0.011023
0.006364
0.000000
0.000000
0.012728
0.000000
0.000000
0.000000
0.022029
0.00000
0.00000
0.00000
Koshiyama, T.
Shirai, M.
Hikage, T.
Tabe, H.
Tanaka, K.
Kitagawa, S.
Ueno, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
90.722
90.722
45.395
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
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
O Ru3
319.209
oxo-centered triruthenium cluster
non-polymer
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
C34 H32 N4 O4 Zn
626.051
PROTOPORPHYRIN IX CONTAINING ZN
non-polymer
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
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
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
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
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
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
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
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
N
267
N
H
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
O
N
277
N
RU
N
278
N
RU
N
279
N
RU
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
O
N
286
N
O
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
S
N
295
N
O
N
296
N
O
N
297
N
O
N
298
N
O
N
299
N
N
N
300
S
C
N
301
N
C
N
302
N
O
N
303
R
C
N
304
N
O
N
305
N
C
N
306
N
O
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
N
N
317
S
C
N
318
N
C
N
319
N
O
N
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
N
Y
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
N
330
N
O
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
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
O
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
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
N
C
N
372
N
C
N
373
N
C
N
374
N
O
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
ZN
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
C
N
391
R
N
N
392
N
C
N
393
N
C
N
394
N
C
N
395
N
C
N
396
N
C
N
397
N
C
N
398
N
C
N
399
N
C
N
400
N
O
N
401
N
O
N
402
N
N
N
403
N
C
N
404
N
C
N
405
N
C
N
406
N
C
N
407
N
C
N
408
N
C
N
409
N
C
Y
410
N
N
Y
411
N
C
Y
412
N
C
Y
413
N
C
Y
414
N
C
N
415
N
C
N
416
N
C
N
417
N
C
N
418
N
N
N
419
N
C
N
420
N
C
N
421
N
C
N
422
N
C
N
423
N
C
N
424
N
C
N
425
N
C
N
426
N
C
N
427
N
O
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
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
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
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
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
sing
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
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
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
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
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
doub
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
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
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
doub
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
doub
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
doub
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
Y
311
N
doub
Y
312
N
sing
Y
313
N
sing
N
314
N
sing
Y
315
N
doub
Y
316
N
sing
Y
317
N
sing
N
318
N
sing
Y
319
N
sing
Y
320
N
doub
N
321
N
sing
Y
322
N
doub
N
323
N
sing
Y
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
doub
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
Y
339
N
doub
Y
340
N
sing
Y
341
N
sing
N
342
N
sing
Y
343
N
doub
N
344
N
sing
Y
345
N
doub
N
346
N
sing
Y
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
doub
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
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
doub
N
375
N
sing
N
376
N
sing
N
377
N
doub
N
378
N
sing
N
379
N
sing
N
380
N
doub
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
doub
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
doub
N
403
N
sing
N
404
N
sing
N
405
N
doub
N
406
N
sing
N
407
N
sing
N
408
N
doub
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
doub
N
416
N
sing
N
417
N
sing
N
418
N
sing
Y
419
N
sing
Y
420
N
sing
Y
421
N
doub
Y
422
N
sing
N
423
N
sing
Y
424
N
doub
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
doub
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
doub
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
doub
N
450
N
sing
N
451
N
sing
GE
Angew.Chem.Int.Ed.Engl.
ACIEAY
0179
1521-3773
10.1002/anie.201008004
21495132
Post-Crystal Engineering of Zinc-Substituted Myoglobin to Construct a Long-Lived Photoinduced Charge-Separation System
2011
10.2210/pdb3ase/pdb
pdb_00003ase
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
IMAGE PLATE
2009-12-16
RIGAKU RAXIS VII
CONFOCAL MIRRORS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
17365.164
Myoglobin
1
man
polymer
96.063
SULFATE ION
2
syn
non-polymer
319.209
oxo-centered triruthenium cluster
2
syn
non-polymer
626.051
PROTOPORPHYRIN IX CONTAINING ZN
1
syn
non-polymer
18.015
water
71
nat
water
no
no
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKK
GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKK
GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG
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
n
Sperm whale
sample
MB
9755
Physeter catodon
562
Escherichia coli
TB-1
PLASMID
pUC19
1
3.11
60.39
VAPOR DIFFUSION, SITTING DROP
6.4
3.2-2.9M ammonium sulfate in 0.1 M Bis-Tris-propane, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
pdbx_validate_chiral
struct_conn
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2011-04-27
1
1
2011-07-13
1
2
2024-03-13
_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.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_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.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_seq_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PDBJ
Y
PDBJ
2010-12-11
REL
REL
SO4
SULFATE ION
RUO
oxo-centered triruthenium cluster
ZNH
PROTOPORPHYRIN IX CONTAINING ZN
HOH
water
THE SEQUENCE WAS BASED ON REFERENCE 2 OF DATABASE P02185 (MYG_PHYMC).
