ID code: '1ZL3' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' G B 401 beta 4 10 7 32 C1' G B 402 beta 27 33 30 55 C1' C B 403 beta 50 56 53 75 C1' A B 404 beta 70 76 73 97 C1' A B 405 beta 92 98 95 119 C1' C B 406 beta 114 120 117 139 C1' G B 407 beta 134 140 137 162 C1' G B 408 beta 157 163 160 185 C1' U B 409 beta 180 186 183 205 C1' UD5 B 410 beta 200 206 203 226 C1' C B 411 beta 221 227 224 246 C1' G B 412 beta 241 247 244 269 C1' A B 413 beta 264 270 267 291 C1' U B 414 beta 286 292 289 311 C1' C B 415 beta 306 312 309 331 C1' C B 416 beta 326 332 329 351 C1' C B 417 beta 346 352 349 371 C1' G B 418 beta 366 372 369 394 C1' U B 419 beta 389 395 392 414 C1' U B 420 beta 409 415 412 434 C1' G B 421 beta 429 435 432 457 C1' C B 422 beta 452 458 455 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 401 OK 9 5 8 30 C2' G B 402 OK 32 28 31 53 C2' C B 403 OK 55 51 54 73 C2' A B 404 OK 75 71 74 95 C2' A B 405 OK 97 93 96 117 C2' C B 406 OK 119 115 118 137 C2' G B 407 OK 139 135 138 160 C2' G B 408 OK 162 158 161 183 C2' U B 409 OK 185 181 184 203 C2' UD5 B 410 OK 205 201 204 224 C2' C B 411 OK 226 222 225 244 C2' G B 412 OK 246 242 245 267 C2' A B 413 OK 269 265 268 289 C2' U B 414 OK 291 287 290 309 C2' C B 415 OK 311 307 310 329 C2' C B 416 OK 331 327 330 349 C2' C B 417 OK 351 347 350 369 C2' G B 418 OK 371 367 370 392 C2' U B 419 OK 394 390 393 412 C2' U B 420 OK 414 410 413 432 C2' G B 421 OK 434 430 433 455 C2' C B 422 OK 457 453 456 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 401 OK 3 6 7 28 C3' G B 402 OK 26 29 30 51 C3' C B 403 OK 49 52 53 71 C3' A B 404 OK 69 72 73 93 C3' A B 405 OK 91 94 95 115 C3' C B 406 OK 113 116 117 135 C3' G B 407 OK 133 136 137 158 C3' G B 408 OK 156 159 160 181 C3' U B 409 OK 179 182 183 201 C3' UD5 B 410 OK 199 202 203 222 C3' C B 411 OK 220 223 224 242 C3' G B 412 OK 240 243 244 265 C3' A B 413 OK 263 266 267 287 C3' U B 414 OK 285 288 289 307 C3' C B 415 OK 305 308 309 327 C3' C B 416 OK 325 328 329 347 C3' C B 417 OK 345 348 349 367 C3' G B 418 OK 365 368 369 390 C3' U B 419 OK 388 391 392 410 C3' U B 420 OK 408 411 412 430 C3' G B 421 OK 428 431 432 453 C3' C B 422 OK 451 454 455 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 401 OK 5 2 4 26 C4' G B 402 OK 28 25 27 49 C4' C B 403 OK 51 48 50 69 C4' A B 404 OK 71 68 70 91 C4' A B 405 OK 93 90 92 113 C4' C B 406 OK 115 112 114 133 C4' G B 407 OK 135 132 134 156 C4' G B 408 OK 158 155 157 179 C4' U B 409 OK 181 178 180 199 C4' UD5 B 410 OK 201 198 200 220 C4' C B 411 OK 222 219 221 240 C4' G B 412 OK 242 239 241 263 C4' A B 413 OK 265 262 264 285 C4' U B 414 OK 287 284 286 305 C4' C B 415 OK 307 304 306 325 C4' C B 416 OK 327 324 326 345 C4' C B 417 OK 347 344 346 365 C4' G B 418 OK 367 364 366 388 C4' U B 419 OK 390 387 389 408 C4' U B 420 OK 410 407 409 428 C4' G B 421 OK 430 427 429 451 C4' C B 422 OK 453 450 452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 401 1 3 25 C5' G B 402 24 26 48 C5' C B 403 47 49 68 C5' A B 404 67 69 90 C5' A B 405 89 91 112 C5' C B 406 111 113 132 C5' G B 407 131 133 155 C5' G B 408 154 156 178 C5' U B 409 177 179 198 C5' UD5 B 410 197 199 219 C5' C B 411 218 220 239 C5' G B 412 238 240 262 C5' A B 413 261 263 284 C5' U B 414 283 285 304 C5' C B 415 303 305 324 C5' C B 416 323 325 344 C5' C B 417 343 345 364 C5' G B 418 363 365 387 C5' U B 419 386 388 407 C5' U B 420 406 408 427 C5' G B 421 426 428 450 C5' C B 422 449 451 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G B 402 distorted distorted 6 22 23 24 44 P C B 403 distorted distorted 29 45 46 47 64 P A B 404 distorted distorted 52 65 66 67 86 P A B 405 distorted distorted 72 87 88 89 108 P C B 406 distorted distorted 94 109 110 111 128 P G B 407 distorted distorted 116 129 130 131 151 P G B 408 distorted distorted 136 152 153 154 174 P U B 409 distorted distorted 159 175 176 177 194 P UD5 B 410 distorted distorted 182 195 196 197 215 P C B 411 distorted distorted 202 216 217 218 235 P G B 412 distorted distorted 223 236 237 238 258 P A B 413 distorted distorted 243 259 260 261 280 P U B 414 distorted distorted 266 281 282 283 300 P C B 415 distorted distorted 288 301 302 303 320 P C B 416 distorted distorted 308 321 322 323 340 P C B 417 distorted distorted 328 341 342 343 360 P G B 418 distorted distorted 348 361 362 363 383 P U B 419 distorted distorted 368 384 385 386 403 P U B 420 distorted distorted 391 404 405 406 423 P G B 421 distorted distorted 411 424 425 426 446 P C B 422 distorted distorted 431 447 448 449 ---------------------------------------------------------------------------------