ID code: '3PEW' 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' --------------------------------------------------------------------------------- 3266 C1' U B 1 beta 3261 3267 3264 3286 C1' U B 2 beta 3281 3287 3284 3306 C1' U B 3 beta 3301 3307 3304 3326 C1' U B 4 beta 3321 3327 3324 3346 C1' U B 5 beta 3341 3347 3344 3376 C1' ADP A1000 beta 3371 3377 3374 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3264 C2' U B 1 OK 3266 3262 3265 3284 C2' U B 2 OK 3286 3282 3285 3304 C2' U B 3 OK 3306 3302 3305 3324 C2' U B 4 OK 3326 3322 3325 3344 C2' U B 5 OK 3346 3342 3345 3374 C2' ADP A1000 OK 3376 3372 3375 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3262 C3' U B 1 OK 3260 3263 3264 3282 C3' U B 2 OK 3280 3283 3284 3302 C3' U B 3 OK 3300 3303 3304 3322 C3' U B 4 OK 3320 3323 3324 3342 C3' U B 5 OK 3340 3343 3344 3372 C3' ADP A1000 OK 3370 3373 3374 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3260 C4' U B 1 OK 3262 3259 3261 3280 C4' U B 2 OK 3282 3279 3281 3300 C4' U B 3 OK 3302 3299 3301 3320 C4' U B 4 OK 3322 3319 3321 3340 C4' U B 5 OK 3342 3339 3341 3370 C4' ADP A1000 OK 3372 3369 3371 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3259 C5' U B 1 3258 3260 3279 C5' U B 2 3278 3280 3299 C5' U B 3 3298 3300 3319 C5' U B 4 3318 3320 3339 C5' U B 5 3338 3340 3369 C5' ADP A1000 3368 3370 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3255 P U B 1 distorted distorted 3256 3257 3258 3275 P U B 2 distorted distorted 3263 3276 3277 3278 3295 P U B 3 distorted distorted 3283 3296 3297 3298 3315 P U B 4 distorted distorted 3303 3316 3317 3318 3335 P U B 5 distorted distorted 3323 3336 3337 3338 3355 P U B 6 distorted distorted 3343 3356 3357 3358 ---------------------------------------------------------------------------------