SO4
200
2
SO4
SO4
200
A
SO4
201
2
SO4
SO4
201
A
RUO
1
3
RUO
RUO
154
A
RUO
1
3
RUO
RUO
155
A
ZNH
1
4
ZNH
ZNH
156
A
HOH
1
5
HOH
HOH
157
A
HOH
2
5
HOH
HOH
158
A
HOH
3
5
HOH
HOH
159
A
HOH
4
5
HOH
HOH
160
A
HOH
5
5
HOH
HOH
161
A
HOH
6
5
HOH
HOH
162
A
HOH
7
5
HOH
HOH
163
A
HOH
8
5
HOH
HOH
164
A
HOH
9
5
HOH
HOH
165
A
HOH
10
5
HOH
HOH
166
A
HOH
11
5
HOH
HOH
167
A
HOH
12
5
HOH
HOH
168
A
HOH
13
5
HOH
HOH
169
A
HOH
14
5
HOH
HOH
170
A
HOH
15
5
HOH
HOH
171
A
HOH
16
5
HOH
HOH
172
A
HOH
17
5
HOH
HOH
173
A
HOH
18
5
HOH
HOH
174
A
HOH
19
5
HOH
HOH
175
A
HOH
20
5
HOH
HOH
176
A
HOH
21
5
HOH
HOH
177
A
HOH
22
5
HOH
HOH
178
A
HOH
23
5
HOH
HOH
179
A
HOH
24
5
HOH
HOH
180
A
HOH
25
5
HOH
HOH
181
A
HOH
26
5
HOH
HOH
182
A
HOH
27
5
HOH
HOH
183
A
HOH
28
5
HOH
HOH
184
A
HOH
29
5
HOH
HOH
185
A
HOH
30
5
HOH
HOH
186
A
HOH
31
5
HOH
HOH
187
A
HOH
32
5
HOH
HOH
188
A
HOH
33
5
HOH
HOH
189
A
HOH
34
5
HOH
HOH
190
A
HOH
35
5
HOH
HOH
191
A
HOH
36
5
HOH
HOH
192
A
HOH
37
5
HOH
HOH
193
A
HOH
38
5
HOH
HOH
194
A
HOH
39
5
HOH
HOH
195
A
HOH
40
5
HOH
HOH
196
A
HOH
41
5
HOH
HOH
197
A
HOH
42
5
HOH
HOH
198
A
HOH
43
5
HOH
HOH
199
A
HOH
44
5
HOH
HOH
202
A
HOH
45
5
HOH
HOH
203
A
HOH
46
5
HOH
HOH
204
A
HOH
47
5
HOH
HOH
205
A
HOH
48
5
HOH
HOH
206
A
HOH
49
5
HOH
HOH
207
A
HOH
50
5
HOH
HOH
208
A
HOH
51
5
HOH
HOH
209
A
HOH
52
5
HOH
HOH
210
A
HOH
53
5
HOH
HOH
211
A
HOH
54
5
HOH
HOH
212
A
HOH
55
5
HOH
HOH
213
A
HOH
56
5
HOH
HOH
214
A
HOH
57
5
HOH
HOH
215
A
HOH
58
5
HOH
HOH
216
A
HOH
59
5
HOH
HOH
217
A
HOH
60
5
HOH
HOH
218
A
HOH
61
5
HOH
HOH
219
A
HOH
62
5
HOH
HOH
220
A
HOH
63
5
HOH
HOH
221
A
HOH
64
5
HOH
HOH
222
A
HOH
65
5
HOH
HOH
223
A
HOH
66
5
HOH
HOH
224
A
HOH
67
5
HOH
HOH
225
A
HOH
68
5
HOH
HOH
226
A
HOH
69
5
HOH
HOH
227
A
HOH
70
5
HOH
HOH
228
A
HOH
71
5
HOH
HOH
229
A
MET
0
n
1
MET
0
A
VAL
1
n
2
VAL
1
A
LEU
2
n
3
LEU
2
A
SER
3
n
4
SER
3
A
GLU
4
n
5
GLU
4
A
GLY
5
n
6
GLY
5
A
GLU
6
n
7
GLU
6
A
TRP
7
n
8
TRP
7
A
GLN
8
n
9
GLN
8
A
LEU
9
n
10
LEU
9
A
VAL
10
n
11
VAL
10
A
LEU
11
n
12
LEU
11
A
HIS
12
n
13
HIS
12
A
VAL
13
n
14
VAL
13
A
TRP
14
n
15
TRP
14
A
ALA
15
n
16
ALA
15
A
LYS
16
n
17
LYS
16
A
VAL
17
n
18
VAL
17
A
GLU
18
n
19
GLU
18
A
ALA
19
n
20
ALA
19
A
ASP
20
n
21
ASP
20
A
VAL
21
n
22
VAL
21
A
ALA
22
n
23
ALA
22
A
GLY
23
n
24
GLY
23
A
HIS
24
n
25
HIS
24
A
GLY
25
n
26
GLY
25
A
GLN
26
n
27
GLN
26
A
ASP
27
n
28
ASP
27
A
ILE
28
n
29
ILE
28
A
LEU
29
n
30
LEU
29
A
ILE
30
n
31
ILE
30
A
ARG
31
n
32
ARG
31
A
