DG
5
B
N2
DG
5
1_555
C
DC
26
C
O2
DC
9
1_555
hydrog
WATSON-CRICK
B
DG
5
B
O6
DG
5
1_555
C
DC
26
C
N4
DC
9
1_555
hydrog
WATSON-CRICK
B
DA
6
B
N1
DA
6
1_555
C
DT
25
C
N3
DT
8
1_555
hydrog
WATSON-CRICK
B
DA
6
B
N6
DA
6
1_555
C
DT
25
C
O4
DT
8
1_555
hydrog
WATSON-CRICK
B
DC
7
B
N3
DC
7
1_555
C
DG
24
C
N1
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
7
B
N4
DC
7
1_555
C
DG
24
C
O6
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
7
B
O2
DC
7
1_555
C
DG
24
C
N2
DG
7
1_555
hydrog
WATSON-CRICK
B
DT
9
B
N3
DT
9
1_555
C
DA
22
C
N1
DA
5
1_555
hydrog
WATSON-CRICK
B
DT
9
B
O4
DT
9
1_555
C
DA
22
C
N6
DA
5
1_555
hydrog
DG-DC PAIR
B
DG
10
B
N1
DG
10
1_555
C
DC
21
C
N3
DC
4
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N1
DG
11
1_555
C
DC
20
C
N3
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N2
DG
11
1_555
C
DC
20
C
O2
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
O6
DG
11
1_555
C
DC
20
C
N4
DC
3
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N1
DA
12
1_555
C
DT
19
C
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N6
DA
12
1_555
C
DT
19
C
O4
DT
2
1_555
hydrog
DC-DG PAIR
B
DC
13
B
N3
DC
13
1_555
C
DG
18
C
N2
DG
1
1_555
HYDROLASE,LYASE/DNA
8-oxoGuanine, 2'-fluoro-8-oxoGuanine, protein-DNA complex, DNA glycosylase, Base Excsion Repair, DNA damage, DNA repair, HYDROLASE, LYASE-DNA complex
OGG1_HUMAN
UNP
1
12
O15527
GHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPD
ELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLI
QLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVA
DCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ
3KTU
PDB
2
1
3KTU
GGTAGACCTGGAC
3KTU
PDB
3
1
3KTU
GTCCA(FDG)GTCTAC
12
325
3KTU
12
325
O15527
A
1
4
317
1
13
3KTU
1
13
3KTU
B
2
1
13
18
29
3KTU
18
29
3KTU
C
3
1
12
1
expression tag
SER
9
3KTU
A
O15527
UNP
1
1
expression tag
GLU
10
3KTU
A
O15527
UNP
2
1
expression tag
PHE
11
3KTU
A
O15527
UNP
3
1
ASN
engineered mutation
CYS
149
3KTU
A
O15527
UNP
149
141
5
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ALA
24
A
ALA
16
A
PRO
27
A
PRO
19
A
GLN
72
A
GLN
64
A
TYR
78
A
TYR
70
A
GLN
62
A
GLN
54
A
GLN
68
A
GLN
60
A
HIS
54
A
HIS
46
A
LEU
59
A
LEU
51
A
ARG
48
A
ARG
40
A
SER
51
A
SER
43
A
ARG
169
A
ARG
161
A
LEU
173
A
LEU
165
A
VAL
176
A
VAL
168
A
HIS
179
A
HIS
171
BINDING SITE FOR RESIDUE FDG C 23
C
FDG
23
Software
15
BINDING SITE FOR RESIDUE CA A 2
A
CA
2
Software
4
BINDING SITE FOR RESIDUE CA C 1
C
CA
1
Software
2
A
GLY
42
A
GLY
34
15
1_555
A
SER
147
A
SER
139
15
1_555
A
ASN
150
A
ASN
142
15
1_555
A
ASN
151
A
ASN
143
15
1_555
A
ILE
152
A
ILE
144
15
1_555
A
LYS
249
A
LYS
241
15
1_555
A
MET
257
A
MET
249
15
1_555
A
PRO
266
A
PRO
258
15
1_555
A
ASP
268
A
ASP
260
15
1_555
A
HIS
270
A
HIS
262
15
1_555
A
GLN
315
A
GLN
307
15
1_555
A
PHE
319
A
PHE
311
15
1_555
C
DA
22
C
DA
5
15
1_555
C
DG
24
C
DG
7
15
1_555
C
HOH
109
G
HOH
15
1_555
A
CYS
241
A
CYS
233
4
1_555
A
LEU
243
A
LEU
235
4
1_555
A
VAL
246
A
VAL
238
4
1_555
C
DC
26
C
DC
9
4
1_555
A
VAL
269
A
VAL
261
2
1_555
C
DG
24
C
DG
7
2
1_555
179
P 65 2 2