0.016261
0.000000
0.000000
0.000000
0.016261
0.000000
0.000000
0.000000
0.004133
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
61.50
61.50
241.97
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/pdb1kb4/pdb
pdb_00001kb4
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
Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element
5534.607
5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3'
1
syn
polymer
Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element
5498.551
5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*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
31
nat
water
VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR
no
no
(DC)(DA)(DC)(DA)(DG)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DA)(DG)(DG)(DT)(DC)(DA)
CACAGGTCACGAAGGTCA
C
polydeoxyribonucleotide
no
no
(DT)(DG)(DA)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DG)(DA)(DC)(DC)(DT)(DG)(DT)(DG)
TGACCTTCGTGACCTGTG
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
3.06
59.79
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
4.788
1
19
C
401
D
436
-1.570
C_DC401:DG436_D
1
-11.089
0.041
-0.117
-0.119
1.446
1
20
C
402
D
435
-0.360
C_DA402:DT435_D
2
-7.069
-0.312
0.365
-0.363
7.680
1
19
C
403
D
434
1.001
C_DC403:DG434_D
3
-3.022
0.018
-0.358
-0.219
-6.854
1
20
C
404
D
433
-0.167
C_DA404:DT433_D
4
-10.808
-0.409
0.056
0.149
3.738
1
19
C
405
D
432
3.645
C_DG405:DC432_D
5
0.263
-0.224
0.290
-0.257
-14.069
1
19
C
406
D
431
0.409
C_DG406:DC431_D
6
-9.547
-0.272
-0.337
-0.264
-7.867
1
20
C
407
D
430
3.558
C_DT407:DA430_D
7
-15.209
-0.591
0.339
-0.065
1.404
1
19
C
408
D
429
-0.910
C_DC408:DG429_D
8
-0.186
-0.180
-0.144
-0.220
11.639
1
20
C
409
D
428
1.007
C_DA409:DT428_D
9
-12.029
0.063
0.356
-0.052
4.712
1
19
C
410
D
427
-3.337
C_DC410:DG427_D
10
-9.837
0.588
0.244
-0.200
-2.520
1
19
C
411
D
426
-0.691
C_DG411:DC426_D
11
-4.998
-0.119
-0.130
-0.136
5.827
1
20
C
412
D
425
2.757
C_DA412:DT425_D
12
-3.932
0.200
0.162
-0.176
-6.099
1
20
C
413
D
424
-0.792
C_DA413:DT424_D
13
-11.264
-0.091
0.220
0.137
0.150
1
19
C
414
D
423
0.323
C_DG414:DC423_D
14
-5.999
-0.115
0.038
-0.211
-5.081
1
19
C
415
D
422
-4.685
C_DG415:DC422_D
15
-6.581
-0.103
-0.129
-0.367
-1.463
1
20
C
416
D
421
-4.503
C_DT416:DA421_D
16
-9.254
-0.227
0.130
-0.456
7.773
1
19
C
417
D
420
3.215
C_DC417:DG420_D
17
-1.523
0.476
-0.389
-0.202
16.882
1
20
C
418
D
419
0.288
C_DA418:DT419_D
18
-14.916
0.378
0.311
-0.147
3.389
35.827
C
C
401
402
13.204
D
D
436
435
3.467
8.055
-0.166
0.003
CC_DC401DA402:DT435DG436_DD
1
-1.604
2.629
34.903
-1.224
0.024
3.320
33.058
C
C
402
403
6.127
D
D
435
434
3.334
3.467
0.473
-0.290
CC_DA402DC403:DG434DT435_DD
2
4.994
-8.825
32.509
-1.110
0.036
3.623
38.636
C
C
403
404
5.526
D
D
434
433
3.528
3.625
-0.772
0.294
CC_DC403DA404:DT433DG434_DD
3
-8.332
12.703
37.592
-0.051
0.028
2.984
34.978
C
C
404
405
4.026
D
D
433
432
3.093
2.416
0.533
-0.801
CC_DA404DG405:DC432DT433_DD
4
-2.730
4.549
34.794
-1.671
-1.270
3.522
36.662
C
C
405
406
4.374
D
D
432
431
3.723
2.742
-0.757
-0.967
CC_DG405DG406:DC431DC432_DD
5
4.669
-7.449
36.273
-1.956
1.916
3.163
27.988
C
C
406
407
2.751
D
D
431
430
3.156
1.324
-0.530
-0.711
CC_DG406DT407:DA430DC431_DD
6
-4.634
9.628
27.578
-1.775
0.027
3.485
37.791
C
C
407
408
1.487
D
D
430
429
3.339
0.958
0.934
1.495
CC_DT407DC408:DG429DA430_DD
7
6.684
-10.372
37.204
2.179
-0.536
3.277
37.280
C
C
408
409
4.645
D
D
429
428
3.137
2.958
-0.502
