ID code: '5JBG' 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' --------------------------------------------------------------------------------- 5377 C1' GTP X 1 beta 5372 5378 5375 5400 C1' G X 2 beta 5395 5401 5398 5423 C1' A X 3 beta 5418 5424 5421 5445 C1' G X 4 beta 5440 5446 5443 5468 C1' C X 5 beta 5463 5469 5466 5488 C1' G X 6 beta 5483 5489 5486 5511 C1' U X 7 beta 5506 5512 5509 5531 C1' G X 8 beta 5526 5532 5529 5554 C1' C X 9 beta 5549 5555 5552 5574 C1' C X 10 beta 5569 5575 5572 5594 C1' G X 11 beta 5589 5595 5592 5617 C1' G X 15 beta 5612 5618 5615 5640 C1' G X 16 beta 5635 5641 5638 5663 C1' C X 17 beta 5658 5664 5661 5683 C1' A X 18 beta 5678 5684 5681 5705 C1' C X 19 beta 5700 5706 5703 5725 C1' G X 20 beta 5720 5726 5723 5748 C1' C X 21 beta 5743 5749 5746 5768 C1' U X 22 beta 5763 5769 5766 5788 C1' C X 23 beta 5783 5789 5786 5808 C1' C X 24 beta 5803 5809 5806 5828 C1' G X 25 beta 5823 5829 5826 5851 C1' G X 26 beta 5846 5852 5849 5881 C1' ADP A 702 beta 5876 5882 5879 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5375 C2' GTP X 1 OK 5377 5373 5376 5398 C2' G X 2 OK 5400 5396 5399 5421 C2' A X 3 OK 5423 5419 5422 5443 C2' G X 4 OK 5445 5441 5444 5466 C2' C X 5 OK 5468 5464 5467 5486 C2' G X 6 OK 5488 5484 5487 5509 C2' U X 7 OK 5511 5507 5510 5529 C2' G X 8 OK 5531 5527 5530 5552 C2' C X 9 OK 5554 5550 5553 5572 C2' C X 10 OK 5574 5570 5573 5592 C2' G X 11 OK 5594 5590 5593 5615 C2' G X 15 OK 5617 5613 5616 5638 C2' G X 16 OK 5640 5636 5639 5661 C2' C X 17 OK 5663 5659 5662 5681 C2' A X 18 OK 5683 5679 5682 5703 C2' C X 19 OK 5705 5701 5704 5723 C2' G X 20 OK 5725 5721 5724 5746 C2' C X 21 OK 5748 5744 5747 5766 C2' U X 22 OK 5768 5764 5767 5786 C2' C X 23 OK 5788 5784 5787 5806 C2' C X 24 OK 5808 5804 5807 5826 C2' G X 25 OK 5828 5824 5827 5849 C2' G X 26 OK 5851 5847 5850 5879 C2' ADP A 702 OK 5881 5877 5880 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5373 C3' GTP X 1 OK 5371 5374 5375 5396 C3' G X 2 OK 5394 5397 5398 5419 C3' A X 3 OK 5417 5420 5421 5441 C3' G X 4 OK 5439 5442 5443 5464 C3' C X 5 OK 5462 5465 5466 5484 C3' G X 6 OK 5482 5485 5486 5507 C3' U X 7 OK 5505 5508 5509 5527 C3' G X 8 OK 5525 5528 5529 5550 C3' C X 9 OK 5548 5551 5552 5570 C3' C X 10 OK 5568 5571 5572 5590 C3' G X 11 OK 5588 5591 5592 5613 C3' G X 15 OK 5611 5614 5615 5636 C3' G X 16 OK 5634 5637 5638 5659 C3' C X 17 OK 5657 5660 5661 5679 C3' A X 18 OK 5677 5680 5681 5701 C3' C X 19 OK 5699 5702 5703 5721 C3' G X 20 OK 5719 5722 5723 5744 C3' C X 21 OK 5742 5745 5746 5764 C3' U X 22 OK 5762 5765 5766 5784 C3' C X 23 OK 5782 5785 5786 5804 C3' C X 24 OK 5802 5805 5806 5824 C3' G X 25 OK 5822 5825 5826 5847 C3' G X 26 OK 5845 5848 5849 5877 C3' ADP A 702 OK 5875 5878 5879 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5371 