ID code: '2MQQ' 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' --------------------------------------------------------------------------------- 3325 C1' A B 1 alpha beta 3320 3342 3326 3323 3358 C1' C B 2 alpha beta 3353 3373 3359 3356 3389 C1' A B 3 alpha beta 3384 3406 3390 3387 3422 C1' C B 4 alpha beta 3417 3437 3423 3420 3453 C1' A B 5 alpha beta 3448 3470 3454 3451 3484 C1' A C 1 alpha beta 3479 3501 3485 3482 3517 C1' C C 2 alpha beta 3512 3532 3518 3515 3548 C1' A C 3 alpha beta 3543 3565 3549 3546 3581 C1' C C 4 alpha beta 3576 3596 3582 3579 3612 C1' A C 5 alpha beta 3607 3629 3613 3610 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3323 C2' A B 1 OK OK 3325 3321 3340 3324 3356 C2' C B 2 OK OK 3358 3354 3371 3357 3387 C2' A B 3 OK OK 3389 3385 3404 3388 3420 C2' C B 4 OK OK 3422 3418 3435 3421 3451 C2' A B 5 OK OK 3453 3449 3468 3452 3482 C2' A C 1 OK OK 3484 3480 3499 3483 3515 C2' C C 2 OK OK 3517 3513 3530 3516 3546 C2' A C 3 OK OK 3548 3544 3563 3547 3579 C2' C C 4 OK OK 3581 3577 3594 3580 3610 C2' A C 5 OK OK 3612 3608 3627 3611 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3321 C3' A B 1 OK OK 3319 3339 3322 3323 3354 C3' C B 2 OK OK 3352 3370 3355 3356 3385 C3' A B 3 OK OK 3383 3403 3386 3387 3418 C3' C B 4 OK OK 3416 3434 3419 3420 3449 C3' A B 5 OK OK 3447 3467 3450 3451 3480 C3' A C 1 OK OK 3478 3498 3481 3482 3513 C3' C C 2 OK OK 3511 3529 3514 3515 3544 C3' A C 3 OK OK 3542 3562 3545 3546 3577 C3' C C 4 OK OK 3575 3593 3578 3579 3608 C3' A C 5 OK OK 3606 3626 3609 3610 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3319 C4' A B 1 OK OK 3321 3338 3318 3320 3352 C4' C B 2 OK OK 3354 3369 3351 3353 3383 C4' A B 3 OK OK 3385 3402 3382 3384 3416 C4' C B 4 OK OK 3418 3433 3415 3417 3447 C4' A B 5 OK OK 3449 3466 3446 3448 3478 C4' A C 1 OK OK 3480 3497 3477 3479 3511 C4' C C 2 OK OK 3513 3528 3510 3512 3542 C4' A C 3 OK OK 3544 3561 3541 3543 3575 C4' C C 4 OK OK 3577 3592 3574 3576 3606 C4' A C 5 OK OK 3608 3625 3605 3607 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3318 C5' A B 1 OK OK 3317 3336 3337 3319 3351 C5' C B 2 OK OK 3350 3367 3368 3352 3382 C5' A B 3 OK OK 3381 3400 3401 3383 3415 C5' C B 4 OK OK 3414 3431 3432 3416 3446 C5' A B 5 OK OK 3445 3464 3465 3447 3477 C5' A C 1 OK OK 3476 3495 3496 3478 3510 C5' C C 2 OK OK 3509 3526 3527 3511 3541 C5' A C 3 OK OK 3540 3559 3560 3542 3574 C5' C C 4 OK OK 3573 3590 3591 3575 3605 C5' A C 5 OK OK 3604 3623 3624 3606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3347 P C B 2 distorted distorted 3322 3348 3349 3350 3378 P A B 3 distorted distorted 3355 3379 3380 3381 3411 P C B 4 distorted distorted 3386 3412 3413 3414 3442 P A B 5 distorted distorted 3419 3443 3444 3445 3506 P C C 2 distorted distorted 3481 3507 3508 3509 3537 P A C 3 distorted distorted 3514 3538 3539 3540 3570 P C C 4 distorted distorted 3545 3571 3572 3573 3601 P A C 5 distorted distorted 3578 3602 3603 3604 ---------------------------------------------------------------------------------