1.456
CC_DC408DA409:DT428DG429_DD
8
-4.867
7.641
36.858
1.891
0.149
3.545
35.703
C
C
409
410
-0.836
D
D
428
427
3.525
-0.512
0.351
-0.661
CC_DA409DC410:DG427DT428_DD
9
1.595
-2.603
35.665
-0.999
-0.324
3.514
40.306
C
C
410
411
8.583
D
D
427
426
3.518
5.873
0.179
0.304
CC_DC410DG411:DC426DG427_DD
10
6.199
-9.059
39.428
-0.281
0.501
3.199
30.041
C
C
411
412
13.235
D
D
426
425
3.195
6.790
-0.025
0.449
CC_DG411DA412:DT425DC426_DD
11
-3.240
6.314
29.105
-0.519
-0.613
3.561
38.489
C
C
412
413
-1.053
D
D
425
424
3.441
-0.691
-1.015
-0.232
CC_DA412DA413:DT424DT425_DD
12
-6.273
9.556
37.987
-0.259
0.701
3.124
34.473
C
C
413
414
9.737
D
D
424
423
3.253
5.744
0.324
-0.578
CC_DA413DG414:DC423DT424_DD
13
0.940
-1.594
33.993
-1.851
-0.403
3.467
35.795
C
C
414
415
2.093
D
D
423
422
3.507
1.286
-0.656
-0.971
CC_DG414DG415:DC422DC423_DD
14
0.186
-0.302
35.772
-1.778
1.096
3.253
29.184
C
C
415
416
2.201
D
D
422
421
3.263
1.109
-0.461
-0.364
CC_DG415DT416:DA421DC422_DD
15
-0.403
0.799
29.161
-0.963
0.828
3.401
42.042
C
C
416
417
3.329
D
D
421
420
3.149
2.376
1.259
1.658
CC_DT416DC417:DG420DA421_DD
16
7.409
-10.382
41.348
2.062
-0.980
3.351
33.678
C
C
417
418
1.004
D
D
420
419
3.268
0.580
-0.679
1.382
CC_DC417DA418:DT419DG420_DD
17
-4.418
7.647
33.391
2.289
0.441
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 Rat Osteocalcin (OC) Response Element
RCSB
Y
RCSB
2001-11-05
REL
REL
ZN
ZINC ION
HOH
water
2NLL
TR Half-Complex from PDB Entry 2NLL
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
607
5
HOH
HOH
607
C
WAT
613
5
HOH
HOH
613
C
WAT
620
5
HOH
HOH
620
C
WAT
624
5
HOH
HOH
624
C
WAT
626
5
HOH
HOH
626
C
WAT
628
5
HOH
HOH
628
C
WAT
629
5
HOH
HOH
629
C
WAT
617
5
HOH
HOH
617
D
WAT
622
5
HOH
HOH
622
D
WAT
627
5
HOH
HOH
627
D
WAT
601
5
HOH
HOH
601
A
WAT
603
5
HOH
HOH
603
A
WAT
604
5
HOH
HOH
604
A
WAT
605
5
HOH
HOH
605
A
WAT
608
5
HOH
HOH
608
A
WAT
609
5
HOH
HOH
609
A
WAT
612
5
HOH
HOH
612
A
WAT
614
5
HOH
HOH
614
A
WAT
615
5
HOH
HOH
615
A
WAT
616
5
HOH
HOH
616
A
WAT
618
5
HOH
HOH
618
A
WAT
623
5
HOH
HOH
623
A
WAT
625
5
HOH
HOH
625
A
WAT
602
5
HOH
HOH
602
B
WAT
606
5
HOH
HOH
606
B
WAT
610
5
HOH
HOH
610
B
WAT
611
5
HOH
HOH
611
B
WAT
619
5
HOH
HOH
619
B
WAT
621
5
HOH
HOH
621
B
WAT
630
5
HOH
HOH
630
B
WAT
631
5
HOH
HOH
631
B
C
401
n
1
DC
401
C
A
402
n
2
DA
402
C
C
403
n
3
DC
403
C
A
404
n
4
DA
404
C
G
405
n
5
DG
405
C
G
406
n
6
DG
406
C
T
407
n
7
DT
407
C
C
408
n
8
DC
408
C
A
409
n
9
DA
409
C
C
410
n
10
DC
410
C
G
411
n
11
DG
411
C
A
412
n
12
DA
412
C
A
413
n
13
DA
413
C
G
414
n
14
DG
414
C
G
415
n
15
DG
415
C
T
416
n
16
DT
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
A
421
n
3
DA
421
D
C
422
n
4
DC
422
D
C
423
n
5
DC
423
D
T
424
n
6
DT
424
D
T
425
n
7
DT
425
D
C
426
n
8
DC
426
D
G
427
n
9
DG
427
D
T
428
n
10
DT
428
D
G
429
n
11
DG
429
D
A
430
n
12
DA
430
D
C
431
n
13
DC
431
D
C
432
n
14
DC
432
D
T
433
n
15
DT
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
n
6
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
n
6
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
n
106
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
113.3
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
107.4
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
99.1
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
122.9
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
110.9
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
99.3
