0.016353
0.000000
0.000000
0.000000
0.016353
0.000000
0.000000
0.000000
0.004136
0.00000
0.00000
0.00000
Shaffer, P.L.
Gewirth, D.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
61.15
61.15
241.80
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
N
1
N
N
N
2
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
O
N
89
N
P
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
C
N
94
R
C
N
95
N
O
N
96
S
C
N
97
N
O
N
98
N
C
N
99
R
C
Y
100
N
N
Y
101
N
C
Y
102
N
N
Y
103
N
C
Y
104
N
C
N
105
N
N
Y
106
N
N
Y
107
N
C
Y
108
N
N
Y
109
N
C
N
110
N
H
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
O
N
125
N
P
N
126
N
O
N
127
N
O
N
128
N
O
N
129
N
C
N
130
R
C
N
131
N
O
N
132
S
C
N
133
N
O
N
134
N
C
N
135
R
C
N
136
N
N
N
137
N
C
N
138
N
O
N
139
N
N
N
140
N
C
N
141
N
N
N
142
N
C
N
143
N
C
N
144
N
H
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
O
N
159
N
P
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
C
N
164
R
C
N
165
N
O
N
166
S
C
N
167
N
O
N
168
N
C
N
169
R
C
Y
170
N
N
Y
171
N
C
Y
172
N
N
Y
173
N
C
N
174
N
C
N
175
N
O
N
176
N
N
N
177
N
C
N
178
N
N
N
179
N
N
Y
180
N
C
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
O
N
196
N
P
N
197
N
O
N
198
N
O
N
199
N
O
N
200
N
C
N
201
R
C
N
202
N
O
N
203
S
C
N
204
N
O
N
205
N
C
N
206
R
C
N
207
N
N
N
208
N
C
N
209
N
O
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
C
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
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
O
N
239
N
N
N
240
N
O
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
H
N
249
N
H
N
250
N
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
O
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
N
N
271
N
C
N
272
N
C
N
273
N
O
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
N
Y
287
N
C
Y
288
N
C
Y
289
N
N
N
290
N
O
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
O
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
S
C
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
O
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
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
O
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
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
N
N
357
N
O
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
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
S
N
380
N
C
N
381
N
O
N
382
N
H
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
N
N
394
S
C
N
395
N
C
N
396
N
O
N
397
N
C
Y
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
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
H
N
415
N
H
N
416
N
N
N
417
S
C
N
418
N
C
N
419
N
O
N
420
N
C
N
421
N
C
N
422
N
C
N
423
N
O
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
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
N
C
N
438
N
O
N
439
N
O
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
N
N
448
S
C
N
449
N
C
N
450
N
O
N
451
R
C
N
452
N
O
N
453
N
C
N
454
N
O
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
N
N
465
S
C
N
466
N
C
N
467
N
O
N
468
N
C
N
469
N
C
N
470
N
C
N
471
N
O
N
472
N
H
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
ZN
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
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
doub
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
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
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
doub
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
Y
289
N
sing
Y
290
N
doub
Y
291
N
doub
N
292
N
sing
Y
293
N
sing
N
294
N
sing
Y
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
doub
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
doub
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
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
sing
N
348
N
sing
N
349
N
doub
