0.028706
0.000000
0.008014
0.000000
0.034819
0.000000
0.000000
0.000000
0.016388
0.00000
0.00000
0.00000
Mizohata, E.
Morita, Y.
Oohora, K.
Hirata, K.
Ohbayashi, J.
Inoue, T.
Hisaeda, Y.
Hayashi, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
105.60
90.00
34.836
28.720
63.352
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
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
C33 H37 Co N4 O4 1
612.604
(1R,19R) cobalt tetradehydrocorrin
non-polymer
C33 H37 Co N4 O4 1
612.604
(1S,19S) cobalt tetradehydrocorrin
non-polymer
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
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
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
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
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
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
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
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
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
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
O
N
170
N
C
N
171
N
O
N
172
N
C
N
173
N
C
Y
174
N
C
Y
175
N
C
N
176
N
C
Y
177
N
C
Y
178
N
N
Y
179
N
C
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
N
N
184
N
CO
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
R
C
N
190
N
C
N
191
R
C
N
192
N
N
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
C
N
202
N
C
N
203
N
N
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
O
N
210
N
O
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
O
N
249
N
C
N
250
N
O
N
251
N
C
N
252
N
C
Y
253
N
C
Y
254
N
C
N
255
N
C
Y
256
N
C
Y
257
N
N
Y
258
N
C
N
259
N
C
N
260
N
C
N
261
N
C
N
262
N
N
N
263
N
CO
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
C
N
268
S
C
N
269
N
C
N
270
S
C
N
271
N
N
N
272
N
C
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
N
N
283
N
C
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
C
N
288
N
O
N
289
N
O
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
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
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
C
N
335
N
O
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
C
N
357
N
N
N
358
N
O
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
N
C
N
379
N
C
N
380
N
S
N
381
N
C
N
382
N
O
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
N
N
418
S
C
N
419
N
C
N
420
N
O
N
421
N
C
N
422
N
C
N
423
N
C
N
424
N
O
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
N
C
N
439
N
O
N
440
N
O
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
S
N
449
N
O
N
450
N
O
N
451
N
O
N
452
N
O
N
453
N
N
N
454
S
C
N
455
N
C
N
456
N
O
N
457
R
C
N
458
N
O
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
Y
475
N
C
Y
476
N
C
Y
477
N
C
Y
478
N
N
Y
479
N
C
Y
480
N
C
Y
481
N
C
Y
482
N
C
Y
483
N
C
N
484
N
O
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
N
N
498
S
C
N
499
N
C
N
500
N
O
N
501
N
C
Y
502
N
C
Y
503
N
C
Y
504
N
C
Y
505
N
C
Y
506
N
C
Y
507
N
C
N
508
N
O
N
509
N
O
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
N
N
522
S
C
N
523
N
C
N
524
N
O
N
525
N
C
N
526
N
C
N
527
N
C
N
528
N
O
N
529
N
H
N
530
N
H
N
531
N
H
N
532
N
H
N
533
N
H
N
534
N
H
N
535
N
H
N
536
N
H
N
537
N
H
N
538
N
H
N
539
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
doub
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
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
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
doub
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
doub
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
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
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
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
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
doub
N
167
N
sing
Y
168
N
sing
Y
169
N
doub
N
170
N
doub
N
171
N
sing
N
172
N
sing
N
173
N
doub
N
174
N
sing
Y
175
N
sing
Y
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
Y
183
N
sing
N
184
N
doub
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
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
doub
N
203
N
doub
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
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
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
doub
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
Y
254
N
sing
Y
255
N
doub
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
doub
Y
260
N
sing
N
261
N
sing
N
262
N
doub
Y
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
Y
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
doub
N
272
N
sing
N
273
N
sing
N
274
N
doub
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
N
280
N
sing
N
281
N
sing
N
282
N
doub
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
doub
N
289
N
sing
N
290
N
sing
N
291
N
doub
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
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
doub
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
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
doub
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
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
doub
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
Y
407
N
doub
Y
408
N
sing
Y
409
N
sing
N
410
N
sing
Y
411
N
doub
N
412
N
sing
Y
413
N
doub
N
414
N
sing
Y
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
doub
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
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
doub
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
doub
N
450
N
doub
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
doub
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
sing
N
473
N
sing
N
474
N
sing
N
475
N
doub
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
Y
480
N
doub
Y
481
N
sing
Y
482
N
sing
N
483
N
sing
Y
484
N
doub
Y
485
N
sing
Y
486
N
sing
N
487
N
sing
Y
488
N
sing
Y
489
N
doub
N
490
N
sing
Y
491
N
doub
N
492
N
sing
Y
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
sing
N
502
N
sing
N
503
N
doub
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
Y
508
N
doub
Y
509
N
sing
Y
510
N
sing
N
511
N
sing
Y
512
N
doub
N
513
N
sing
Y
514
N
doub
N
515
N
sing
Y
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
doub
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
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
sing
UK
Chem.Commun.(Camb.)
