0.024217
0.000000
0.000000
0.000000
0.024217
0.000000
0.000000
0.000000
0.008562
0.00000
0.00000
0.00000
Yu, B.
Benach, J.
Edstrom, W.C.
Gibney, B.R.
Hunt, J.F.
Northeast Structural Genomics Consortium (NESG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.294
41.294
116.797
C5 H6 O5
146.098
2-OXOGLUTARIC ACID
non-polymer
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
Co 2
58.933
COBALT (II) ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide 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
C11 H17 N5 O6 P 1
346.256
n
1N-METHYLADENOSINE-5'-MONOPHOSPHATE
DNA 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
C
N
2
N
O
N
3
N
O
N
4
N
C
N
5
N
O
N
6
N
C
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
O
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
N
N
18
S
C
N
19
N
C
N
20
N
O
N
21
N
C
N
22
N
O
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
N
N
31
S
C
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
N
N
38
N
C
N
39
N
N
N
40
N
N
N
41
N
O
N
42
N
H
N
43
N
H
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
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
N
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
C
N
62
N
C
N
63
N
O
N
64
N
N
N
65
N
O
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
O
N
81
N
O
N
82
N
O
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
CO
N
91
N
N
N
92
R
C
N
93
N
C
N
94
N
O
N
95
N
C
N
96
N
S
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
O
N
106
N
P
N
107
N
O
N
108
N
O
N
109
N
O
N
110
N
C
N
111
R
C
N
112
N
O
N
113
S
C
N
114
N
O
N
115
N
C
N
116
R
C
N
117
N
N
N
118
N
C
N
119
N
O
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
C
N
124
N
C
N
125
N
C
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
O
N
149
N
N
N
150
N
O
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
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
N
C
N
166
N
C
N
167
N
C
N
168
N
O
N
169
N
O
N
170
N
O
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
N
N
181
N
C
N
182
N
C
N
183
N
O
N
184
N
O
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
N
N
191
S
C
N
192
N
C
N
193
N
O
N
194
N
C
Y
195
N
C
Y
196
N
N
Y
197
N
C
Y
198
N
C
Y
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
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
O
N
212
N
H
N
213
N
H
N
214
N
N
N
215
S
C
N
216
N
C
N
217
N
O
N
218
S
C
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
O
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
C
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
N
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
Y
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
N
288
N
P
N
289
N
O
N
290
N
O
N
291
N
O
Y
292
N
N
Y
293
N
N
Y
294
N
N
N
295
N
N
Y
296
N
N
N
297
N
C
N
298
N
C
N
299
N
C
N
300
R
C
N
301
N
O
N
302
R
C
N
303
S
C
N
304
N
O
N
305
N
O
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
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
N
328
N
C
N
329
N
S
N
330
N
C
N
331
N
O
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
H
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
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
Y
353
N
C
N
354
N
O
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
H
N
366
N
N
N
367
S
C
N
368
N
C
N
369
N
O
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
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
N
388
N
O
N
389
N
O
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
R
C
N
402
N
O
N
403
N
C
N
404
N
O
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
H
N
413
N
H
N
414
N
N
N
415
S
C
N
416
N
C
N
417
N
O
N
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
C
Y
422
N
N
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
C
N
428
N
O
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
N
N
442
S
C
N
443
N
C
N
444
N
O
N
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
Y
451
N
C
N
452
N
O
N
453
N
O
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
N
N
466
S
C
N
467
N
C
N
468
N
O
N
469
N
C
N
470
N
C
N
471
N
C
N
472
N
O
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
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
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
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
doub
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
sing
N
58
N
sing
N
59
N
sing
N
60
N
doub
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
N
66
N
sing
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
doub
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
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
doub
N
128
N
sing
N
129
N
sing
N
130
N
doub
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
doub
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
doub
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
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
Y
192
N
sing
Y
193
N
doub
Y
194
N
doub
N
195
N
sing
Y
196
N
sing
N
197
N
sing
Y
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
doub
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
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
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
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
Y
270
N
doub
Y
271
N
sing
N
272
N
sing
Y
273
N
doub
Y
274
N
sing
Y
275
N
sing
Y
276
N
sing
Y
277
N
sing
Y
278
N
doub
N
279
N
sing
Y
280
N
sing
Y
281
N
doub
N
282
N
sing
N
283
N
doub
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
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
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
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
doub
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
sing
N
336
N
sing
N
337
N
doub
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
Y
342
N
doub
Y
343
N
sing
Y
344
N
sing
N
345
N
sing
Y
346
N
doub
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
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
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
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
doub
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
doub
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
Y
411
N
doub
Y
412
N
sing
Y
413
N
sing
N
414
N
sing
Y
415
N
doub
Y
416
N
sing
Y
417
N
sing
N
418
N
sing
Y
419
N
sing
Y
420
N
doub
N
421
N
sing
Y
422
N
doub
N
423
N
sing
Y
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
doub
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
Y
439
N
doub
Y
440
N
sing
Y
441
N
sing
N
442
N
sing
Y
443
N
doub
N
444
N
sing
Y
445
N
doub
N
446
N
sing
Y
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
doub
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
UK
Nature
NATUAS
0006
0028-0836
439
879
884
10.1038/nature04561
16482161
Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB.