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
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
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
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
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
sing
N
414
N
sing
N
415
N
doub
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
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
doub
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
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
doub
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
UK
EMBO J.
EMJODG
0897
0261-4189
21
2242
2252
10.1093/emboj/21.9.2242
11980721
Structural basis of VDR-DNA interactions on direct repeat response elements.
2002
10.2210/pdb1kb6/pdb
pdb_00001kb6
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
2001-09-15
APS-1
SINGLE WAVELENGTH
M
x-ray
1
1.0332
1.0
19-BM
APS
1.0332
SYNCHROTRON
APS BEAMLINE 19-BM
Rat Osteocalcin (OC) Response Element
5614.655
5'-D(*CP*AP*CP*GP*GP*GP*TP*GP*AP*AP*TP*GP*AP*GP*GP*AP*CP*A)-3'
1
syn
polymer
Rat Osteocalcin (OC) Response Element
5418.503
5'-D(*TP*GP*TP*CP*CP*TP*CP*AP*TP*TP*CP*AP*CP*CP*CP*GP*TP*G)-3'
1
syn
polymer
12953.305
Vitamin D3 Receptor
DNA-binding Domain (Residues 16-125)
2
man
polymer
65.409
ZINC ION
4
syn
non-polymer
18.015
water
34
nat
water
VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR
no
no
(DC)(DA)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DA)(DT)(DG)(DA)(DG)(DG)(DA)(DC)(DA)
CACGGGTGAATGAGGACA
C
polydeoxyribonucleotide
no
no
(DT)(DG)(DT)(DC)(DC)(DT)(DC)(DA)(DT)(DT)(DC)(DA)(DC)(DC)(DC)(DG)(DT)(DG)
TGTCCTCATTCACCCGTG
D
polydeoxyribonucleotide
no
no
FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFIL
TDEEVQRKREMILKRKEEEALKDSLRPKLS
FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFIL
TDEEVQRKREMILKRKEEEALKDSLRPKLS
A,B
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
human
Homo
Escherichia
Escherichia coli
sample
VDR
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
PET11A-VDR-N1-RPLKS
1
3.02
59.30
VAPOR DIFFUSION, HANGING DROP
5.6
PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
PEG 8000
1
MgCl2
1
MES
1
glycerol
1
DTT
1
2.226
1
19
C
401
D
436
-0.893
C_DC401:DG436_D
1
-11.903
-0.603
0.300
-0.290
0.203
1
20
C
402
D
435
-2.156
C_DA402:DT435_D
2
-3.521
0.371
0.204
0.021
11.995
1
19
C
403
D
434
-5.712
C_DC403:DG434_D
3
-4.706
-0.126
-0.323
-0.368
-3.947
1
19
C
404
D
433
-1.873
C_DG404:DC433_D
4
-7.380
-0.190
0.194
-0.148
-3.257
1
19
C
405
D
432
-2.591
C_DG405:DC432_D
5
-6.603
0.045
-0.134
-0.248
-17.822
1
19
C
406
D
431
0.150
C_DG406:DC431_D
6
-7.180
-0.476
-0.796
-0.335
-3.857
1
20
C
407
D
430
1.121
C_DT407:DA430_D
7
-7.001
-0.937
-0.078
-0.094
3.281
1
19
C
408
D
429
-0.530
C_DG408:DC429_D
8
-0.415
0.080
-0.012
-0.275
9.409
1
20
C
409
D
428
0.144
C_DA409:DT428_D
9
-17.402
-0.041
0.144
-0.047
7.810
1
20
C
410
D
427
0.214
C_DA410:DT427_D
10
-15.800
0.136
0.355
-0.067
-1.695
1
20
C
411
D
426
1.710
C_DT411:DA426_D
11
-10.790
0.263
0.101
-0.262
-1.997
1
19
C
412
D
425
-1.256
C_DG412:DC425_D
12
1.066
-0.138
-0.416
-0.315
-10.278
1
20
C
413
D
424
-2.202
C_DA413:DT424_D
13
-7.702
0.252
-0.205
-0.198
-3.023
1
19
C
414
D
423
-4.556
C_DG414:DC423_D
14
1.031
0.300
-0.150
-0.119
-3.257
1
19
C
415
D
422
-0.163
C_DG415:DC422_D
15
-9.492
-0.592
-0.385
-0.299
8.292
1
20
C
416
D
421
0.419
C_DA416:DT421_D
16
-9.551
0.435
0.161
-0.346
2.627
1
19
C
417
D
420
-0.574
C_DC417:DG420_D
17
-4.516
0.533
0.071
-0.469
10.072
1
20
C
418
D
419
3.874
C_DA418:DT419_D
18
-6.139
0.457
0.225
-0.236
3.431
41.991
C
C
401
402
6.448
D
D
436
435
3.464
4.611
-0.230
-0.058
CC_DC401DA402:DT435DG436_DD
1
1.210
-1.691
41.732
-0.588
0.454
3.222
31.651
C
C
402
403
-0.857
D
D
435
434
3.164
-0.465
0.609
-0.024
CC_DA402DC403:DG434DT435_DD
2
6.399
-11.810
31.010
0.041
0.050
3.594
40.898