1359-7345
50
12560
12563
10.1039/c4cc05448b
25197974
Co(II)/Co(I) reduction-induced axial histidine-flipping in myoglobin reconstituted with a cobalt tetradehydrocorrin as a methionine synthase model.
2014
10.2210/pdb3wfu/pdb
pdb_00003wfu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2012-04-22
RAYONIX MX225HE
SINGLE WAVELENGTH
M
x-ray
1
0.90000
1.0
BL44XU
SPring-8
0.90000
SYNCHROTRON
SPRING-8 BEAMLINE BL44XU
16983.514
Myoglobin
1
nat
polymer
612.604
(1R,19R) cobalt tetradehydrocorrin
1
syn
non-polymer
612.604
(1S,19S) cobalt tetradehydrocorrin
1
syn
non-polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
130
nat
water
no
no
GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKG
HHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKG
HHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
domestic horse,equine
sample
9796
Equus caballus
1
1.80
31.56
VAPOR DIFFUSION, HANGING DROP
7.4
0.1M Tris-HCl, 3.4M ammonium sulfate, 10% treharose, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
1
0
2014-12-03
1
1
2024-03-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The same protein in different redox state.
PDBJ
Y
PDBJ
2013-07-23
REL
REL
J1R
(1R,19R) cobalt tetradehydrocorrin
J1S
(1S,19S) cobalt tetradehydrocorrin
SO4
SULFATE ION
HOH
water
THE COBALT COMPLEX J1R, J1S ARE CHARACTERIZED BY TETRA-COORDINATE CO IN 1+ OXIDATION STATE, AS CONFIRMED BY UV-VIS AND EPR SPECTROSCOPY.
J1R AND J1S ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.
CRC
1001
2
J1R
J1R
1001
A
CSC
1002
3
J1S
J1S
1002
A
SO4
1156
4
SO4
SO4
1003
A
SO4
1157
4
SO4
SO4
1004
A
HOH
1
5
HOH
HOH
1101
A
HOH
2
5
HOH
HOH
1102
A
HOH
3
5
HOH
HOH
1103
A
HOH
4
5
HOH
HOH
1104
A
HOH
5
5
HOH
HOH
1105
A
HOH
6
5
HOH
HOH
1106
A
HOH
7
5
HOH
HOH
1107
A
HOH
8
5
HOH
HOH
1108
A
HOH
9
5
HOH
HOH
1109
A
HOH
10
5
HOH
HOH
1110
A
HOH
11
5
HOH
HOH
1111
A
HOH
12
5
HOH
HOH
1112
A
HOH
13
5
HOH
HOH
1113
A
HOH
14
5
HOH
HOH
1114
A
HOH
15
5
HOH
HOH
1115
A
HOH
16
5
HOH
HOH
1116
A
HOH
17
5
HOH
HOH
1117
A
HOH
18
5
HOH
HOH
1118
A
HOH
19
5
HOH
HOH
1119
A
HOH
20
5
HOH
HOH
1120
A
HOH
21
5
HOH
HOH
1121
A
HOH
22
5
HOH
HOH
1122
A
HOH
23
5
HOH
HOH
1123
A
HOH
24
5
HOH
HOH
1124
A
HOH
25
5
HOH
HOH
1125
A
HOH
26
5
HOH
HOH
1126
A
HOH
27
5
HOH
HOH
1127
A
HOH
28
5
HOH
HOH
1128
A
HOH
29
5
HOH
HOH
1129
A
HOH
30
5
HOH
HOH
1130