LEU
32
n
33
LEU
32
A
PHE
33
n
34
PHE
33
A
LYS
34
n
35
LYS
34
A
SER
35
n
36
SER
35
A
HIS
36
n
37
HIS
36
A
PRO
37
n
38
PRO
37
A
GLU
38
n
39
GLU
38
A
THR
39
n
40
THR
39
A
LEU
40
n
41
LEU
40
A
GLU
41
n
42
GLU
41
A
LYS
42
n
43
LYS
42
A
PHE
43
n
44
PHE
43
A
ASP
44
n
45
ASP
44
A
ARG
45
n
46
ARG
45
A
PHE
46
n
47
PHE
46
A
LYS
47
n
48
LYS
47
A
HIS
48
n
49
HIS
48
A
LEU
49
n
50
LEU
49
A
LYS
50
n
51
LYS
50
A
THR
51
n
52
THR
51
A
GLU
52
n
53
GLU
52
A
ALA
53
n
54
ALA
53
A
GLU
54
n
55
GLU
54
A
MET
55
n
56
MET
55
A
LYS
56
n
57
LYS
56
A
ALA
57
n
58
ALA
57
A
SER
58
n
59
SER
58
A
GLU
59
n
60
GLU
59
A
ASP
60
n
61
ASP
60
A
LEU
61
n
62
LEU
61
A
LYS
62
n
63
LYS
62
A
LYS
63
n
64
LYS
63
A
HIS
64
n
65
HIS
64
A
GLY
65
n
66
GLY
65
A
VAL
66
n
67
VAL
66
A
THR
67
n
68
THR
67
A
VAL
68
n
69
VAL
68
A
LEU
69
n
70
LEU
69
A
THR
70
n
71
THR
70
A
ALA
71
n
72
ALA
71
A
LEU
72
n
73
LEU
72
A
GLY
73
n
74
GLY
73
A
ALA
74
n
75
ALA
74
A
ILE
75
n
76
ILE
75
A
LEU
76
n
77
LEU
76
A
LYS
77
n
78
LYS
77
A
LYS
78
n
79
LYS
78
A
LYS
79
n
80
LYS
79
A
GLY
80
n
81
GLY
80
A
HIS
81
n
82
HIS
81
A
HIS
82
n
83
HIS
82
A
GLU
83
n
84
GLU
83
A
ALA
84
n
85
ALA
84
A
GLU
85
n
86
GLU
85
A
LEU
86
n
87
LEU
86
A
LYS
87
n
88
LYS
87
A
PRO
88
n
89
PRO
88
A
LEU
89
n
90
LEU
89
A
ALA
90
n
91
ALA
90
A
GLN
91
n
92
GLN
91
A
SER
92
n
93
SER
92
A
HIS
93
n
94
HIS
93
A
ALA
94
n
95
ALA
94
A
THR
95
n
96
THR
95
A
LYS
96
n
97
LYS
96
A
HIS
97
n
98
HIS
97
A
LYS
98
n
99
LYS
98
A
ILE
99
n
100
ILE
99
A
PRO
100
n
101
PRO
100
A
ILE
101
n
102
ILE
101
A
LYS
102
n
103
LYS
102
A
TYR
103
n
104
TYR
103
A
LEU
104
n
105
LEU
104
A
GLU
105
n
106
GLU
105
A
PHE
106
n
107
PHE
106
A
ILE
107
n
108
ILE
107
A
SER
108
n
109
SER
108
A
GLU
109
n
110
GLU
109
A
ALA
110
n
111
ALA
110
A
ILE
111
n
112
ILE
111
A
ILE
112
n
113
ILE
112
A
HIS
113
n
114
HIS
113
A
VAL
114
n
115
VAL
114
A
LEU
115
n
116
LEU
115
A
HIS
116
n
117
HIS
116
A
SER
117
n
118
SER
117
A
ARG
118
n
119
ARG
118
A
HIS
119
n
120
HIS
119
A
PRO
120
n
121
PRO
120
A
GLY
121
n
122
GLY
121
A
ASN
122
n
123
ASN
122
A
PHE
123
n
124
PHE
123
A
GLY
124
n
125
GLY
124
A
ALA
125
n
126
ALA
125
A
ASP
126
n
127
ASP
126
A
ALA
127
n
128
ALA
127
A
GLN
128
n
129
GLN
128
A
GLY
129
n
130
GLY
129
A
ALA
130
n
131
ALA
130
A
MET
131
n
132
MET
131
A
ASN
132
n
133
ASN
132
A
LYS
133
n
134
LYS
133
A
ALA
134
n
135
ALA
134
A
LEU
135
n
136
LEU
135
A
GLU
136
n
137
GLU
136
A
LEU
137
n
138
LEU
137
A
PHE
138
n
139
PHE
138
A
ARG
139
n
140
ARG