C
C
403
404
10.422
D
D
434
433
3.643
7.199
-0.290
0.116
CC_DC403DG404:DC433DG434_DD
3
-8.426
12.199
39.430
-0.725
-0.628
3.280
38.097
C
C
404
405
12.425
D
D
433
432
3.499
8.047
0.279
-0.766
CC_DG404DG405:DC432DC433_DD
4
2.724
-4.206
37.172
-2.244
-0.065
3.414
30.351
C
C
405
406
10.378
D
D
432
431
3.682
5.377
-0.220
-0.660
CC_DG405DG406:DC431DC432_DD
5
5.498
-10.611
29.383
-2.453
1.640
3.057
28.051
C
C
406
407
0.648
D
D
431
430
3.006
0.312
-0.574
-0.274
CC_DG406DT407:DA430DC431_DD
6
-5.630
11.691
27.489
-0.633
-0.059
3.340
43.072
C
C
407
408
2.013
D
D
430
429
3.238
1.476
0.704
1.679
CC_DT407DG408:DC429DA430_DD
7
4.005
-5.463
42.870
2.140
-0.561
3.587
33.804
C
C
408
409
11.213
D
D
429
428
3.408
6.481
-0.417
1.230
CC_DG408DA409:DT428DC429_DD
8
-0.916
1.585
33.182
0.984
0.557
3.216
37.120
C
C
409
410
2.227
D
D
428
427
3.233
1.417
0.152
-0.218
CC_DA409DA410:DT427DT428_DD
9
-1.281
2.013
37.073
-0.529
-0.408
3.473
38.055
C
C
410
411
2.657
D
D
427
426
3.511
1.731
0.054
-0.737
CC_DA410DT411:DA426DT427_DD
10
2.030
-3.115
37.964
-1.365
0.193
3.532
32.639
C
C
411
412
13.832
D
D
426
425
3.445
7.677
0.772
0.458
CC_DT411DG412:DC425DA426_DD
11
4.827
-8.697
31.387
-0.634
-0.461
3.632
38.727
C
C
412
413
2.977
D
D
425
424
3.478
1.964
-1.135
0.330
CC_DG412DA413:DT424DC425_DD
12
-6.808
10.321
38.097
0.234
0.797
3.039
35.080
C
C
413
414
17.764
D
D
424
423
3.390
10.551
0.069
-0.690
CC_DA413DG414:DC423DT424_DD
13
-0.395
0.665
33.501
-2.738
-0.174
3.338
29.565
C
C
414
415
4.467
D
D
423
422
3.411
2.271
0.011
-0.466
CC_DG414DG415:DC422DC423_DD
14
3.998
-7.866
29.213
-1.413
0.858
3.315
43.047
C
C
415
416
0.202
D
D
422
421
3.186
0.148
-1.035
1.154
CC_DG415DA416:DT421DC422_DD
15
-7.268
9.948
42.458
1.558
0.693
3.476
32.663
C
C
416
417
4.134
D
D
421
420
3.439
2.320
0.651
-0.012
CC_DA416DC417:DG420DT421_DD
16
3.141
-5.598
32.435
-0.448
-0.581
3.407
34.291
C
C
417
418
3.901
D
D
420
419
3.337
2.298
-0.520
0.955
CC_DC417DA418:DT419DG420_DD
17
-1.154
1.958
34.198
1.247
0.695
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-05-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element
Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element
RCSB
Y
RCSB
2001-11-05
REL
REL
ZN
ZINC ION
HOH
water
1KB4
PDB ENTRY 1KB4
PDB
experimental model
ZN
150
4
ZN
ZN
150
A
ZN
151
4
ZN
ZN
151
A
ZN
350
4
ZN
ZN
350
B
ZN
351
4
ZN
ZN
351
B
WAT
609
5
HOH
HOH
609
C
WAT
614
5
HOH
HOH
614
C
WAT
634
5
HOH
HOH
634
C
WAT
602
5
HOH
HOH
602
D
WAT
605
5
HOH
HOH
605
D
WAT
607
5
HOH
HOH
607
D
WAT
612
5
HOH
HOH
612
D
WAT
613
5
HOH
HOH
613
D
WAT
623
5
HOH
HOH
623
D
WAT
626
5
HOH
HOH
626
D
WAT
629
5
HOH
HOH
629
D
WAT
630
5
HOH
HOH
630
D
WAT
633
5
HOH
HOH
633
D
WAT
601
5
HOH
HOH
601
A
WAT
603
5
HOH
HOH
603
A
WAT
604
5
HOH
HOH
604
A
WAT
606
5
HOH
HOH
606
A
WAT
608
5
HOH
HOH
608
A
WAT
610
5
HOH
HOH
610
A
WAT
611
5
HOH
HOH
611
A
WAT
616
5
HOH
HOH
616
A
WAT
617
5
HOH
HOH
617
A
WAT
619
5
HOH
HOH
619
A
WAT
621
5
HOH
HOH
621
A
WAT
622
5
HOH
HOH
622
A
WAT
625
5
HOH
HOH
625
A
WAT
628
5
HOH
HOH
628
A
WAT
631
5
HOH
HOH
631
A
WAT
615
5
HOH
HOH
615
B
WAT
618
5
HOH
HOH
618
B
WAT
620
5
HOH
HOH
620
B
WAT
624
5
HOH
HOH
624
B
WAT
627
5
HOH
HOH
627
B
WAT
632
5
HOH
HOH
632
B
C
401
n
1
DC
401
C
A
402
n
2
DA
402
C
C
403
n
3
DC
403
C
G
404
n
4
DG
404
C
G
405
n
5
DG
405
C
G
406
n
6
DG
406
C
T
407
n
7
DT
407
C
G
408
n
8
DG
408
C
A
409
n
9
DA
409
C
A
410
n
10
DA
410
C
T
411
n
11
DT
411
C
G
412
n
12
DG
412
C
A
413
n
13
DA
413
C
G
414
n
14
DG
414
C
G
415
n
15
DG
415
C
A
416
n
16
DA
416
C
C
417
n
17
DC
417
C
A
418
n
18
DA
418
C
T
419
n
1
DT
419
D
G
420
n
2
DG
420
D
T
421
n
3
DT
421
D
C
422
n
4
DC
422
D
C
423
n
5
DC
423
D
T
424
n
6
DT
424
D
C
425
n
7
DC
425
D
A
426
n
8
DA
426
D
T
427
n
9
DT
427
D
T
428
n
10
DT
428
D
C
429
n
11
DC
429
D
A
430
n
12
DA
430
D
C
431
n
13
DC
431
D
C
432
n
14
DC
432
D
C
433
n
15