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
104.8
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
104.0
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
116.6
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
107.8
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
115.3
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
113.1
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
106.6
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
105.7
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
115.2
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
111.8
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
103.4
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
131.0
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
94.3
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
104.5
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
111.2
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
111.2
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
96.3
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
HIS
35
C
N
HIS
20
A
O
ALA
38
C
O
ALA
23
B
N
HIS
235
D
N
HIS
20
B
O
ALA
238
D
O
ALA
23
1
A
CG
ARG
30
C
CG
ARG
15
1
Y
1
A
CD
ARG
30
C
CD
ARG
15
1
Y
1
A
NE
ARG
30
C
NE
ARG
15
1
Y
1
A
CZ
ARG
30
C
CZ
ARG
15
1
Y
1
A
NH1
ARG
30
C
NH1
ARG
15
1
Y
1
A
NH2
ARG
30
C
NH2
ARG
15
1
Y
1
A
CG
GLN
101
C
CG
GLN
86
1
Y
1
A
CD
GLN
101
C
CD
GLN
86
1
Y
1
A
OE1
GLN
101
C
OE1
GLN
86
1
Y
1
A
NE2
GLN
101
C
NE2
GLN
86
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
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
GLU
312
D
CG
GLU
97
1
Y
1
B
CD
GLU
312
D
CD
GLU
97
1
Y
1
B
OE1
GLU
312
D
OE1
GLU
97
1
Y
1
B
OE2
GLU
312
D
OE2
GLU
97
1
Y
1
B
CG
GLU
313
D
CG
GLU
98
1
Y
1
B
CD
GLU
313
D
CD
GLU
98
1
Y
1
B
OE1
GLU
313
D
OE1
GLU
98
1
Y
1
B
OE2
GLU
313
D
OE2
GLU
98
1
Y
1
B
CG
GLU
314
D
CG
GLU
99
1
Y
1
B
CD
GLU
314
D
CD
GLU
99
1
Y
1
B
OE1
GLU
314
D
OE1
GLU
99
1
Y
1
B
OE2
GLU
314
D
OE2
GLU
99
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
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
PRO
21
C
PRO
6
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
221
D
PRO
6
1
Y
1
B
ARG
321
D
ARG
106
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
B
B
NH1
O
ARG
HOH
250
630
2.12
1
C
DC
401
0.069
SIDE CHAIN
1
C
DG
414
0.058
SIDE CHAIN
1
B
B
CB
SG
CYS
CYS
260
260
-0.099
0.016
1.812
1.713
N
1
A
LYS
55
54.49
15.78
1
A
PHE
62
-104.91
-119.01
1
A
ASP
65
-152.02
41.55
1
A
LYS
70
-39.25
-38.18
1
A
ARG
104
-72.54
25.09
1
A
LYS
111
-97.47
-69.97
1
A
GLU
112
-64.01
32.21
1
A
GLU
113
-146.46
18.16
1
B
PHE
262
-112.90
-122.20
1
B
ASN
263
-79.67
-70.31
1
B
ASP
265
-156.13
56.96
1
B
MET
306
-55.74
13.65
1
B
ASP
318
-90.70
39.37
1
B
SER
319
-137.17
-48.80
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
PARAM_ZN
76.0
24.32
0.00
0.00
24.32
0.00
-48.64
0.2720000
0.008
0.2140000
2.80
50
1124
11200
11200
10.0
91.6
RANDOM
464135.50
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
TR Half-Complex from PDB Entry 2NLL
MAXIMUM LIKELIHOOD FUNCTION
FLAT MODEL
37.5931
0.309478
0.49
0.40
5.00
0.78
0.64
2.80
50
31
2235
4
732
1468
0.015
1.7
21.6
1.31
1.08
1.50
1.91
2.00
1.54
2.00
2.53
2.50
0.4860000
0.054
0.4720000
2.90
81
828
10
8.9
77.0
79.8
2.8
50
1KB4
12384
-3
0.1000000
1
27.2
14.1
99.5
0.3900000
2.80
2.90
2.3
1173
99.0
refinement
CNS
data reduction
HKL-2000
data scaling
HKL-2000
phasing
CNS
Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) 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