139
A
LYS
140
n
141
LYS
140
A
ASP
141
n
142
ASP
141
A
ILE
142
n
143
ILE
142
A
ALA
143
n
144
ALA
143
A
ALA
144
n
145
ALA
144
A
LYS
145
n
146
LYS
145
A
TYR
146
n
147
TYR
146
A
LYS
147
n
148
LYS
147
A
GLU
148
n
149
GLU
148
A
LEU
149
n
150
LEU
149
A
GLY
150
n
151
GLY
150
A
TYR
151
n
152
TYR
151
A
ALA
152
n
153
GLN
152
A
GLY
153
n
154
GLY
153
A
author_and_software_defined_assembly
PISA
1
monomeric
A
HIS
12
A
ND1
HIS
13
1_555
A
RUO
154
D
RU2
RUO
1_555
A
RUO
154
D
O1
RUO
1_555
177.4
A
HIS
93
A
NE2
HIS
94
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NA
ZNH
1_555
94.3
A
HIS
93
A
NE2
HIS
94
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NB
ZNH
1_555
96.8
A
ZNH
156
F
NA
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NB
ZNH
1_555
87.8
A
HIS
93
A
NE2
HIS
94
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NC
ZNH
1_555
105.2
A
ZNH
156
F
NA
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NC
ZNH
1_555
160.5
A
ZNH
156
F
NB
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
NC
ZNH
1_555
88.8
A
HIS
93
A
NE2
HIS
94
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
ND
ZNH
1_555
102.3
A
ZNH
156
F
NA
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
ND
ZNH
1_555
89.2
A
ZNH
156
F
NB
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
ND
ZNH
1_555
160.8
A
ZNH
156
F
NC
ZNH
1_555
A
ZNH
156
F
ZN
ZNH
1_555
A
ZNH
156
F
ND
ZNH
1_555
87.8
A
HOH
216
G
O
HOH
1_555
A
RUO
154
D
RU1
RUO
1_555
A
RUO
154
D
O1
RUO
1_555
166.2
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
CG
GLN
152
A
CG
GLN
153
1
Y
1
A
CD
GLN
152
A
CD
GLN
153
1
Y
1
A
OE1
GLN
152
A
OE1
GLN
153
1
Y
1
A
NE2
GLN
152
A
NE2
GLN
153
1
Y
1
A
NA
ZNH
156
PLANAR
1
A
ASP
20
-155.83
73.22
1
A
HIS
81
-92.93
58.21
1
A
PHE
123
-140.52
54.50
18.328
0.00
0.00
0.00
0.00
0.00
0.00
0.942
0.923
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.23246
0.20118
0.20275
1.75
19.65
1106
20500
5.1
99.70
2.094
0.069
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.106
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.75
19.65
71
1353
61
0
1221
0.013
0.021
1313
3.019
2.011
1778
4.535
5.000
153
36.283
24.151
53
15.541
15.000
237
27.713
15.000
4
0.084
0.200
185
0.009
0.020
962
0.204
0.200
637
0.301
0.200
877
0.121
0.200
73
0.188
0.200
27
0.104
0.200
10
0.887
1.500
787
1.425
2.000
1214
2.506
3.000
612
3.952
4.500
562
0.291
0.238
1.795
93
1452
20
99.23
1.75
100
3ASE
21608
0.054
1
29.9