DC
433
D
G
434
n
16
DG
434
D
T
435
n
17
DT
435
D
G
436
n
18
DG
436
D
n
1
16
A
n
2
17
A
n
3
18
A
n
4
19
A
n
5
20
A
PRO
21
n
6
PRO
21
A
ARG
22
n
7
ARG
22
A
ILE
23
n
8
ILE
23
A
CYS
24
n
9
CYS
24
A
GLY
25
n
10
GLY
25
A
VAL
26
n
11
VAL
26
A
CYS
27
n
12
CYS
27
A
GLY
28
n
13
GLY
28
A
ASP
29
n
14
ASP
29
A
ARG
30
n
15
ARG
30
A
ALA
31
n
16
ALA
31
A
THR
32
n
17
THR
32
A
GLY
33
n
18
GLY
33
A
PHE
34
n
19
PHE
34
A
HIS
35
n
20
HIS
35
A
PHE
36
n
21
PHE
36
A
ASN
37
n
22
ASN
37
A
ALA
38
n
23
ALA
38
A
MET
39
n
24
MET
39
A
THR
40
n
25
THR
40
A
CYS
41
n
26
CYS
41
A
GLU
42
n
27
GLU
42
A
GLY
43
n
28
GLY
43
A
CYS
44
n
29
CYS
44
A
LYS
45
n
30
LYS
45
A
GLY
46
n
31
GLY
46
A
PHE
47
n
32
PHE
47
A
PHE
48
n
33
PHE
48
A
ARG
49
n
34
ARG
49
A
ARG
50
n
35
ARG
50
A
SER
51
n
36
SER
51
A
MET
52
n
37
MET
52
A
LYS
53
n
38
LYS
53
A
ARG
54
n
39
ARG
54
A
LYS
55
n
40
LYS
55
A
ALA
56
n
41
ALA
56
A
LEU
57
n
42
LEU
57
A
PHE
58
n
43
PHE
58
A
THR
59
n
44
THR
59
A
CYS
60
n
45
CYS
60
A
PRO
61
n
46
PRO
61
A
PHE
62
n
47
PHE
62
A
ASN
63
n
48
ASN
63
A
GLY
64
n
49
GLY
64
A
ASP
65
n
50
ASP
65
A
CYS
66
n
51
CYS
66
A
ARG
67
n
52
ARG
67
A
ILE
68
n
53
ILE
68
A
THR
69
n
54
THR
69
A
LYS
70
n
55
LYS
70
A
ASP
71
n
56
ASP
71
A
ASN
72
n
57
ASN
72
A
ARG
73
n
58
ARG
73
A
ARG
74
n
59
ARG
74
A
HIS
75
n
60
HIS
75
A
CYS
76
n
61
CYS
76
A
GLN
77
n
62
GLN
77
A
ALA
78
n
63
ALA
78
A
CYS
79
n
64
CYS
79
A
ARG
80
n
65
ARG
80
A
LEU
81
n
66
LEU
81
A
LYS
82
n
67
LYS
82
A
ARG
83
n
68
ARG
83
A
CYS
84
n
69
CYS
84
A
VAL
85
n
70
VAL
85
A
ASP
86
n
71
ASP
86
A
ILE
87
n
72
ILE
87
A
GLY
88
n
73
GLY
88
A
MET
89
n
74
MET
89
A
MET
90
n
75
MET
90
A
LYS
91
n
76
LYS
91
A
GLU
92
n
77
GLU
92
A
PHE
93
n
78
PHE
93
A
ILE
94
n
79
ILE
94
A
LEU
95
n
80
LEU
95
A
THR
96
n
81
THR
96
A
ASP
97
n
82
ASP
97
A
GLU
98
n
83
GLU
98
A
GLU
99
n
84
GLU
99
A
VAL
100
n
85
VAL
100
A
GLN
101
n
86
GLN
101
A
ARG
102
n
87
ARG
102
A
LYS
103
n
88
LYS
103
A
ARG
104
n
89
ARG
104
A
GLU
105
n
90
GLU
105
A
MET
106
n
91
MET
106
A
ILE
107
n
92
ILE
107
A
LEU
108
n
93
LEU
108
A
LYS
109
n
94
LYS
109
A
ARG
110
n
95
ARG
110
A
LYS
111
n
96
LYS
111
A
GLU
112
n
97
GLU
112
A
GLU
113
n
98
GLU
113
A
GLU
114
n
99
GLU
114
A
n
100
115
A
n
101
116
A
n
102
117
A
n
103
118
A
n
104
119
A
n
105
120
A
n
106
121
A
n
107
122
A
n
108
123
A
n
109
124
A
n
110
125
A
n
1
216
B
n
2
217
B
n
3
218
B
n
4
219
B
n
5
220
B
PRO
221
n
6
PRO
221
B
ARG
222
n
7
ARG
222
B
ILE
223
n
8
ILE
223
B
CYS
224
n
9
CYS
224
B
GLY
225
n
10
GLY
225
B
VAL
226
n
11
VAL
226
B
CYS
227
n
12
CYS
227
B
GLY
228
n
13
GLY
228
B
ASP
229
n
14
ASP
229
B
ARG
230
n
15
ARG
230
B
ALA
231
n
16
ALA
231
B
THR
232
n
17
THR
232
B
GLY
233
n
18
GLY
233
B
PHE
234
n
19
PHE
234
B
HIS
235
n
20
HIS
235
B
PHE
236
n
21
PHE
236
B
ASN
237
n
22
ASN
237
B
ALA
238
n
23
ALA
238
B
MET
239
n
24
MET
239
B
THR
240
n
25
THR
240
B
CYS
241
n
26
CYS
241
B
GLU
242
n
27
GLU
242
B
GLY
243
n
28
GLY
243
B
CYS
244
n
29
CYS
244
B
LYS
245
n
30
LYS
245
B
GLY
246
n
31
GLY
246
B
PHE
247
n
32
PHE
247
B
PHE
248
n
33
PHE
248
B
ARG
249
n
34
ARG
249
B
ARG
250
n
35
ARG
250
B
SER
251
n
36
SER
251
B
MET
252
n
37
MET
252
B
LYS
253
n
38
LYS
253
B
ARG
254
n
39
ARG
254
B
LYS
255
n
40
LYS
255
B
ALA
256
n
41
ALA
256
B
LEU
257
n
42
LEU
257
B
PHE
258
n
43
PHE
258
B
THR
259
n
44
THR
259
B
CYS
260
n
45
CYS
260
B
PRO
261
n
46
PRO
261
B
PHE
262
n
47
PHE
262
B
ASN
263
n
48
ASN
263
B
GLY
264
n
49
GLY
264
B
ASP
265
n
50
ASP
265
B
CYS
266
n
51
CYS
266
B
ARG
267
n
52
ARG
267
B
ILE
268
n
53
ILE
268
B
THR
269
n
54
THR
269
B
LYS
270
n
55
LYS
270
B
ASP
271
n
56
ASP
271
B
ASN
272
n
57
ASN
272
B
ARG
273
n
58
ARG
273
B
ARG
274
n
59
ARG
274
B
HIS
275
n
60
HIS
275
B
CYS
276
n
61
CYS
276
B
GLN
277
n
62
GLN
277
B
ALA
278
n
63
ALA
278
B
CYS
279
n
64
CYS
279
B
ARG
280
n
65
ARG
280
B
LEU
281
n
66
LEU
281
B
LYS
282
n
67
LYS
282
B
ARG
283
n
68
ARG
283
B
CYS
284
n
69
CYS
284
B
VAL
285
n
70
VAL