A
HOH
31
5
HOH
HOH
1131
A
HOH
32
5
HOH
HOH
1132
A
HOH
33
5
HOH
HOH
1133
A
HOH
34
5
HOH
HOH
1134
A
HOH
35
5
HOH
HOH
1135
A
HOH
36
5
HOH
HOH
1136
A
HOH
37
5
HOH
HOH
1137
A
HOH
38
5
HOH
HOH
1138
A
HOH
39
5
HOH
HOH
1139
A
HOH
40
5
HOH
HOH
1140
A
HOH
41
5
HOH
HOH
1141
A
HOH
42
5
HOH
HOH
1142
A
HOH
43
5
HOH
HOH
1143
A
HOH
44
5
HOH
HOH
1144
A
HOH
45
5
HOH
HOH
1145
A
HOH
46
5
HOH
HOH
1146
A
HOH
47
5
HOH
HOH
1147
A
HOH
48
5
HOH
HOH
1148
A
HOH
49
5
HOH
HOH
1149
A
HOH
50
5
HOH
HOH
1150
A
HOH
51
5
HOH
HOH
1151
A
HOH
52
5
HOH
HOH
1152
A
HOH
53
5
HOH
HOH
1153
A
HOH
54
5
HOH
HOH
1154
A
HOH
55
5
HOH
HOH
1155
A
HOH
56
5
HOH
HOH
1156
A
HOH
57
5
HOH
HOH
1157
A
HOH
58
5
HOH
HOH
1158
A
HOH
59
5
HOH
HOH
1159
A
HOH
60
5
HOH
HOH
1160
A
HOH
61
5
HOH
HOH
1161
A
HOH
62
5
HOH
HOH
1162
A
HOH
63
5
HOH
HOH
1163
A
HOH
64
5
HOH
HOH
1164
A
HOH
65
5
HOH
HOH
1165
A
HOH
66
5
HOH
HOH
1166
A
HOH
67
5
HOH
HOH
1167
A
HOH
68
5
HOH
HOH
1168
A
HOH
69
5
HOH
HOH
1169
A
HOH
70
5
HOH
HOH
1170
A
HOH
71
5
HOH
HOH
1171
A
HOH
72
5
HOH
HOH
1172
A
HOH
73
5
HOH
HOH
1173
A
HOH
74
5
HOH
HOH
1174
A
HOH
75
5
HOH
HOH
1175
A
HOH
76
5
HOH
HOH
1176
A
HOH
77
5
HOH
HOH
1177
A
HOH
78
5
HOH
HOH
1178
A
HOH
79
5
HOH
HOH
1179
A
HOH
80
5
HOH
HOH
1180
A
HOH
81
5
HOH
HOH
1181
A
HOH
82
5
HOH
HOH
1182
A
HOH
83
5
HOH
HOH
1183
A
HOH
84
5
HOH
HOH
1184
A
HOH
85
5
HOH
HOH
1185
A
HOH
86
5
HOH
HOH
1186
A
HOH
87
5
HOH
HOH
1187
A
HOH
88
5
HOH
HOH
1188
A
HOH
89
5
HOH
HOH
1189
A
HOH
90
5
HOH
HOH
1190
A
HOH
91
5
HOH
HOH
1191
A
HOH
92
5
HOH
HOH
1192
A
HOH
93
5
HOH
HOH
1193
A
HOH
94
5
HOH
HOH
1194
A
HOH
95
5
HOH
HOH
1195
A
HOH
96
5
HOH
HOH
1196
A
HOH
97
5
HOH
HOH
1197
A
HOH
98
5
HOH
HOH
1198
A
HOH
99
5
HOH
HOH
1199
A
HOH
100
5
HOH
HOH
1200
A
HOH
101
5
HOH
HOH
1201
A
HOH
102
5
HOH
HOH
1202
A
HOH
103
5
HOH
HOH
1203
A
HOH
104
5
HOH
HOH
1204
A
HOH
105
5
HOH
HOH
1205
A
HOH
106
5
HOH
HOH
1206
A
HOH
107
5
HOH
HOH
1207
A
HOH
108
5
HOH
HOH
1208
A
HOH
109
5
HOH
HOH
1209
A
HOH
110
5
HOH
HOH
1210
A
HOH
111
5
HOH
HOH
1211
A
HOH
112
5
HOH
HOH
1212
A
HOH
113
5
HOH
HOH
1213
A
HOH
114
5
HOH
HOH
1214
A
HOH
115
5
HOH
HOH
1215
A
HOH
116
5
HOH
HOH
1216
A
HOH
117
5
HOH
HOH
1217
A
HOH
118
5
HOH
HOH
1218
A
HOH
119
5
HOH
HOH
1219
A
HOH
120
5
HOH
HOH
1220
A
HOH
121
5
HOH
HOH
1221
A
HOH
122
5
HOH
HOH
1222
A
HOH
123
5
HOH
HOH
1223
A
HOH
124
5
HOH
HOH
1224
A
HOH
125