2006
10.2210/pdb2fdf/pdb
pdb_00002fdf
1.00000
0.00000
0.00000
0.00000
1.00000
0.00000
0.00000
0.00000
1.00000
0.00000
0.00000
0.00000
100
1
Yale/MSC mirrors
IMAGE PLATE
2005-07-14
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.54180
1.0
1.54180
ROTATING ANODE
RIGAKU RU200
891.669
5'-D(P*TP*(MA7)P*T)-3'
1
syn
polymer
23610.975
Alkylated DNA repair protein alkB
residues 12-216
1
man
polymer
58.933
COBALT (II) ION
1
syn
non-polymer
146.098
2-OXOGLUTARIC ACID
1
syn
non-polymer
18.015
water
246
nat
water
no
yes
(DT)(MA7)(DT)
TAT
B
polydeoxyribonucleotide
no
no
MQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWP
AMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLL
EHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKENLYFQ
MQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWP
AMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLL
EHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKENLYFQ
A
ER126
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
Escherichia coli
K-12
Escherichia
Escherichia coli
sample
alkB, aidD
83333
Escherichia coli K12
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pET26
1
2.03
39.43
VAPOR DIFFUSION, HANGING DROP
22-24% (w/v) PEG 3350, 10% glycerol and 200 mM sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
Northeast Structural Genomics Consortium
NESG
PSI, Protein Structure Initiative
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2006-02-21
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2023-08-30
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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_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.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_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The same protein complexed with Fe(II), 2-oxoglutarate, and methylated trinucleotide
Y
RCSB
Y
RCSB
2005-12-13
REL
REL
CO
COBALT (II) ION
AKG
2-OXOGLUTARIC ACID
HOH
water
2FD8
PDB ENTRY 2FD8
PDB
experimental model
CO
300
3
CO
CO
300
A
AKG
400
4
AKG
AKG
400
A
HOH
602
5
HOH
HOH
602
B
HOH
603
5
HOH
HOH
603
B
HOH
622
5
HOH
HOH
622
B
HOH
638
5
HOH
HOH
638
B
HOH
640
5
HOH
HOH
640
B
HOH
656
5
HOH
HOH
656
B
HOH
663
5
HOH
HOH
663
B
HOH
699
5
HOH
HOH
699
B
HOH
701
5
HOH
HOH
701
B
HOH
721
5
HOH
HOH
721
B
HOH
723
5
HOH
HOH
723
B
HOH
742
5
HOH
HOH
742
B
HOH
799
5
HOH
HOH
799
B
HOH
825
5
HOH
HOH
825
B
HOH
601
5
HOH
HOH
601
A
HOH
604
5
HOH
HOH
604
A
HOH
605
5
HOH
HOH
605
A
HOH
606
5
HOH
HOH
606
A
HOH
607
5
HOH
HOH
607
A
HOH
608
5
HOH
HOH
608
A
HOH
609
5
HOH
HOH
609
A
HOH
610
5
HOH
HOH
610
A
HOH
611
5
HOH
HOH
611
A
HOH
612
5
HOH
HOH
612
A
HOH
613
5
HOH
HOH
613
A
HOH
614
5
HOH
HOH
614
A
HOH
615
5
HOH
HOH
615
A
HOH
616
5
HOH
HOH
616
A
HOH
617
5
HOH
HOH
617
A
HOH
618
5
HOH