285
B
ASP
286
n
71
ASP
286
B
ILE
287
n
72
ILE
287
B
GLY
288
n
73
GLY
288
B
MET
289
n
74
MET
289
B
MET
290
n
75
MET
290
B
LYS
291
n
76
LYS
291
B
GLU
292
n
77
GLU
292
B
PHE
293
n
78
PHE
293
B
ILE
294
n
79
ILE
294
B
LEU
295
n
80
LEU
295
B
THR
296
n
81
THR
296
B
ASP
297
n
82
ASP
297
B
GLU
298
n
83
GLU
298
B
GLU
299
n
84
GLU
299
B
VAL
300
n
85
VAL
300
B
GLN
301
n
86
GLN
301
B
ARG
302
n
87
ARG
302
B
LYS
303
n
88
LYS
303
B
ARG
304
n
89
ARG
304
B
GLU
305
n
90
GLU
305
B
MET
306
n
91
MET
306
B
ILE
307
n
92
ILE
307
B
LEU
308
n
93
LEU
308
B
LYS
309
n
94
LYS
309
B
ARG
310
n
95
ARG
310
B
LYS
311
n
96
LYS
311
B
GLU
312
n
97
GLU
312
B
GLU
313
n
98
GLU
313
B
GLU
314
n
99
GLU
314
B
ALA
315
n
100
ALA
315
B
LEU
316
n
101
LEU
316
B
LYS
317
n
102
LYS
317
B
ASP
318
n
103
ASP
318
B
SER
319
n
104
SER
319
B
LEU
320
n
105
LEU
320
B
ARG
321
n
106
ARG
321
B
n
107
322
B
n
108
323
B
n
109
324
B
n
110
325
B
author_defined_assembly
4
tetrameric
A
CYS
24
C
SG
CYS
9
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
27
C
SG
CYS
12
1_555
111.6
A
CYS
24
C
SG
CYS
9
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
41
C
SG
CYS
26
1_555
122.1
A
CYS
27
C
SG
CYS
12
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
41
C
SG
CYS
26
1_555
104.5
A
CYS
24
C
SG
CYS
9
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
44
C
SG
CYS
29
1_555
111.9
A
CYS
27
C
SG
CYS
12
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
44
C
SG
CYS
29
1_555
110.8
A
CYS
41
C
SG
CYS
26
1_555
A
ZN
150
E
ZN
ZN
1_555
A
CYS
44
C
SG
CYS
29
1_555
94.7
A
CYS
60
C
SG
CYS
45
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
66
C
SG
CYS
51
1_555
109.2
A
CYS
60
C
SG
CYS
45
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
76
C
SG
CYS
61
1_555
107.4
A
CYS
66
C
SG
CYS
51
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
76
C
SG
CYS
61
1_555
107.7
A
CYS
60
C
SG
CYS
45
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
79
C
SG
CYS
64
1_555
114.3
A
CYS
66
C
SG
CYS
51
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
79
C
SG
CYS
64
1_555
109.1
A
CYS
76
C
SG
CYS
61
1_555
A
ZN
151
F
ZN
ZN
1_555
A
CYS
79
C
SG
CYS
64
1_555
109.0
B
CYS
224
D
SG
CYS
9
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
227
D
SG
CYS
12
1_555
106.5
B
CYS
224
D
SG
CYS
9
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
241
D
SG
CYS
26
1_555
123.0
B
CYS
227
D
SG
CYS
12
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
241
D
SG
CYS
26
1_555
105.6
B
CYS
224
D
SG
CYS
9
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
244
D
SG
CYS
29
1_555
109.7
B
CYS
227
D
SG
CYS
12
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
244
D
SG
CYS
29
1_555
119.6
B
CYS
241
D
SG
CYS
26
1_555
B
ZN
350
G
ZN
ZN
1_555
B
CYS
244
D
SG
CYS
29
1_555
93.0
B
CYS
260
D
SG
CYS
45
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
266
D
SG
CYS
51
1_555
123.6
B
CYS
260
D
SG
CYS
45
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
276
D
SG
CYS
61
1_555
108.0
B
CYS
266
D
SG
CYS
51
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
276
D
SG
CYS
61
1_555
112.8
B
CYS
260
D
SG
CYS
45
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
279
D
SG
CYS
64
1_555
109.9
B
CYS
266
D
SG
CYS
51
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
279
D
SG
CYS
64
1_555
100.7
B
CYS
276
D
SG
CYS
61
1_555
B
ZN
351
H
ZN
ZN
1_555
B
CYS
279
D
SG
CYS
64
1_555
98.7
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
GLY
33
C
N
GLY
18
A
O
THR
40
C
O
THR
25
B
N
HIS
235
D
N
HIS
20
B
O
ALA
238
D
O
ALA
23
1
A
CG
LYS
109
C
CG
LYS
94
1
Y
1
A
CD
LYS
109
C
CD
LYS
94
1
Y
1
A
CE
LYS
109
C
CE
LYS
94
1
Y
1
A
NZ
LYS
109
C
NZ
LYS
94
1
Y
1
A
CG
ARG
110
C
CG
ARG
95
1
Y
1
A
CD
ARG
110
C
CD
ARG
95
1
Y
1
A
NE
ARG
110
C
NE
ARG
95
1
Y
1
A
CZ
ARG
110
C
CZ
ARG
95
1
Y
1
A
NH1
ARG
110
C
NH1
ARG
95
1
Y
1
A
NH2
ARG
110
C
NH2
ARG
95
1
Y
1
A
CG
LYS
