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