HOH
618
A
HOH
619
5
HOH
HOH
619
A
HOH
620
5
HOH
HOH
620
A
HOH
621
5
HOH
HOH
621
A
HOH
623
5
HOH
HOH
623
A
HOH
624
5
HOH
HOH
624
A
HOH
625
5
HOH
HOH
625
A
HOH
626
5
HOH
HOH
626
A
HOH
627
5
HOH
HOH
627
A
HOH
628
5
HOH
HOH
628
A
HOH
629
5
HOH
HOH
629
A
HOH
630
5
HOH
HOH
630
A
HOH
631
5
HOH
HOH
631
A
HOH
632
5
HOH
HOH
632
A
HOH
633
5
HOH
HOH
633
A
HOH
634
5
HOH
HOH
634
A
HOH
635
5
HOH
HOH
635
A
HOH
636
5
HOH
HOH
636
A
HOH
637
5
HOH
HOH
637
A
HOH
639
5
HOH
HOH
639
A
HOH
641
5
HOH
HOH
641
A
HOH
642
5
HOH
HOH
642
A
HOH
643
5
HOH
HOH
643
A
HOH
644
5
HOH
HOH
644
A
HOH
645
5
HOH
HOH
645
A
HOH
646
5
HOH
HOH
646
A
HOH
647
5
HOH
HOH
647
A
HOH
648
5
HOH
HOH
648
A
HOH
649
5
HOH
HOH
649
A
HOH
650
5
HOH
HOH
650
A
HOH
651
5
HOH
HOH
651
A
HOH
652
5
HOH
HOH
652
A
HOH
653
5
HOH
HOH
653
A
HOH
654
5
HOH
HOH
654
A
HOH
655
5
HOH
HOH
655
A
HOH
657
5
HOH
HOH
657
A
HOH
658
5
HOH
HOH
658
A
HOH
659
5
HOH
HOH
659
A
HOH
660
5
HOH
HOH
660
A
HOH
661
5
HOH
HOH
661
A
HOH
662
5
HOH
HOH
662
A
HOH
664
5
HOH
HOH
664
A
HOH
665
5
HOH
HOH
665
A
HOH
666
5
HOH
HOH
666
A
HOH
667
5
HOH
HOH
667
A
HOH
668
5
HOH
HOH
668
A
HOH
669
5
HOH
HOH
669
A
HOH
670
5
HOH
HOH
670
A
HOH
671
5
HOH
HOH
671
A
HOH
672
5
HOH
HOH
672
A
HOH
673
5
HOH
HOH
673
A
HOH
674
5
HOH
HOH
674
A
HOH
675
5
HOH
HOH
675
A
HOH
676
5
HOH
HOH
676
A
HOH
677
5
HOH
HOH
677
A
HOH
678
5
HOH
HOH
678
A
HOH
679
5
HOH
HOH
679
A
HOH
680
5
HOH
HOH
680
A
HOH
681
5
HOH
HOH
681
A
HOH
682
5
HOH
HOH
682
A
HOH
683
5
HOH
HOH
683
A
HOH
684
5
HOH
HOH
684
A
HOH
685
5
HOH
HOH
685
A
HOH
686
5
HOH
HOH
686
A
HOH
687
5
HOH
HOH
687
A
HOH
688
5
HOH
HOH
688
A
HOH
689
5
HOH
HOH
689
A
HOH
690
5
HOH
HOH
690
A
HOH
691
5
HOH
HOH
691
A
HOH
692
5
HOH
HOH
692
A
HOH
693
5
HOH
HOH
693
A
HOH
694
5
HOH
HOH
694
A
HOH
695
5
HOH
HOH
695
A
HOH
696
5
HOH
HOH
696
A
HOH
697
5
HOH
HOH
697
A
HOH
698
5
HOH
HOH
698
A
HOH
700
5
HOH
HOH
700
A
HOH
702
5
HOH
HOH
702
A
HOH
703
5
HOH
HOH
703
A
HOH
704
5
HOH
HOH
704
A
HOH
705
5
HOH
HOH
705
A
HOH
706
5
HOH
HOH
706
A
HOH
707
5
HOH
HOH
707
A
HOH
708
5
HOH
HOH
708
A
HOH
709
5
HOH
HOH
709
A
HOH
710
5
HOH
HOH
710
A
HOH
711
5
HOH
HOH
711
A
HOH
712
5
HOH
HOH
712
A
HOH
713
5
HOH
HOH
713
A
HOH
714
5
HOH
HOH
714
A
HOH
715
5
HOH
HOH
715
A
HOH
716
5
HOH
HOH
716
A
HOH
717
5
HOH
HOH
717
A
HOH
718
5
HOH
HOH
718
A
HOH
719
5
HOH
HOH
719
A
HOH
720
5
HOH
HOH
720
A
HOH
722
5
HOH
HOH
722
A
HOH
724
5
HOH
HOH
724
A
HOH
725
5
HOH
HOH
725
A
HOH
726
5
HOH
HOH
726
A
HOH
727
5
HOH
HOH
727
A
HOH
728
5
HOH
HOH
728
A
HOH
729
5
HOH
HOH
729
A
HOH
730
5
HOH
HOH
730
A
HOH
731
5
HOH
HOH
731
A
HOH
732
5
HOH
HOH
732
A
HOH
733
5
HOH
HOH
733
A
HOH
734
5
HOH
HOH
734
A
HOH
735
5
HOH
HOH
735
A
HOH
736
5
HOH
HOH
736
A
HOH
737
5
HOH
HOH
737
A
HOH
738
5
HOH
HOH
738
A
HOH
739
5
HOH
HOH
739
A
HOH
740
5
HOH
HOH
740
A
HOH
741
5
HOH