111
C
CG
LYS
96
1
Y
1
A
CD
LYS
111
C
CD
LYS
96
1
Y
1
A
CE
LYS
111
C
CE
LYS
96
1
Y
1
A
NZ
LYS
111
C
NZ
LYS
96
1
Y
1
A
CG
GLU
112
C
CG
GLU
97
1
Y
1
A
CD
GLU
112
C
CD
GLU
97
1
Y
1
A
OE1
GLU
112
C
OE1
GLU
97
1
Y
1
A
OE2
GLU
112
C
OE2
GLU
97
1
Y
1
A
CG
GLU
113
C
CG
GLU
98
1
Y
1
A
CD
GLU
113
C
CD
GLU
98
1
Y
1
A
OE1
GLU
113
C
OE1
GLU
98
1
Y
1
A
OE2
GLU
113
C
OE2
GLU
98
1
Y
1
A
CG
GLU
114
C
CG
GLU
99
1
Y
1
A
CD
GLU
114
C
CD
GLU
99
1
Y
1
A
OE1
GLU
114
C
OE1
GLU
99
1
Y
1
A
OE2
GLU
114
C
OE2
GLU
99
1
Y
1
B
CG
ARG
230
D
CG
ARG
15
1
Y
1
B
CD
ARG
230
D
CD
ARG
15
1
Y
1
B
NE
ARG
230
D
NE
ARG
15
1
Y
1
B
CZ
ARG
230
D
CZ
ARG
15
1
Y
1
B
NH1
ARG
230
D
NH1
ARG
15
1
Y
1
B
NH2
ARG
230
D
NH2
ARG
15
1
Y
1
B
CG
ARG
267
D
CG
ARG
52
1
Y
1
B
CD
ARG
267
D
CD
ARG
52
1
Y
1
B
NE
ARG
267
D
NE
ARG
52
1
Y
1
B
CZ
ARG
267
D
CZ
ARG
52
1
Y
1
B
NH1
ARG
267
D
NH1
ARG
52
1
Y
1
B
NH2
ARG
267
D
NH2
ARG
52
1
Y
1
B
CG
ARG
302
D
CG
ARG
87
1
Y
1
B
CD
ARG
302
D
CD
ARG
87
1
Y
1
B
NE
ARG
302
D
NE
ARG
87
1
Y
1
B
CZ
ARG
302
D
CZ
ARG
87
1
Y
1
B
NH1
ARG
302
D
NH1
ARG
87
1
Y
1
B
NH2
ARG
302
D
NH2
ARG
87
1
Y
1
B
CG
LYS
303
D
CG
LYS
88
1
Y
1
B
CD
LYS
303
D
CD
LYS
88
1
Y
1
B
CE
LYS
303
D
CE
LYS
88
1
Y
1
B
NZ
LYS
303
D
NZ
LYS
88
1
Y
1
B
CG
ARG
304
D
CG
ARG
89
1
Y
1
B
CD
ARG
304
D
CD
ARG
89
1
Y
1
B
NE
ARG
304
D
NE
ARG
89
1
Y
1
B
CZ
ARG
304
D
CZ
ARG
89
1
Y
1
B
NH1
ARG
304
D
NH1
ARG
89
1
Y
1
B
NH2
ARG
304
D
NH2
ARG
89
1
Y
1
B
CG
GLU
305
D
CG
GLU
90
1
Y
1
B
CD
GLU
305
D
CD
GLU
90
1
Y
1
B
OE1
GLU
305
D
OE1
GLU
90
1
Y
1
B
OE2
GLU
305
D
OE2
GLU
90
1
Y
1
B
CG
MET
306
D
CG
MET
91
1
Y
1
B
SD
MET
306
D
SD
MET
91
1
Y
1
B
CE
MET
306
D
CE
MET
91
1
Y
1
B
CG
LYS
309
D
CG
LYS
94
1
Y
1
B
CD
LYS
309
D
CD
LYS
94
1
Y
1
B
CE
LYS
309
D
CE
LYS
94
1
Y
1
B
NZ
LYS
309
D
NZ
LYS
94
1
Y
1
B
CG
ARG
310
D
CG
ARG
95
1
Y
1
B
CD
ARG
310
D
CD
ARG
95
1
Y
1
B
NE
ARG
310
D
NE
ARG
95
1
Y
1
B
CZ
ARG
310
D
CZ
ARG
95
1
Y
1
B
NH1
ARG
310
D
NH1
ARG
95
1
Y
1
B
NH2
ARG
310
D
NH2
ARG
95
1
Y
1
B
CG
LYS
317
D
CG
LYS
102
1
Y
1
B
CD
LYS
317
D
CD
LYS
102
1
Y
1
B
CE
LYS
317
D
CE
LYS
102
1
Y
1
B
NZ
LYS
317
D
NZ
LYS
102
1
Y
1
B
CG
ASP
318
D
CG
ASP
103
1
Y
1
B
OD1
ASP
318
D
OD1
ASP
103
1
Y
1
B
OD2
ASP
318
D
OD2
ASP
103
1
Y
1
B
CG
ARG
321
D
CG
ARG
106
1
Y
1
B
CD
ARG
321
D
CD
ARG
106
1
Y
1
B
NE
ARG
321
D
NE
ARG
106
1
Y
1
B
CZ
ARG
321
D
CZ
ARG
106
1
Y
1
B
NH1
ARG
321
D
NH1
ARG
106
1
Y
1
B
NH2
ARG
321
D
NH2
ARG
106
1
Y
1
A
PHE
16
C
PHE
1
1
Y
1
A
ASP
17
C
ASP
2
1
Y
1
A
ARG
18
C
ARG
3
1
Y
1
A
ASN
19
C
ASN
4
1
Y
1
A
VAL
20
C
VAL
5
1
Y
1
A
ALA
115
C
ALA
100
1
Y
1
A
LEU
116
C
LEU
101
1
Y
1
A
LYS
117
C
LYS
102
1
Y
1
A
ASP
118
C
ASP
103
1
Y
1
A
SER
119
C
SER
104
1
Y
1
A
LEU
120
C
LEU
105
1
Y
1
A
ARG
121
C
ARG
106
1
Y
1
A
PRO
122
C
PRO
107
1
Y
1
A
LYS
123
C
LYS
108
1
Y
1
A
LEU
124
C
LEU
109
1
Y
1
A
SER
125
C
SER
110
1
Y
1
B
PHE
216
D
PHE
1
1
Y
1
B
ASP
217
D
ASP
2
1
Y
1
B
ARG
218
D
ARG
3
1
Y
1
B
ASN
219
D
ASN
4
1
Y
1
B
VAL
220
D
VAL
5
1
Y
1
B
PRO
322
D
PRO
107
1
Y
1
B
LYS
323
D
LYS
108
1
Y
1
B
LEU
324
D
LEU
109
1
Y
1
B
SER
325
D
SER
110
1
Y
1
D
A
OP2
NH2
DT
ARG
427
50
2.19
1
C
DA
413
0.055
SIDE CHAIN
1
D
DC
423
0.061
SIDE CHAIN
1
D
DT
428
0.065
SIDE CHAIN
1
D
DC
429
0.076
SIDE CHAIN
1
D
DA
430
0.061
SIDE CHAIN
1
D
DC
432
0.066
SIDE CHAIN
1
2.43
0.30
108.30
110.73
D
D
D
O4'
C1'
N1
DC
DC
DC
432
432
432
N
1
6.78
1.10
114.20
120.98
A
A
A
CA
CB
SG
CYS
CYS
CYS
41
41
41
N
1
C
C
O3'
C3'
DG
DG
404
404
-0.043
0.006
1.419
1.376
N
1
B
B
OD1
OD1
ASP
ASP
286
286
2.03
1_555
8_555
1
A
ARG
22
-54.95
41.49
1
A
ASP
29
-60.58
-179.61
1
A
ASN
37
88.26
20.57
1
A
MET
39
-58.75
104.78
1
A
LYS
53
-62.78
-78.44
1
A
ARG
54
-51.51
19.15
1
A
LYS
55
29.00
64.70
1
A
PHE
62
-128.50
-106.18
1
A
ASP
65
-162.01
42.98
1
A
GLU
105
-75.03
32.23
1
A
MET
106
-154.88
-23.35
1
A
GLU
112
-146.96
15.25
1
B
ARG
222
68.83
-175.02
1
B
ILE
223
67.10
111.33
1
B
ASP
229
-60.57
-171.28
1
B