8.2
99.6
0.325
1.75
1.81
3.8
5.4
99.4
data reduction
DENZO
phasing
MOLREP
refinement
REFMAC
5.2.0019
data scaling
SCALEPACK
Crystal Structure of Zinc myoglobin soaked with Ru3O cluster
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
A
SER
3
A
SER
4
HELX_P
A
GLU
18
A
GLU
19
1
1
16
A
ASP
20
A
ASP
21
HELX_P
A
HIS
36
A
HIS
37
1
2
17
A
PRO
37
A
PRO
38
HELX_P
A
PHE
43
A
PHE
44
5
3
7
A
THR
51
A
THR
52
HELX_P
A
SER
58
A
SER
59
1
4
8
A
SER
58
A
SER
59
HELX_P
A
LYS
78
A
LYS
79
1
5
21
A
HIS
82
A
HIS
83
HELX_P
A
LYS
96
A
LYS
97
1
6
15
A
PRO
100
A
PRO
101
HELX_P
A
HIS
119
A
HIS
120
1
7
20
A
GLY
124
A
GLY
125
HELX_P
A
GLY
150
A
GLY
151
1
8
27
metalc
2.291
A
HIS
12
A
ND1
HIS
13
1_555
A
RUO
154
D
RU2
RUO
1_555
metalc
2.167
A
HIS
93
A
NE2
HIS
94
1_555
A
ZNH
156
F
ZN
ZNH
1_555
metalc
2.597
A
RUO
154
D
RU1
RUO
1_555
A
HOH
216
G
O
HOH
1_555
OXYGEN TRANSPORT
Electron transfer, OXYGEN TRANSPORT
MYG_PHYMC
UNP
1
1
P02185
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKK
GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
1
154
3ASE
0
153
P02185
A
1
1
154
1
ASP
SEE REMARK 999
ASN
122
3ASE
A
P02185
UNP
123
123
BINDING SITE FOR RESIDUE SO4 A 200
A
SO4
200
Software
6
BINDING SITE FOR RESIDUE SO4 A 201
A
SO4
201
Software
5
BINDING SITE FOR RESIDUE RUO A 154
A
RUO
154
Software
2
BINDING SITE FOR RESIDUE RUO A 155
A
RUO
155
Software
2
BINDING SITE FOR RESIDUE ZNH A 156
A
ZNH
156
Software
22
A
SER
3
A
SER
4
6
1_556
A
GLU
4
A
GLU
5
6
1_556
A
THR
51
A
THR
52
6
1_555
A
GLU
52
A
GLU
53
6
1_555
A
ALA
53
A
ALA
54
6
1_555
A
HOH
192
G
HOH
6
1_555
A
LYS
87
A
LYS
88
5
6_555
A
GLY
124
A
GLY
125
5
1_555
A
ALA
125
A
ALA
126
5
1_555
A
ASP
126
A
ASP
127
5
1_555
A
HOH
169
G
HOH
5
1_555
A
HIS
12
A
HIS
13
2
1_555
A
HOH
216
G
HOH
2
1_555
A
HIS
48
A
HIS
49
2
1_554
A
HIS
81
A
HIS
82
2
1_555
A
LYS
42
A
LYS
43
22
1_555
A
PHE
43
A
PHE
44
22
1_555
A
ARG
45
A
ARG
46
22
1_555
A
HIS
64
A
HIS
65
22
1_555
A
THR
67
A
THR
68
22
1_555
A
VAL
68
A
VAL
69
22
1_555
A
ALA
71
A
ALA
72
22
1_555
A
LEU
89
A
LEU
90
22
1_555
A
SER
92
A
SER
93
22
1_555
A
HIS
93
A
HIS
94
22
1_555
A
HIS
97
A
HIS
98
22
1_555
A
ILE
99
A
ILE
100
22
1_555
A
TYR
103
A
TYR
104
22
1_555
A
LEU
104
A
LEU
105
22
1_555
A
ILE
107
A
ILE
108
22
1_555
A
PHE
138
A
PHE
139
22
1_555
A
HOH
178
G
HOH
22
1_555
A
HOH
180
G
HOH
22
1_555
A
HOH
191
G
HOH
22
1_555
A
HOH
204
G
HOH
22
1_555
A
HOH
210
G
HOH
22
1_555
A
HOH
224
G
HOH
22
1_555
168
P 6