HOH
741
A
HOH
743
5
HOH
HOH
743
A
HOH
744
5
HOH
HOH
744
A
HOH
745
5
HOH
HOH
745
A
HOH
746
5
HOH
HOH
746
A
HOH
747
5
HOH
HOH
747
A
HOH
748
5
HOH
HOH
748
A
HOH
749
5
HOH
HOH
749
A
HOH
750
5
HOH
HOH
750
A
HOH
751
5
HOH
HOH
751
A
HOH
752
5
HOH
HOH
752
A
HOH
753
5
HOH
HOH
753
A
HOH
754
5
HOH
HOH
754
A
HOH
755
5
HOH
HOH
755
A
HOH
756
5
HOH
HOH
756
A
HOH
757
5
HOH
HOH
757
A
HOH
758
5
HOH
HOH
758
A
HOH
759
5
HOH
HOH
759
A
HOH
760
5
HOH
HOH
760
A
HOH
761
5
HOH
HOH
761
A
HOH
762
5
HOH
HOH
762
A
HOH
763
5
HOH
HOH
763
A
HOH
764
5
HOH
HOH
764
A
HOH
765
5
HOH
HOH
765
A
HOH
766
5
HOH
HOH
766
A
HOH
767
5
HOH
HOH
767
A
HOH
768
5
HOH
HOH
768
A
HOH
769
5
HOH
HOH
769
A
HOH
770
5
HOH
HOH
770
A
HOH
771
5
HOH
HOH
771
A
HOH
772
5
HOH
HOH
772
A
HOH
773
5
HOH
HOH
773
A
HOH
774
5
HOH
HOH
774
A
HOH
775
5
HOH
HOH
775
A
HOH
776
5
HOH
HOH
776
A
HOH
777
5
HOH
HOH
777
A
HOH
778
5
HOH
HOH
778
A
HOH
779
5
HOH
HOH
779
A
HOH
780
5
HOH
HOH
780
A
HOH
781
5
HOH
HOH
781
A
HOH
782
5
HOH
HOH
782
A
HOH
783
5
HOH
HOH
783
A
HOH
784
5
HOH
HOH
784
A
HOH
785
5
HOH
HOH
785
A
HOH
786
5
HOH
HOH
786
A
HOH
787
5
HOH
HOH
787
A
HOH
788
5
HOH
HOH
788
A
HOH
789
5
HOH
HOH
789
A
HOH
790
5
HOH
HOH
790
A
HOH
791
5
HOH
HOH
791
A
HOH
792
5
HOH
HOH
792
A
HOH
793
5
HOH
HOH
793
A
HOH
794
5
HOH
HOH
794
A
HOH
795
5
HOH
HOH
795
A
HOH
796
5
HOH
HOH
796
A
HOH
797
5
HOH
HOH
797
A
HOH
798
5
HOH
HOH
798
A
HOH
800
5
HOH
HOH
800
A
HOH
801
5
HOH
HOH
801
A
HOH
802
5
HOH
HOH
802
A
HOH
803
5
HOH
HOH
803
A
HOH
804
5
HOH
HOH
804
A
HOH
805
5
HOH
HOH
805
A
HOH
806
5
HOH
HOH
806
A
HOH
807
5
HOH
HOH
807
A
HOH
808
5
HOH
HOH
808
A
HOH
809
5
HOH
HOH
809
A
HOH
810
5
HOH
HOH
810
A
HOH
811
5
HOH
HOH
811
A
HOH
812
5
HOH
HOH
812
A
HOH
813
5
HOH
HOH
813
A
HOH
814
5
HOH
HOH
814
A
HOH
815
5
HOH
HOH
815
A
HOH
816
5
HOH
HOH
816
A
HOH
817
5
HOH
HOH
817
A
HOH
818
5
HOH
HOH
818
A
HOH
819
5
HOH
HOH
819
A
HOH
820
5
HOH
HOH
820
A
HOH
821
5
HOH
HOH
821
A
HOH
822
5
HOH
HOH
822
A
HOH
823
5
HOH
HOH
823
A
HOH
824
5
HOH
HOH
824
A
HOH
826
5
HOH
HOH
826
A
HOH
827
5
HOH
HOH
827
A
HOH
828
5
HOH
HOH
828
A
HOH
829
5
HOH
HOH
829
A
HOH
830
5
HOH
HOH
830
A
HOH
831
5
HOH
HOH
831
A
HOH
832
5
HOH
HOH
832
A
HOH
833
5
HOH
HOH
833
A
HOH
834
5
HOH
HOH
834
A
HOH
835
5
HOH
HOH
835
A
HOH
836
5
HOH
HOH
836
A
HOH
837
5
HOH
HOH
837
A
HOH
838
5
HOH
HOH
838
A
HOH
839
5
HOH
HOH
839
A
HOH
840
5
HOH
HOH
840
A
HOH
841
5
HOH
HOH
841
A
HOH
842
5
HOH
HOH
842
A
HOH
843
5
HOH
HOH
843
A
HOH
844
5
HOH
HOH
844
A
HOH
845
5
HOH
HOH
845
A
HOH
846
5
HOH
HOH
846
A
T
501
n
1
DT
501
B
MA7
502
n
2
MA7
502
B
T
503
n
3
DT
503
B
n
1
11
A
n
2
12
A
n
3
13
A
n
4
14
A
LEU
15
n
5
LEU
15
A
ALA
16
n
6
ALA
16
A
ALA
17
n
7
ALA
17
A
GLY
18
n
8
GLY
18
A
ALA
19
n
9
ALA
19
A
VAL
20
n
10
VAL
20
A
ILE
21
n
11
ILE
21
A
LEU
22
n
12
LEU
22
A
ARG
23
n
13
ARG
