ID code: '2RN1' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 46 C1' A A 2 alpha beta 41 63 47 44 79 C1' G A 3 alpha beta 74 97 80 77 113 C1' C A 4 alpha beta 108 128 114 111 144 C1' C A 5 alpha beta 139 159 145 142 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' U A 7 alpha beta 201 221 207 204 236 C1' G A 8 alpha beta 231 254 237 234 270 C1' G A 9 alpha beta 265 288 271 268 304 C1' G A 10 alpha beta 299 322 305 302 338 C1' A A 11 alpha beta 333 355 339 336 371 C1' G A 12 alpha beta 366 389 372 369 405 C1' G A 13 alpha beta 400 423 406 403 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' U A 15 alpha beta 465 485 471 468 500 C1' C A 16 alpha beta 495 515 501 498 532 C1' G B 17 alpha beta 527 550 533 530 566 C1' C B 18 alpha beta 561 581 567 564 597 C1' U B 19 alpha beta 592 612 598 595 627 C1' G B 20 alpha beta 622 645 628 625 661 C1' G B 21 alpha beta 656 679 662 659 695 C1' U B 22 alpha beta 690 710 696 693 725 C1' C B 23 alpha beta 720 740 726 723 756 C1' C B 24 alpha beta 751 771 757 754 787 C1' C B 25 alpha beta 782 802 788 785 818 C1' A B 26 alpha beta 813 835 819 816 851 C1' G B 27 alpha beta 846 869 852 849 885 C1' A B 28 alpha beta 880 902 886 883 918 C1' C B 29 alpha beta 913 933 919 916 949 C1' A B 30 alpha beta 944 966 950 947 982 C1' G B 31 alpha beta 977 1000 983 980 1016 C1' C B 32 alpha beta 1011 1031 1017 1014 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' A A 2 OK OK 46 42 61 45 77 C2' G A 3 OK OK 79 75 95 78 111 C2' C A 4 OK OK 113 109 126 112 142 C2' C A 5 OK OK 144 140 157 143 173 C2' C A 6 OK OK 175 171 188 174 204 C2' U A 7 OK OK 206 202 219 205 234 C2' G A 8 OK OK 236 232 252 235 268 C2' G A 9 OK OK 270 266 286 269 302 C2' G A 10 OK OK 304 300 320 303 336 C2' A A 11 OK OK 338 334 353 337 369 C2' G A 12 OK OK 371 367 387 370 403 C2' G A 13 OK OK 405 401 421 404 437 C2' C A 14 OK OK 439 435 452 438 468 C2' U A 15 OK OK 470 466 483 469 498 C2' C A 16 OK OK 500 496 513 499 530 C2' G B 17 OK OK 532 528 548 531 564 C2' C B 18 OK OK 566 562 579 565 595 C2' U B 19 OK OK 597 593 610 596 625 C2' G B 20 OK OK 627 623 643 626 659 C2' G B 21 OK OK 661 657 677 660 693 C2' U B 22 OK OK 695 691 708 694 723 C2' C B 23 OK OK 725 721 738 724 754 C2' C B 24 OK OK 756 752 769 755 785 C2' C B 25 OK OK 787 783 800 786 816 C2' A B 26 OK OK 818 814 833 817 849 C2' G B 27 OK OK 851 847 867 850 883 C2' A B 28 OK OK 885 881 900 884 916 C2' C B 29 OK OK 918 914 931 917 947 C2' A B 30 OK OK 949 945 964 948 980 C2' G B 31 OK OK 982 978 998 981 1014 C2' C B 32 OK OK 1016 1012 1029 1015 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' A A 2 OK OK 40 60 43 44 75 C3' G A 3 OK OK 73 94 76 77 109 C3' C A 4 OK OK 107 125 110 111 140 C3' C A 5 OK OK 138 156 141 142 171 C3' C A 6 OK OK 169 187 172 173 202 C3' U A 7 OK OK 200 218 203 204 232 C3' G A 8 OK OK 230 251 233 234 266 C3' G A 9 OK OK 264 285 267 268 300 C3' G A 10 OK OK 298 319 301 302 334 C3' A A 11 OK OK 332 352 335 336 367 C3' G A 12 OK OK 365 386 368 369 401 C3' G A 13 OK OK 399 420 402 403 435 C3' C A 14 OK OK 433 451 436 437 466 C3' U A 15 OK OK 464 482 467 468 496 C3' C A 16 OK OK 494 512 497 498 528 C3' G B 17 OK OK 526 547 529 530 562 C3' C B 18 OK OK 560 578 563 564 593 C3' U B 19 OK OK 591 609 594 595 623 C3' G B 20 OK OK 