ID code: '4J6W' 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' --------------------------------------------------------------------------------- 3271 C1' CTP A 101 beta 3276 3263 3272 3304 C1' C A 102 beta 3299 3305 3302 3323 C1' CTP B 101 beta 3328 3315 3324 3353 C1' CTP C 101 beta 3358 3345 3354 3386 C1' C C 102 beta 3381 3387 3384 3409 C1' C D 101 beta 3404 3410 3407 3426 C1' CTP D 102 beta 3431 3418 3427 3480 C1' C E 101 beta 3475 3481 3478 3497 C1' CTP E 102 beta 3502 3489 3498 3537 C1' CDP F 101 beta 3532 3538 3535 3554 C1' CTP F 102 beta 3559 3546 3555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3272 C2' CTP A 101 OK 3271 3274 3273 3302 C2' C A 102 OK 3304 3300 3303 3324 C2' CTP B 101 OK 3323 3326 3325 3354 C2' CTP C 101 OK 3353 3356 3355 3384 C2' C C 102 OK 3386 3382 3385 3407 C2' C D 101 OK 3409 3405 3408 3427 C2' CTP D 102 OK 3426 3429 3428 3478 C2' C E 101 OK 3480 3476 3479 3498 C2' CTP E 102 OK 3497 3500 3499 3535 C2' CDP F 101 OK 3537 3533 3536 3555 C2' CTP F 102 OK 3554 3557 3556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3274 C3' CTP A 101 OK 3275 3277 3272 3300 C3' C A 102 OK 3298 3301 3302 3326 C3' CTP B 101 OK 3327 3329 3324 3356 C3' CTP C 101 OK 3357 3359 3354 3382 C3' C C 102 OK 3380 3383 3384 3405 C3' C D 101 OK 3403 3406 3407 3429 C3' CTP D 102 OK 3430 3432 3427 3476 C3' C E 101 OK 3474 3477 3478 3500 C3' CTP E 102 OK 3501 3503 3498 3533 C3' CDP F 101 OK 3531 3534 3535 3557 C3' CTP F 102 OK 3558 3560 3555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3275 C4' CTP A 101 OK 3274 3278 3276 3298 C4' C A 102 OK 3300 3297 3299 3327 C4' CTP B 101 OK 3326 3330 3328 3357 C4' CTP C 101 OK 3356 3360 3358 3380 C4' C C 102 OK 3382 3379 3381 3403 C4' C D 101 OK 3405 3402 3404 3430 C4' CTP D 102 OK 3429 3433 3431 3474 C4' C E 101 OK 3476 3473 3475 3501 C4' CTP E 102 OK 3500 3504 3502 3531 C4' CDP F 101 OK 3533 3530 3532 3558 C4' CTP F 102 OK 3557 3561 3559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3278 C5' CTP A 101 3279 3275 3297 C5' C A 102 3296 3298 3330 C5' CTP B 101 3331 3327 3360 C5' CTP C 101 3361 3357 3379 C5' C C 102 3378 3380 3402 C5' C D 101 3401 3403 3433 C5' CTP D 102 3434 3430 3473 C5' C E 101 3472 3474 3504 C5' CTP E 102 3505 3501 3530 C5' CDP F 101 3529 3531 3561 C5' CTP F 102 3562 3558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3293 P C A 102 OK OK 3294 3295 3296 3375 P C C 102 distorted distorted 3376 3377 3378 3398 P C D 101 OK OK 3399 3400 3401 3469 P C E 101 OK OK 3470 3471 3472 ---------------------------------------------------------------------------------