ID code: '3UZS' 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' --------------------------------------------------------------------------------- 8123 C1' G C 41 beta 8118 8124 8121 8146 C1' G C 42 beta 8141 8147 8144 8169 C1' C C 43 beta 8164 8170 8167 8189 C1' A C 44 beta 8184 8190 8187 8211 C1' G C 45 beta 8206 8212 8209 8234 C1' A C 46 beta 8229 8235 8232 8256 C1' C C 47 beta 8251 8257 8254 8276 C1' C C 48 beta 8271 8277 8274 8296 C1' A C 49 beta 8291 8297 8294 8318 C1' U C 50 beta 8313 8319 8316 8338 C1' A C 51 beta 8333 8339 8336 8360 C1' C C 52 beta 8355 8361 8358 8380 C1' G C 53 beta 8375 8381 8378 8403 C1' G C 54 beta 8398 8404 8401 8426 C1' G C 55 beta 8421 8427 8424 8446 C1' U C 64 beta 8441 8447 8444 8466 C1' U C 65 beta 8461 8467 8464 8486 C1' G C 66 beta 8481 8487 8484 8509 C1' C C 67 beta 8504 8510 8507 8529 C1' C C 68 beta 8524 8530 8527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8121 C2' G C 41 OK 8123 8119 8122 8144 C2' G C 42 OK 8146 8142 8145 8167 C2' C C 43 OK 8169 8165 8168 8187 C2' A C 44 OK 8189 8185 8188 8209 C2' G C 45 OK 8211 8207 8210 8232 C2' A C 46 OK 8234 8230 8233 8254 C2' C C 47 OK 8256 8252 8255 8274 C2' C C 48 OK 8276 8272 8275 8294 C2' A C 49 OK 8296 8292 8295 8316 C2' U C 50 OK 8318 8314 8317 8336 C2' A C 51 OK 8338 8334 8337 8358 C2' C C 52 OK 8360 8356 8359 8378 C2' G C 53 OK 8380 8376 8379 8401 C2' G C 54 OK 8403 8399 8402 8424 C2' G C 55 OK 8426 8422 8425 8444 C2' U C 64 OK 8446 8442 8445 8464 C2' U C 65 OK 8466 8462 8465 8484 C2' G C 66 OK 8486 8482 8485 8507 C2' C C 67 OK 8509 8505 8508 8527 C2' C C 68 OK 8529 8525 8528 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8119 C3' G C 41 OK 8117 8120 8121 8142 C3' G C 42 OK 8140 8143 8144 8165 C3' C C 43 OK 8163 8166 8167 8185 C3' A C 44 OK 8183 8186 8187 8207 C3' G C 45 OK 8205 8208 8209 8230 C3' A C 46 OK 8228 8231 8232 8252 C3' C C 47 OK 8250 8253 8254 8272 C3' C C 48 OK 8270 8273 8274 8292 C3' A C 49 OK 8290 8293 8294 8314 C3' U C 50 OK 8312 8315 8316 8334 C3' A C 51 OK 8332 8335 8336 8356 C3' C C 52 OK 8354 8357 8358 8376 C3' G C 53 OK 8374 8377 8378 8399 C3' G C 54 OK 8397 8400 8401 8422 C3' G C 55 OK 8420 8423 8424 8442 C3' U C 64 OK 8440 8443 8444 8462 C3' U C 65 OK 8460 8463 8464 8482 C3' G C 66 OK 8480 8483 8484 8505 C3' C C 67 OK 8503 8506 8507 8525 C3' C C 68 OK 8523 8526 8527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8117 C4' G C 41 OK 8119 8116 8118 8140 C4' G C 42 OK 8142 8139 8141 8163 C4' C C 43 OK 8165 8162 8164 8183 C4' A C 44 OK 8185 8182 8184 8205 C4' G C 45 OK 8207 8204 8206 8228 C4' A C 46 OK 8230 8227 8229 8250 C4' C C 47 OK 8252 8249 8251 8270 C4' C C 48 OK 8272 8269 8271 8290 C4' A C 49 OK 8292 8289 8291 8312 C4' U C 50 OK 8314 8311 8313 8332 C4' A C 51 OK 8334 8331 8333 8354 C4' C C 52 OK 8356 8353 8355 8374 C4' G C 53 OK 8376 8373 8375 8397 C4' G C 54 OK 8399 8396 8398 8420 C4' G C 55 OK 8422 8419 8421 8440 C4' U C 64 OK 8442 8439 8441 8460 C4' U C 65 OK 8462 8459 8461 8480 C4' G C 66 OK 8482 8479 8481 8503 C4' C C 67 OK 8505 8502 8504 8523 C4' C C 68 OK 8525 8522 8524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8116 C5' G C 41 8115 8117 8139 C5' G C 42 8138 8140 8162 C5' C C 43 8161 8163 8182 C5' A C 44 8181 8183 8204 C5' G C 45 8203 8205 8227 C5' A C 46 8226 8228 8249 C5' C C 47 8248 8250 8269 C5' C C 48 8268 8270 8289 C5' A C 49 8288 8290 8311 C5' U C 50 8310 8312 8331 C5' A C 51 8330 8332 8353 C5' C C 52 8352 8354 8373 C5' G C 53 8372 8374 8396 C5' G C 54 8395 8397 8419 C5' G C 55 8418 8420 8439 C5' U C 64 8438 8440 8459 C5' U C 65 8458 8460 8479 C5' G C 66 8478 8480 8502 C5' C C 67 8501 8503 8522 C5' C C 68 8521 8523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8135 P G C 42 distorted distorted 8120 8136 8137 8138 8158 P C C 43 distorted distorted 8143 8159 8160 8161 8178 P A C 44 distorted distorted 8166 8179 8180 8181 8200 P G C 45 distorted distorted 8186 8201 8202 8203 8223 P A C 46 distorted distorted 8208 8224 8225 8226 8245 P C C 47 distorted distorted 8231 8246 8247 8248 8265 P C C 48 distorted distorted 8253 8266 8267 8268 8285 P A C 49 distorted distorted 8273 8286 8287 8288 8307 P U C 50 distorted distorted 8293 8308 8309 8310 8327 P A C 51 distorted distorted 8315 8328 8329 8330 8349 P C C 52 distorted distorted 8335 8350 8351 8352 8369 P G C 53 distorted distorted 8357 8370 8371 8372 8392 P G C 54 distorted distorted 8377 8393 8394 8395 8415 P G C 55 distorted distorted 8400 8416 8417 8418 8455 P U C 65 distorted distorted 8443 8456 8457 8458 8475 P G C 66 distorted distorted 8463 8476 8477 8478 8498 P C C 67 distorted distorted 8483 8499 8500 8501 8518 P C C 68 distorted distorted 8506 8519 8520 8521 ---------------------------------------------------------------------------------