23
A
ARG
24
n
14
ARG
24
A
PHE
25
n
15
PHE
25
A
ALA
26
n
16
ALA
26
A
PHE
27
n
17
PHE
27
A
ASN
28
n
18
ASN
28
A
ALA
29
n
19
ALA
29
A
ALA
30
n
20
ALA
30
A
GLU
31
n
21
GLU
31
A
GLN
32
n
22
GLN
32
A
LEU
33
n
23
LEU
33
A
ILE
34
n
24
ILE
34
A
ARG
35
n
25
ARG
35
A
ASP
36
n
26
ASP
36
A
ILE
37
n
27
ILE
37
A
ASN
38
n
28
ASN
38
A
ASP
39
n
29
ASP
39
A
VAL
40
n
30
VAL
40
A
ALA
41
n
31
ALA
41
A
SER
42
n
32
SER
42
A
GLN
43
n
33
GLN
43
A
SER
44
n
34
SER
44
A
PRO
45
n
35
PRO
45
A
PHE
46
n
36
PHE
46
A
ARG
47
n
37
ARG
47
A
GLN
48
n
38
GLN
48
A
MET
49
n
39
MET
49
A
VAL
50
n
40
VAL
50
A
THR
51
n
41
THR
51
A
PRO
52
n
42
PRO
52
A
GLY
53
n
43
GLY
53
A
GLY
54
n
44
GLY
54
A
TYR
55
n
45
TYR
55
A
THR
56
n
46
THR
56
A
MET
57
n
47
MET
57
A
SER
58
n
48
SER
58
A
VAL
59
n
49
VAL
59
A
ALA
60
n
50
ALA
60
A
MET
61
n
51
MET
61
A
THR
62
n
52
THR
62
A
ASN
63
n
53
ASN
63
A
CYS
64
n
54
CYS
64
A
GLY
65
n
55
GLY
65
A
HIS
66
n
56
HIS
66
A
LEU
67
n
57
LEU
67
A
GLY
68
n
58
GLY
68
A
TRP
69
n
59
TRP
69
A
THR
70
n
60
THR
70
A
THR
71
n
61
THR
71
A
HIS
72
n
62
HIS
72
A
ARG
73
n
63
ARG
73
A
GLN
74
n
64
GLN
74
A
GLY
75
n
65
GLY
75
A
TYR
76
n
66
TYR
76
A
LEU
77
n
67
LEU
77
A
TYR
78
n
68
TYR
78
A
SER
79
n
69
SER
79
A
PRO
80
n
70
PRO
80
A
ILE
81
n
71
ILE
81
A
ASP
82
n
72
ASP
82
A
PRO
83
n
73
PRO
83
A
GLN
84
n
74
GLN
84
A
THR
85
n
75
THR
85
A
ASN
86
n
76
ASN
86
A
LYS
87
n
77
LYS
87
A
PRO
88
n
78
PRO
88
A
TRP
89
n
79
TRP
89
A
PRO
90
n
80
PRO
90
A
ALA
91
n
81
ALA
91
A
MET
92
n
82
MET
92
A
PRO
93
n
83
PRO
93
A
GLN
94
n
84
GLN
94
A
SER
95
n
85
SER
95
A
PHE
96
n
86
PHE
96
A
HIS
97
n
87
HIS
97
A
ASN
98
n
88
ASN
98
A
LEU
99
n
89
LEU
99
A
CYS
100
n
90
CYS
100
A
GLN
101
n
91
GLN
101
A
ARG
102
n
92
ARG
102
A
ALA
103
n
93
ALA
103
A
ALA
104
n
94
ALA
104
A
THR
105
n
95
THR
105
A
ALA
106
n
96
ALA
106
A
ALA
107
n
97
ALA
107
A
GLY
108
n
98
GLY
108
A
TYR
109
n
99
TYR
109
A
PRO
110
n
100
PRO
110
A
ASP
111
n
101
ASP
111
A
PHE
112
n
102
PHE
112
A
GLN
113
n
103
GLN
113
A
PRO
114
n
104
PRO
114
A
ASP
115
n
105
ASP
115
A
ALA
116
n
106
ALA
116
A
CYS
117
n
107
CYS
117
A
LEU
118
n
108
LEU
118
A
ILE
119
n
109
ILE
119
A
ASN
120
n
110
ASN
120
A
ARG
121
n
111
ARG
121
A
TYR
122
n
112
TYR
122
A
ALA
123
n
113
ALA
123
A
PRO
124
n
114
PRO
124
A
GLY
125
n
115
GLY
125
A
ALA
126
n
116
ALA
126
A
LYS
127
n
117
LYS
127
A
LEU
128
n
118
LEU
128
A
SER
129
n
119
SER
129
A
LEU
130
n
120
LEU
130
A
HIS
131
n
121
HIS
131
A
GLN
132
n
122
GLN
132
A
ASP
133
n
123
ASP
133
A
LYS
134
n
124
LYS
134
A
ASP
135
n
125
ASP
135
A
GLU
136
n
126
GLU
136
A
PRO
137
n
127
PRO
137
A
ASP
138
n
128
ASP
138
A
LEU
139
n
129
LEU
139
A
ARG
140
n
130
ARG
140
A
ALA
141
n
131
ALA
141
A
PRO
142
n
132
PRO
142
A
ILE
143
n
133
ILE
143
A
VAL
144
n
134
VAL
144
A
SER
145
n
135
SER
145
A
VAL
146
n
136
VAL
146
A
SER
147
n
137