ASN
237
89.33
12.82
1
B
LYS
255
85.28
-7.71
1
B
ALA
256
-19.51
118.99
1
B
PHE
262
-124.25
-112.76
1
B
LYS
270
-50.15
-4.99
1
B
ASP
271
-112.15
-77.90
1
B
ARG
273
-27.45
-68.37
1
B
LEU
320
-77.51
30.67
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
PARAM_ZN
77.6
22.99
0.00
0.00
22.99
0.00
-45.98
0.2750000
0.008
0.2230000
2.70
50
1222
11999
11999
10.2
89.1
RANDOM
682827.51
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1KB4
MAXIMUM LIKELIHOOD FUNCTION
FLAT MODEL
43.1547
0.29935
0.48
0.42
5.00
0.81
0.63
2.70
50
34
2271
4
732
1501
0.016
1.8
21.5
1.37
1.10
1.50
1.96
2.00
1.49
2.00
2.42
2.50
0.4770000
0.051
0.4200000
2.80
89
723
10
11.0
61.2
44.9
2.7
50
1KB6
13127
-3
0.0710000
1
34.4
12.5
96.7
0.3200000
2.7
2.8
2.9
1027
77.6
refinement
CNS
data reduction
HKL-2000
data scaling
HKL-2000
phasing
CNS
Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
A
CYS
41
C
CYS
26
HELX_P
A
ARG
54
C
ARG
39
1
1
14
A
CYS
76
C
CYS
61
HELX_P
A
ILE
87
C
ILE
72
1
2
12
A
MET
90
C
MET
75
HELX_P
A
ILE
94
C
ILE
79
5
3
5
A
THR
96
C
THR
81
HELX_P
A
LEU
108
C
LEU
93
1
4
13
B
CYS
241
D
CYS
26
HELX_P
B
LYS
255
D
LYS
40
1
5
15
B
ASP
271
D
ASP
56
HELX_P
B
HIS
275
D
HIS
60
5
6
5
B
CYS
276
D
CYS
61
HELX_P
B
GLY
288
D
GLY
73
1
7
13
B
MET
290
D
MET
75
HELX_P
B
ILE
294
D
ILE
79
5
8
5
B
THR
296
D
THR
81
HELX_P
B
LEU
320
D
LEU
105
1
9
25
metalc
2.225
A
CYS
24
C
SG
CYS
9
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.252
A
CYS
27
C
SG
CYS
12
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.367
A
CYS
41
C
SG
CYS
26
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.316
A
CYS
44
C
SG
CYS
29
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.177
A
CYS
60
C
SG
CYS
45
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.297
A
CYS
66
C
SG
CYS
51
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.261
A
CYS
76
C
SG
CYS
61
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.217
A
CYS
79
C
SG
CYS
64
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.223
B
CYS
224
D
SG
CYS
9
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.206
B
CYS
227
D
SG
CYS
12
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.362
B
CYS
241
D
SG
CYS
26
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.425
B
CYS
244
D
SG
CYS
29
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.265
B
CYS
260
D
SG
CYS
45
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.422
B
CYS
266
D
SG
CYS
51
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.366
B
CYS
276
D
SG
CYS
61
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.418
B
CYS
279
D
SG
CYS
64
1_555
B
ZN
351
H
ZN
ZN
1_555
hydrog
WATSON-CRICK
C
DC
401
A
N3
DC
1
1_555
D
DG
436
B
N1
DG
18
1_555
hydrog
WATSON-CRICK
C
DC
401
A
N4
DC
1
1_555
D
DG
436
B
O6
DG
18
1_555
hydrog
WATSON-CRICK
C
DC
401
A
O2
DC
1
1_555
D
DG
436
B
N2
DG
18
1_555
hydrog
WATSON-CRICK
C
DA
402
A
N1
DA
2
1_555
D
DT
435
B
N3
DT
17
1_555
hydrog
WATSON-CRICK
C
DA
402
A
N6
DA
2
1_555
D
DT
435
B
O4
DT
17
1_555
hydrog
WATSON-CRICK
C
DC
403
A
N3
DC
3
1_555
D
DG
434
B
N1
DG
16
1_555
hydrog
WATSON-CRICK
C
DC
403
A
N4
DC
3
1_555
D
DG
434
B
O6
DG
16
1_555
hydrog
WATSON-CRICK
C
DC
403
A
O2
DC
3
1_555
D
DG
434
B
N2
DG
16
1_555
hydrog
WATSON-CRICK
C
DG
404
A
N1
DG
4
1_555
D
DC
433
B
N3
DC
15
1_555
hydrog
WATSON-CRICK
C
DG
404
A
N2
DG
4
1_555
D
DC
433
B
O2
DC
15
1_555
hydrog
WATSON-CRICK
C
DG
404
A
O6
DG
4
1_555
D
DC
433
B
N4
DC
15
1_555
hydrog
WATSON-CRICK
C
DG
405
A
N1
DG
5
1_555
D
DC
432
B
N3
DC
14
1_555
hydrog
WATSON-CRICK
C
DG
405
A
N2
DG
5
1_555
D
DC
432
B
O2
DC
14
1_555
hydrog
WATSON-CRICK
C
DG
405
A
O6
DG
5
1_555
D
DC
432
B
N4
DC
14
1_555
hydrog
WATSON-CRICK
C
DG
406
A
N1
DG
6
1_555
D
DC
431
B
N3
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
406
A
N2
DG
6
1_555
D
DC
431
B
O2
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
406
A