5
HOH
HOH
1225
A
HOH
126
5
HOH
HOH
1226
A
HOH
127
5
HOH
HOH
1227
A
HOH
128
5
HOH
HOH
1228
A
HOH
129
5
HOH
HOH
1229
A
HOH
130
5
HOH
HOH
1230
A
GLY
1
n
1
GLY
1
A
LEU
2
n
2
LEU
2
A
SER
3
n
3
SER
3
A
ASP
4
n
4
ASP
4
A
GLY
5
n
5
GLY
5
A
GLU
6
n
6
GLU
6
A
TRP
7
n
7
TRP
7
A
GLN
8
n
8
GLN
8
A
GLN
9
n
9
GLN
9
A
VAL
10
n
10
VAL
10
A
LEU
11
n
11
LEU
11
A
ASN
12
n
12
ASN
12
A
VAL
13
n
13
VAL
13
A
TRP
14
n
14
TRP
14
A
GLY
15
n
15
GLY
15
A
LYS
16
n
16
LYS
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
ALA
19
n
19
ALA
19
A
ASP
20
n
20
ASP
20
A
ILE
21
n
21
ILE
21
A
ALA
22
n
22
ALA
22
A
GLY
23
n
23
GLY
23
A
HIS
24
n
24
HIS
24
A
GLY
25
n
25
GLY
25
A
GLN
26
n
26
GLN
26
A
GLU
27
n
27
GLU
27
A
VAL
28
n
28
VAL
28
A
LEU
29
n
29
LEU
29
A
ILE
30
n
30
ILE
30
A
ARG
31
n
31
ARG
31
A
LEU
32
n
32
LEU
32
A
PHE
33
n
33
PHE
33
A
THR
34
n
34
THR
34
A
GLY
35
n
35
GLY
35
A
HIS
36
n
36
HIS
36
A
PRO
37
n
37
PRO
37
A
GLU
38
n
38
GLU
38
A
THR
39
n
39
THR
39
A
LEU
40
n
40
LEU
40
A
GLU
41
n
41
GLU
41
A
LYS
42
n
42
LYS
42
A
PHE
43
n
43
PHE
43
A
ASP
44
n
44
ASP
44
A
LYS
45
n
45
LYS
45
A
PHE
46
n
46
PHE
46
A
LYS
47
n
47
LYS
47
A
HIS
48
n
48
HIS
48
A
LEU
49
n
49
LEU
49
A
LYS
50
n
50
LYS
50
A
THR
51
n
51
THR
51
A
GLU
52
n
52
GLU
52
A
ALA
53
n
53
ALA
53
A
GLU
54
n
54
GLU
54
A
MET
55
n
55
MET
55
A
LYS
56
n
56
LYS
56
A
ALA
57
n
57
ALA
57
A
SER
58
n
58
SER
58
A
GLU
59
n
59
GLU
59
A
ASP
60
n
60
ASP
60
A
LEU
61
n
61
LEU
61
A
LYS
62
n
62
LYS
62
A
LYS
63
n
63
LYS
63
A
HIS
64
n
64
HIS
64
A
GLY
65
n
65
GLY
65
A
THR
66
n
66
THR
66
A
VAL
67
n
67
VAL
67
A
VAL
68
n
68
VAL
68
A
LEU
69
n
69
LEU
69
A
THR
70
n
70
THR
70
A
ALA
71
n
71
ALA
71
A
LEU
72
n
72
LEU
72
A
GLY
73
n
73
GLY
73
A
GLY
74
n
74
GLY
74
A
ILE
75
n
75
ILE
75
A
LEU
76
n
76
LEU
76
A
LYS
77
n
77
LYS
77
A
LYS
78
n
78
LYS
78
A
LYS
79
n
79
LYS
79
A
GLY
80
n
80
GLY
80
A
HIS
81
n
81
HIS
81
A
HIS
82
n
82
HIS
82
A
GLU
83
n
83
GLU
83
A
ALA
84
n
84
ALA
84
A
GLU
85
n
85
GLU
85
A
LEU
86
n
86
LEU
86
A
LYS
87
n
87
LYS
87
A
PRO
88
n
88
PRO
88
A
LEU
89
n
89
LEU
89
A
ALA
90
n
90
ALA
90
A
GLN
91
n
91
GLN
91
A
SER
92
n
92
SER
92
A
HIS
93
n
93
HIS
93
A
ALA
94
n
94
ALA
94
A
THR
95
n
95
THR
95
A
LYS
96
n
96
LYS
96
A
HIS
97
n
97
HIS
97
A
LYS
98
n
98
LYS
98
A
ILE
99
n
99
ILE
99
A
PRO
100
n
100
PRO
100
A
ILE
101
n
101
ILE
101
A
LYS
102
n
102
LYS
102
A
TYR
103
n
103
TYR