SER
147
A
LEU
148
n
138
LEU
148
A
GLY
149
n
139
GLY
149
A
LEU
150
n
140
LEU
150
A
PRO
151
n
141
PRO
151
A
ALA
152
n
142
ALA
152
A
ILE
153
n
143
ILE
153
A
PHE
154
n
144
PHE
154
A
GLN
155
n
145
GLN
155
A
PHE
156
n
146
PHE
156
A
GLY
157
n
147
GLY
157
A
GLY
158
n
148
GLY
158
A
LEU
159
n
149
LEU
159
A
LYS
160
n
150
LYS
160
A
ARG
161
n
151
ARG
161
A
ASN
162
n
152
ASN
162
A
ASP
163
n
153
ASP
163
A
PRO
164
n
154
PRO
164
A
LEU
165
n
155
LEU
165
A
LYS
166
n
156
LYS
166
A
ARG
167
n
157
ARG
167
A
LEU
168
n
158
LEU
168
A
LEU
169
n
159
LEU
169
A
LEU
170
n
160
LEU
170
A
GLU
171
n
161
GLU
171
A
HIS
172
n
162
HIS
172
A
GLY
173
n
163
GLY
173
A
ASP
174
n
164
ASP
174
A
VAL
175
n
165
VAL
175
A
VAL
176
n
166
VAL
176
A
VAL
177
n
167
VAL
177
A
TRP
178
n
168
TRP
178
A
GLY
179
n
169
GLY
179
A
GLY
180
n
170
GLY
180
A
GLU
181
n
171
GLU
181
A
SER
182
n
172
SER
182
A
ARG
183
n
173
ARG
183
A
LEU
184
n
174
LEU
184
A
PHE
185
n
175
PHE
185
A
TYR
186
n
176
TYR
186
A
HIS
187
n
177
HIS
187
A
GLY
188
n
178
GLY
188
A
ILE
189
n
179
ILE
189
A
GLN
190
n
180
GLN
190
A
PRO
191
n
181
PRO
191
A
LEU
192
n
182
LEU
192
A
LYS
193
n
183
LYS
193
A
ALA
194
n
184
ALA
194
A
GLY
195
n
185
GLY
195
A
PHE
196
n
186
PHE
196
A
HIS
197
n
187
HIS
197
A
PRO
198
n
188
PRO
198
A
LEU
199
n
189
LEU
199
A
THR
200
n
190
THR
200
A
ILE
201
n
191
ILE
201
A
ASP
202
n
192
ASP
202
A
CYS
203
n
193
CYS
203
A
ARG
204
n
194
ARG
204
A
TYR
205
n
195
TYR
205
A
ASN
206
n
196
ASN
206
A
LEU
207
n
197
LEU
207
A
THR
208
n
198
THR
208
A
PHE
209
n
199
PHE
209
A
ARG
210
n
200
ARG
210
A
GLN
211
n
201
GLN
211
A
ALA
212
n
202
ALA
212
A
GLY
213
n
203
GLY
213
A
LYS
214
n
204
LYS
214
A
n
205
215
A
n
206
216
A
n
207
217
A
n
208
218
A
n
209
219
A
n
210
220
A
n
211
221
A
author_defined_assembly
2
dimeric
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
A
ASP
133
B
OD1
ASP
123
1_555
95.6
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
A
HIS
187
B
NE2
HIS
177
1_555
97.1
A
ASP
133
B
OD1
ASP
123
1_555
A
CO
300
C
CO
CO
1_555
A
HIS
187
B
NE2
HIS
177
1_555
91.3
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O2
AKG
1_555
94.2
A
ASP
133
B
OD1
ASP
123
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O2
AKG
1_555
95.1
A
HIS
187
B
NE2
HIS
177
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O2
AKG
1_555
166.4
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O5
AKG
1_555
95.7
A
ASP
133
B
OD1
ASP
123
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O5
AKG
1_555
165.8
A
HIS
187
B
NE2
HIS
177
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O5
AKG
1_555
95.7
A
AKG
400
D
O2
AKG
1_555
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O5
AKG
1_555
75.6
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
172.5
A
ASP
133
B
OD1
ASP
123
1_555