C4' GTP X 1 OK 5373 5370 5372 5394 C4' G X 2 OK 5396 5393 5395 5417 C4' A X 3 OK 5419 5416 5418 5439 C4' G X 4 OK 5441 5438 5440 5462 C4' C X 5 OK 5464 5461 5463 5482 C4' G X 6 OK 5484 5481 5483 5505 C4' U X 7 OK 5507 5504 5506 5525 C4' G X 8 OK 5527 5524 5526 5548 C4' C X 9 OK 5550 5547 5549 5568 C4' C X 10 OK 5570 5567 5569 5588 C4' G X 11 OK 5590 5587 5589 5611 C4' G X 15 OK 5613 5610 5612 5634 C4' G X 16 OK 5636 5633 5635 5657 C4' C X 17 OK 5659 5656 5658 5677 C4' A X 18 OK 5679 5676 5678 5699 C4' C X 19 OK 5701 5698 5700 5719 C4' G X 20 OK 5721 5718 5720 5742 C4' C X 21 OK 5744 5741 5743 5762 C4' U X 22 OK 5764 5761 5763 5782 C4' C X 23 OK 5784 5781 5783 5802 C4' C X 24 OK 5804 5801 5803 5822 C4' G X 25 OK 5824 5821 5823 5845 C4' G X 26 OK 5847 5844 5846 5875 C4' ADP A 702 OK 5877 5874 5876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5370 C5' GTP X 1 5369 5371 5393 C5' G X 2 5392 5394 5416 C5' A X 3 5415 5417 5438 C5' G X 4 5437 5439 5461 C5' C X 5 5460 5462 5481 C5' G X 6 5480 5482 5504 C5' U X 7 5503 5505 5524 C5' G X 8 5523 5525 5547 C5' C X 9 5546 5548 5567 C5' C X 10 5566 5568 5587 C5' G X 11 5586 5588 5610 C5' G X 15 5609 5611 5633 C5' G X 16 5632 5634 5656 C5' C X 17 5655 5657 5676 C5' A X 18 5675 5677 5698 C5' C X 19 5697 5699 5718 C5' G X 20 5717 5719 5741 C5' C X 21 5740 5742 5761 C5' U X 22 5760 5762 5781 C5' C X 23 5780 5782 5801 C5' C X 24 5800 5802 5821 C5' G X 25 5820 5822 5844 C5' G X 26 5843 5845 5874 C5' ADP A 702 5873 5875 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5389 P G X 2 distorted distorted 5374 5390 5391 5392 5412 P A X 3 distorted distorted 5397 5413 5414 5415 5434 P G X 4 distorted distorted 5420 5435 5436 5437 5457 P C X 5 distorted distorted 5442 5458 5459 5460 5477 P G X 6 distorted distorted 5465 5478 5479 5480 5500 P U X 7 distorted distorted 5485 5501 5502 5503 5520 P G X 8 distorted distorted 5508 5521 5522 5523 5543 P C X 9 distorted distorted 5528 5544 5545 5546 5563 P C X 10 distorted distorted 5551 5564 5565 5566 5583 P G X 11 distorted distorted 5571 5584 5585 5586 5606 P G X 15 distorted distorted 5607 5608 5609 5629 P G X 16 distorted distorted 5614 5630 5631 5632 5652 P C X 17 distorted distorted 5637 5653 5654 5655 5672 P A X 18 distorted distorted 5660 5673 5674 5675 5694 P C X 19 distorted distorted 5680 5695 5696 5697 5714 P G X 20 distorted distorted 5702 5715 5716 5717 5737 P C X 21 distorted distorted 5722 5738 5739 5740 5757 P U X 22 distorted distorted 5745 5758 5759 5760 5777 P C X 23 distorted distorted 5765 5778 5779 5780 5797 P C X 24 distorted distorted 5785 5798 5799 5800 5817 P G X 25 distorted distorted 5805 5818 5819 5820 5840 P G X 26 distorted distorted 5825 5841 5842 5843 ---------------------------------------------------------------------------------