103
A
LEU
104
n
104
LEU
104
A
GLU
105
n
105
GLU
105
A
PHE
106
n
106
PHE
106
A
ILE
107
n
107
ILE
107
A
SER
108
n
108
SER
108
A
ASP
109
n
109
ASP
109
A
ALA
110
n
110
ALA
110
A
ILE
111
n
111
ILE
111
A
ILE
112
n
112
ILE
112
A
HIS
113
n
113
HIS
113
A
VAL
114
n
114
VAL
114
A
LEU
115
n
115
LEU
115
A
HIS
116
n
116
HIS
116
A
SER
117
n
117
SER
117
A
LYS
118
n
118
LYS
118
A
HIS
119
n
119
HIS
119
A
PRO
120
n
120
PRO
120
A
GLY
121
n
121
GLY
121
A
ASP
122
n
122
ASP
122
A
PHE
123
n
123
PHE
123
A
GLY
124
n
124
GLY
124
A
ALA
125
n
125
ALA
125
A
ASP
126
n
126
ASP
126
A
ALA
127
n
127
ALA
127
A
GLN
128
n
128
GLN
128
A
GLY
129
n
129
GLY
129
A
ALA
130
n
130
ALA
130
A
MET
131
n
131
MET
131
A
THR
132
n
132
THR
132
A
LYS
133
n
133
LYS
133
A
ALA
134
n
134
ALA
134
A
LEU
135
n
135
LEU
135
A
GLU
136
n
136
GLU
136
A
LEU
137
n
137
LEU
137
A
PHE
138
n
138
PHE
138
A
ARG
139
n
139
ARG
139
A
ASN
140
n
140
ASN
140
A
ASP
141
n
141
ASP
141
A
ILE
142
n
142
ILE
142
A
ALA
143
n
143
ALA
143
A
ALA
144
n
144
ALA
144
A
LYS
145
n
145
LYS
145
A
TYR
146
n
146
TYR
146
A
LYS
147
n
147
LYS
147
A
GLU
148
n
148
GLU
148
A
LEU
149
n
149
LEU
149
A
GLY
150
n
150
GLY
150
A
PHE
151
n
151
PHE
151
A
GLN
152
n
152
GLN
152
A
n
153
153
A
0.1107
-0.0137
-0.0083
0.0086
0.0166
0.0941
0.0004
0.0036
0.0087
-0.0033
-0.0015
-0.0007
-0.0033
-0.0035
0.0011
0.0051
-0.0001
0.0027
0.0131
0.0002
0.0151
refined
12.9304
-4.7141
15.1023
X-RAY DIFFRACTION
A
1
A
152
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
1
monomeric
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
1
A
GLY
153
A
GLY
153
1
Y
1
A
A
O
O
HOH
HOH
1217
1218
1.93
1
A
A
OE1
O
GLN
HOH
152
1191
2.09
1
A
A
O2
O
SO4
HOH
1004
1175
2.09
1
-5.75
0.90
118.30
112.55
A
A
A
CB
CG
OD2
ASP
ASP
ASP
126
126
126
N
1
A
A
CB
CG
ARG
ARG
139
139
-0.176
0.027
1.521
1.345
N
1
A
ASP
20
-152.18
71.23
17.340
1.03
0.00
-0.17
-0.55
0.00
-0.57
0.974
0.960
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.19660
0.14292
0.14575
1.35
15.00
1279
24026
5.1
94.99
2.426
0.045
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.072
0.067
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
1.35
15.00
130
1418
94
0
1194
0.026
0.021
1336
3.000
2.056
1837
5.222
5.000
153
40.480
25.094
53
15.018
15.000
230
10.346
15.000
2
0.172
0.200
184
0.016
0.020
993
2.824
1.500
752
4.053
2.000
1198