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
90.9
A
HIS
187
B
NE2
HIS
177
1_555
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
86.3
A
AKG
400
D
O2
AKG
1_555
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
81.6
A
AKG
400
D
O5
AKG
1_555
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
77.3
B
MA7
502
1N-METHYLADENOSINE-5'-MONOPHOSPHATE
A
MA7
2
DA
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
LEU
22
B
N
LEU
12
A
O
VAL
175
B
O
VAL
165
A
O
VAL
176
B
O
VAL
166
A
N
SER
145
B
N
SER
135
A
N
VAL
144
B
N
VAL
134
A
O
PHE
209
B
O
PHE
199
A
O
ASN
206
B
O
ASN
196
A
N
ASN
120
B
N
ASN
110
A
O
ARG
121
B
O
ARG
111
A
N
ALA
60
B
N
ALA
50
A
N
THR
70
B
N
THR
60
A
O
LEU
77
B
O
LEU
67
A
N
LEU
128
B
N
LEU
118
A
O
ILE
189
B
O
ILE
179
A
O
GLY
188
B
O
GLY
178
A
N
GLN
155
B
N
GLN
145
A
N
PHE
154
B
N
PHE
144
A
O
LEU
168
B
O
LEU
158
1
A
CA
LYS
214
B
CA
LYS
204
1
Y
1
A
C
LYS
214
B
C
LYS
204
1
Y
1
A
O
LYS
214
B
O
LYS
204
1
Y
1
A
CB
LYS
214
B
CB
LYS
204
1
Y
1
A
CG
LYS
214
B
CG
LYS
204
1
Y
1
A
CD
LYS
214
B
CD
LYS
204
1
Y
1
A
CE
LYS
214
B
CE
LYS
204
1
Y
1
A
NZ
LYS
214
B
NZ
LYS
204
1
Y
1
A
MET
11
B
MET
1
1
Y
1
A
GLN
12
B
GLN
2
1
Y
1
A
GLU
13
B
GLU
3
1
Y
1
A
PRO
14
B
PRO
4
1
Y
1
A
LYS
215
B
LYS
205
1
Y
1
A
GLU
216
B
GLU
206
1
Y
1
A
ASN
217
B
ASN
207
1
Y
1
A
LEU
218
B
LEU
208
1
Y
1
A
TYR
219
B
TYR
209
1
Y
1
A
PHE
220
B
PHE
210
1
Y
1
A
GLN
221
B
GLN
211
1
Y
1
B
B
P
OP3
DT
DT
501
501
-0.087
0.012
1.607
1.520
N
1
A
ILE
201
65.30
-92.04
protein_rep.param
protein.top
water_rep.param
water.top
dna-rna_rep.param_by
dna-rna.top_by
ion.param
ion.top
18.400
0.390
0.000
0.000
0.390
0.000
-0.770
0.237
0.007
0.193
2.100
19.470
1174
11115
10.600
97.500
RANDOM
1645109.000
0.000
1
RESTRAINED
THROUGHOUT
1.00
MOLECULAR REPLACEMENT
PDB ENTRY 2FD8
FLAT MODEL
44.950
0.328
0.290
0.220
5.000
0.180
0.120
2.100
19.470
246
1876
11
63
1556
0.012
1.500
26.600
1.510
1.300
1.500
1.980
2.000
2.040
2.000
2.970
2.500
0.256
0.019
0.2
2.230
191
1541
1732
6
11.000
92.500
2.10
20.00
2FDF
11350
0.062
1.033
1
5.600
99.700
0.15
2.10
2.17
1104
1.186
1
3.100
96.800
0.135
2.17
2.26
1117
1.094
1
4.300
100.000
0.13
2.26
2.36
1154
1.092
1
5.900
100.000
0.118
2.36
2.49
1108
1.084
1
6.000
100.000
0.109
2.49
2.64
1140
1.089
1
6.100
99.900
0.084
2.64
2.85
1126
1.093
1
6.100
100.000
0.07
2.85
3.13
1145
1.095
1
6.100
100.000
0.05
3.13
3.59
1131
1.023
1
6.200
100.000
0.038
3.59
4.51
1162
0.848
1
6.200
100.000
0.033
4.51
20.00
1163
0.854
1
6.100
100.000
data reduction
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
DENZO
package
data scaling
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
SCALEPACK
package
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns.csb.yale.edu/v1.1/
CNS
package
1.1
data extraction
PDB
sw-help@rcsb.rutgers.edu
OCT. 28, 2005