O6
DG
6
1_555
D
DC
431
B
N4
DC
13
1_555
hydrog
WATSON-CRICK
C
DT
407
A
N3
DT
7
1_555
D
DA
430
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
C
DT
407
A
O4
DT
7
1_555
D
DA
430
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
C
DG
408
A
N1
DG
8
1_555
D
DC
429
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
C
DG
408
A
N2
DG
8
1_555
D
DC
429
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
C
DG
408
A
O6
DG
8
1_555
D
DC
429
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
C
DA
409
A
N1
DA
9
1_555
D
DT
428
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
C
DA
409
A
N6
DA
9
1_555
D
DT
428
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
C
DA
410
A
N1
DA
10
1_555
D
DT
427
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
C
DA
410
A
N6
DA
10
1_555
D
DT
427
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
C
DT
411
A
N3
DT
11
1_555
D
DA
426
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
C
DT
411
A
O4
DT
11
1_555
D
DA
426
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
C
DG
412
A
N1
DG
12
1_555
D
DC
425
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
412
A
N2
DG
12
1_555
D
DC
425
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
412
A
O6
DG
12
1_555
D
DC
425
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
C
DA
413
A
N1
DA
13
1_555
D
DT
424
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
C
DA
413
A
N6
DA
13
1_555
D
DT
424
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
C
DG
414
A
N1
DG
14
1_555
D
DC
423
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
414
A
N2
DG
14
1_555
D
DC
423
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
414
A
O6
DG
14
1_555
D
DC
423
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
415
A
N1
DG
15
1_555
D
DC
422
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
C
DG
415
A
N2
DG
15
1_555
D
DC
422
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
C
DG
415
A
O6
DG
15
1_555
D
DC
422
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
C
DA
416
A
N1
DA
16
1_555
D
DT
421
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
C
DA
416
A
N6
DA
16
1_555
D
DT
421
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
C
DC
417
A
N3
DC
17
1_555
D
DG
420
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
417
A
N4
DC
17
1_555
D
DG
420
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
417
A
O2
DC
17
1_555
D
DG
420
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
C
DA
418
A
N1
DA
18
1_555
D
DT
419
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
C
DA
418
A
N6
DA
18
1_555
D
DT
419
B
O4
DT
1
1_555
TRANSCRIPTION/DNA
VDR, NUCLEAR RECEPTOR, PROTEIN-DNA COMPLEX, VITAMIN D, TRANSCRIPTION-DNA COMPLEX
VDR_HUMAN
UNP
3
16
P11473
FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFIL
TDEEVQRKREMILKRKEEEALKDSLRPKLS
1KB6
PDB
1
1KB6
1KB6
PDB
2
1KB6
16
125
1KB6
16
125
P11473
A
1
1
110
16
125
1KB6
216
325
P11473
B
1
1
110
401
418
1KB6
401
418
1KB6
C
2
1
18
419
436
1KB6
419
436
1KB6
D
3
1
18
2
2
anti-parallel
anti-parallel
A
GLY
33
C
GLY
18
A
HIS
35
C
HIS
20
A
ALA
38
C
ALA
23
A
THR
40
C
THR
25
B
GLY
233
D
GLY
18
B
HIS
235
D
HIS
20
B
ALA
238
D
ALA
23
B
THR
240
D
THR
25
BINDING SITE FOR RESIDUE ZN A 150
A
ZN
150
Software
4
BINDING SITE FOR RESIDUE ZN A 151
A
ZN
151
Software
4
BINDING SITE FOR RESIDUE ZN B 350
B
ZN
350
Software
4
BINDING SITE FOR RESIDUE ZN B 351
B
ZN
351
Software
4
A
CYS
24
C
CYS
9
4
1_555
A
CYS
27
C
CYS
12
4
1_555
A
CYS
41
C
CYS
26
4
1_555
A
CYS
44
C
CYS
29
4
1_555
A
CYS
60
C
CYS
45
4
1_555
A
CYS
66
C
CYS
51
4
1_555
A
CYS
76
C
CYS
61
4
1_555
A
CYS
79
C
CYS
64
4
1_555
B
CYS
224
D
CYS
9
4
1_555
B
CYS
227
D
CYS
12
4
1_555
B
CYS
241
D
CYS
26
4
1_555
B
CYS
244
D
CYS
29
4
1_555
B
CYS
260
D
CYS
45
4
1_555
B
CYS
266
D
CYS
51
4
1_555
B
CYS
276
D
CYS
61
4
1_555
B
CYS
279
D
CYS
64
4
1_555
96
P 43 21 2