ASN
72
C
ASN
57
HELX_P
A
HIS
75
C
HIS
60
5
2
4
A
CYS
76
C
CYS
61
HELX_P
A
ILE
87
C
ILE
72
1
3
12
A
MET
90
C
MET
75
HELX_P
A
ILE
94
C
ILE
79
5
4
5
A
THR
96
C
THR
81
HELX_P
A
ARG
104
C
ARG
89
1
5
9
B
CYS
241
D
CYS
26
HELX_P
B
LYS
255
D
LYS
40
1
6
15
B
ASP
271
D
ASP
56
HELX_P
B
HIS
275
D
HIS
60
5
7
5
B
CYS
276
D
CYS
61
HELX_P
B
GLY
288
D
GLY
73
1
8
13
B
MET
290
D
MET
75
HELX_P
B
ILE
294
D
ILE
79
5
9
5
B
THR
296
D
THR
81
HELX_P
B
MET
306
D
MET
91
1
10
11
B
LYS
309
D
LYS
94
HELX_P
B
LYS
317
D
LYS
102
1
11
9
metalc
2.163
A
CYS
24
C
SG
CYS
9
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.293
A
CYS
27
C
SG
CYS
12
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.458
A
CYS
41
C
SG
CYS
26
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.361
A
CYS
44
C
SG
CYS
29
1_555
A
ZN
150
E
ZN
ZN
1_555
metalc
2.300
A
CYS
60
C
SG
CYS
45
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.378
A
CYS
66
C
SG
CYS
51
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.211
A
CYS
76
C
SG
CYS
61
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.191
A
CYS
79
C
SG
CYS
64
1_555
A
ZN
151
F
ZN
ZN
1_555
metalc
2.245
B
CYS
224
D
SG
CYS
9
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.211
B
CYS
227
D
SG
CYS
12
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.541
B
CYS
241
D
SG
CYS
26
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.335
B
CYS
244
D
SG
CYS
29
1_555
B
ZN
350
G
ZN
ZN
1_555
metalc
2.176
B
CYS
260
D
SG
CYS
45
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.374
B
CYS
266
D
SG
CYS
51
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.495
B
CYS
276
D
SG
CYS
61
1_555
B
ZN
351
H
ZN
ZN
1_555
metalc
2.347
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
DA
404
A
N1
DA
4
1_555
D
DT
433
B
N3
DT
15
1_555
hydrog
WATSON-CRICK
C
DA
404
A
N6
DA
4
1_555
D
DT
433
B
O4
DT
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
DC
408
A
N3
DC
8
1_555
D
DG
429
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
C
DC
408
A
N4
DC
8
1_555
D
DG
429
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
C
DC
408
A
O2
DC
8
1_555
D
DG
429
B
N2
DG
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
DC
410
A
N3
DC
10
1_555
D
DG
427
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
C
DC
410
A
N4
DC
10
1_555
D
DG
427
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
C
DC
410
A
O2
DC
10
1_555
D
DG
427
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
C
DG
411
A
N1
DG
11
1_555
D
DC
426
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
C
DG
411
A
N2
DG
11
1_555
D
DC
426
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
C
DG
411
A
O6
DG
11
1_555
D
DC
426
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
C
DA
412
A
N1
DA
12
1_555
D
DT
425
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
C
DA
412
A
N6
DA
12
1_555
D
DT
425
B
O4
DT
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
DT
416
A
N3
DT
16
1_555
D
DA
421
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
C
DT
416
A
O4
DT
16
1_555
D
DA
421
B
N6
DA
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
1KB4
PDB
1
1KB4
1KB4
PDB
2
1KB4
16
125
1KB4
16
125
P11473
A
1
1
110
16
125
1KB4
216
325
P11473
B
1
1
110
401
418
1KB4
401
418
1KB4
C
2
1
18
419
436
1KB4
419
436
1KB4
D
3
1
18
2
2
anti-parallel
anti-parallel
A
PHE
34
C
PHE
19
A
HIS
35
C
HIS
20
A
ALA
38
C
ALA
23
A
MET
39
C
MET
24
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