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
1.701
phasing
COMO
Crystal Structure of AlkB in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
A
ALA
29
B
ALA
19
HELX_P
A
SER
44
B
SER
34
1
1
16
A
PRO
93
B
PRO
83
HELX_P
A
ALA
107
B
ALA
97
1
2
15
A
GLY
180
B
GLY
170
HELX_P
A
ARG
183
B
ARG
173
5
3
4
covale
1.610
both
B
DT
501
A
O3'
DT
1
1_555
B
MA7
502
A
P
MA7
2
1_555
covale
1.606
both
B
MA7
502
A
O3'
MA7
2
1_555
B
DT
503
A
P
DT
3
1_555
metalc
2.053
A
HIS
131
B
NE2
HIS
121
1_555
A
CO
300
C
CO
CO
1_555
metalc
2.277
A
ASP
133
B
OD1
ASP
123
1_555
A
CO
300
C
CO
CO
1_555
metalc
2.114
A
HIS
187
B
NE2
HIS
177
1_555
A
CO
300
C
CO
CO
1_555
metalc
2.158
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O2
AKG
1_555
metalc
2.273
A
CO
300
C
CO
CO
1_555
A
AKG
400
D
O5
AKG
1_555
metalc
2.728
A
CO
300
C
CO
CO
1_555
A
HOH
697
F
O
HOH
1_555
OXIDOREDUCTASE/DNA
beta jellyroll, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, OXIDOREDUCTASE-DNA COMPLEX
ALKB_ECOLI
UNP
2
12
P05050
QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPA
MPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLE
HGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKE
2FDF
PDB
1
2FDF
12
216
2FDF
12
216
P05050
A
1
2
206
501
503
2FDF
501
503
2FDF
B
2
1
3
1
initiating methionine
MET
11
2FDF
A
P05050
UNP
1
1
cloning artifact
ASN
217
2FDF
A
P05050
UNP
207
1
cloning artifact
LEU
218
2FDF
A
P05050
UNP
208
1
cloning artifact
TYR
219
2FDF
A
P05050
UNP
209
1
cloning artifact
PHE
220
2FDF
A
P05050
UNP
210
1
cloning artifact
GLN
221
2FDF
A
P05050
UNP
211
6
2
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ALA
19
B
ALA
9
A
LEU
22
B
LEU
12
A
VAL
175
B
VAL
165
A
TRP
178
B
TRP
168
A
ILE
143
B
ILE
133
A
GLY
149
B
GLY
139
A
ARG
204
B
ARG
194
A
ARG
210
B
ARG
200
A
ALA
116
B
ALA
106
A
TYR
122
B
TYR
112
A
ALA
60
B
ALA
50
A
CYS
64
B
CYS
54
A
GLY
68
B
GLY
58
A
THR
71
B
THR
61
A
TYR
76
B
TYR
66
A
SER
79
B
SER
69
A
LEU
128
B
LEU
118
A
HIS
131
B
HIS
121
A
HIS
187
B
HIS
177
A
ILE
189
B
ILE
179
A
ALA
152
B
ALA
142
A
PHE
156
B
PHE
146
A
LYS
166
B
LYS
156
A
LEU
170
B
LEU
160
BINDING SITE FOR RESIDUE CO A 300
A
CO
300
Software
5
BINDING SITE FOR RESIDUE AKG A 400
A
AKG
400
Software
15
A
HIS
131
B
HIS
121
5
1_555
A
ASP
133
B
ASP
123
5
1_555
A
HIS
187
B
HIS
177
5
1_555
A
AKG
400
D
AKG
5
1_555
A
HOH
697
F
HOH
5
1_555
A
LEU
118
B
LEU
108
15
1_555
A
ASN
120
B
ASN
110
15
1_555
A
TYR
122
B
TYR
112
15
1_555
A
LEU
128
B
LEU
118
15
1_555
A
HIS
131
B
HIS
121
15
1_555
A
ASP
133
B
ASP
123
15
1_555
A
HIS
187
B
HIS
177
15
1_555
A
ILE
189
B
ILE
179
15
1_555
A
ARG
204
B
ARG
194
15
1_555
A
ASN
206
B
ASN
196
15
1_555
A
THR
208
B
THR
198
15
1_555
A
ARG
210
B
ARG
200
15
1_555
A
CO
300
C
CO
15
1_555
A
HOH
625
F
HOH
15
1_555
B
MA7
502
A
MA7
2
15
1_555
78
P 43