5.943
3.000
584
7.909
4.500
638
3.237
3.000
1336
0.242
0.182
1.389
86
1679
20
90.89
1.35
50
3WFU
25415
0.037
1
28.9
2.7
95.2
1.35
1.40
4.0
0.221
1
92.2
data collection
BSS
phasing
MOLREP
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of horse heart myoglobin reconstituted with cobalt(I) tetradehydrocorrin
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
A
SER
3
A
SER
3
HELX_P
A
ALA
19
A
ALA
19
1
1
17
A
ASP
20
A
ASP
20
HELX_P
A
HIS
36
A
HIS
36
1
2
17
A
HIS
36
A
HIS
36
HELX_P
A
GLU
41
A
GLU
41
1
3
6
A
THR
51
A
THR
51
HELX_P
A
SER
58
A
SER
58
1
4
8
A
SER
58
A
SER
58
HELX_P
A
LYS
77
A
LYS
77
1
5
20
A
HIS
82
A
HIS
82
HELX_P
A
LYS
96
A
LYS
96
1
6
15
A
PRO
100
A
PRO
100
HELX_P
A
HIS
119
A
HIS
119
1
7
20
A
GLY
124
A
GLY
124
HELX_P
A
GLY
150
A
GLY
150
1
8
27
OXYGEN TRANSPORT
globin fold, Oxygen transport, muscles
MYG_HORSE
UNP
1
2
P68082
GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKG
HHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG
2
154
3WFU
1
153
P68082
A
1
1
153
BINDING SITE FOR RESIDUE J1R A 1001
A
J1R
1001
Software
15
BINDING SITE FOR RESIDUE J1S A 1002
A
J1S
1002
Software
16
BINDING SITE FOR RESIDUE SO4 A 1003
A
SO4
1003
Software
4
BINDING SITE FOR RESIDUE SO4 A 1004
A
SO4
1004
Software
4
A
LYS
42
A
LYS
42
15
1_555
A
PHE
43
A
PHE
43
15
1_555
A
LYS
45
A
LYS
45
15
1_555
A
HIS
64
A
HIS
64
15
1_555
A
VAL
67
A
VAL
67
15
1_555
A
SER
92
A
SER
92
15
1_555
A
HIS
93
A
HIS
93
15
1_555
A
HIS
97
A
HIS
97
15
1_555
A
ILE
99
A
ILE
99
15
1_555
A
HIS
113
A
HIS
113
15
1_565
A
HIS
116
A
HIS
116
15
1_565
A
HOH
1135
F
HOH
15
1_555
A
HOH
1171
F
HOH
15
1_555
A
HOH
1211
F
HOH
15
1_555
A
HOH
1230
F
HOH
15
1_555
A
LYS
42
A
LYS
42
16
1_555
A
PHE
43
A
PHE
43
16
1_555
A
LYS
45
A
LYS
45
16
1_555
A
HIS
64
A
HIS
64
16
1_555
A
VAL
68
A
VAL
68
16
1_555
A
SER
92
A
SER
92
16
1_555
A
HIS
93
A
HIS
93
16
1_555
A
HIS
97
A
HIS
97
16
1_555
A
ILE
99
A
ILE
99
16
1_555
A
HIS
113
A
HIS
113
16
1_565
A
HIS
116
A
HIS
116
16
1_565
A
GLN
128
A
GLN
128
16
1_565
A
HOH
1135
F
HOH
16
1_555
A
HOH
1171
F
HOH
16
1_555
A
HOH
1211
F
HOH
16
1_555
A
HOH
1230
F
HOH
16
1_555
A
LYS
50
A
LYS
50
4
1_555
A
THR
51
A
THR
51
4
1_555
A
GLU
52
A
GLU
52
4
1_555
A
HOH
1156
F
HOH
4
1_555
A
HIS
81
A
HIS
81
4
1_555
A
HIS
82
A
HIS
82
4
1_555
A
GLU
83
A
GLU
83
4
1_555
A
HOH
1175
F
HOH
4
1_555
4
P 1 21 1