621 642 624 625 657 C3' G B 21 OK OK 655 676 658 659 691 C3' U B 22 OK OK 689 707 692 693 721 C3' C B 23 OK OK 719 737 722 723 752 C3' C B 24 OK OK 750 768 753 754 783 C3' C B 25 OK OK 781 799 784 785 814 C3' A B 26 OK OK 812 832 815 816 847 C3' G B 27 OK OK 845 866 848 849 881 C3' A B 28 OK OK 879 899 882 883 914 C3' C B 29 OK OK 912 930 915 916 945 C3' A B 30 OK OK 943 963 946 947 978 C3' G B 31 OK OK 976 997 979 980 1012 C3' C B 32 OK OK 1010 1028 1013 1014 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' A A 2 OK OK 42 59 39 41 73 C4' G A 3 OK OK 75 93 72 74 107 C4' C A 4 OK OK 109 124 106 108 138 C4' C A 5 OK OK 140 155 137 139 169 C4' C A 6 OK OK 171 186 168 170 200 C4' U A 7 OK OK 202 217 199 201 230 C4' G A 8 OK OK 232 250 229 231 264 C4' G A 9 OK OK 266 284 263 265 298 C4' G A 10 OK OK 300 318 297 299 332 C4' A A 11 OK OK 334 351 331 333 365 C4' G A 12 OK OK 367 385 364 366 399 C4' G A 13 OK OK 401 419 398 400 433 C4' C A 14 OK OK 435 450 432 434 464 C4' U A 15 OK OK 466 481 463 465 494 C4' C A 16 OK OK 496 511 493 495 526 C4' G B 17 OK OK 528 546 525 527 560 C4' C B 18 OK OK 562 577 559 561 591 C4' U B 19 OK OK 593 608 590 592 621 C4' G B 20 OK OK 623 641 620 622 655 C4' G B 21 OK OK 657 675 654 656 689 C4' U B 22 OK OK 691 706 688 690 719 C4' C B 23 OK OK 721 736 718 720 750 C4' C B 24 OK OK 752 767 749 751 781 C4' C B 25 OK OK 783 798 780 782 812 C4' A B 26 OK OK 814 831 811 813 845 C4' G B 27 OK OK 847 865 844 846 879 C4' A B 28 OK OK 881 898 878 880 912 C4' C B 29 OK OK 914 929 911 913 943 C4' A B 30 OK OK 945 962 942 944 976 C4' G B 31 OK OK 978 996 975 977 1010 C4' C B 32 OK OK 1012 1027 1009 1011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' A A 2 OK OK 38 57 58 40 72 C5' G A 3 OK OK 71 91 92 73 106 C5' C A 4 OK OK 105 122 123 107 137 C5' C A 5 OK OK 136 153 154 138 168 C5' C A 6 OK OK 167 184 185 169 199 C5' U A 7 OK OK 198 215 216 200 229 C5' G A 8 OK OK 228 248 249 230 263 C5' G A 9 OK OK 262 282 283 264 297 C5' G A 10 OK OK 296 316 317 298 331 C5' A A 11 OK OK 330 349 350 332 364 C5' G A 12 OK OK 363 383 384 365 398 C5' G A 13 OK OK 397 417 418 399 432 C5' C A 14 OK OK 431 448 449 433 463 C5' U A 15 OK OK 462 479 480 464 493 C5' C A 16 OK OK 492 509 510 494 525 C5' G B 17 OK OK 524 544 545 526 559 C5' C B 18 OK OK 558 575 576 560 590 C5' U B 19 OK OK 589 606 607 591 620 C5' G B 20 OK OK 619 639 640 621 654 C5' G B 21 OK OK 653 673 674 655 688 C5' U B 22 OK OK 687 704 705 689 718 C5' C B 23 OK OK 717 734 735 719 749 C5' C B 24 OK OK 748 765 766 750 780 C5' C B 25 OK OK 779 796 797 781 811 C5' A B 26 OK OK 810 829 830 812 844 C5' G B 27 OK OK 843 863 864 845 878 C5' A B 28 OK OK 877 896 897 879 911 C5' C B 29 OK OK 910 927 928 912 942 C5' A B 30 OK OK 941 960 961 943 975 C5' G B 31 OK OK 974 994 995 976 1009 C5' C B 32 OK OK 1008 1025 1026 1010 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 35 P A A 2 distorted distorted 9 36 37 38 68 P G A 3 distorted distorted 43 69 70 71 102 P C A 4 distorted distorted 76 103 104 105 133 P C A 5 distorted distorted 110 134 135 136 164 P C A 6 distorted distorted 141 165 166 167 195 P U A 7 distorted distorted 172 196 197 198 225 P G A 8 distorted distorted 203 226 227 228 259 P G A 9 distorted distorted 233 260 261 262 293 P G A 10 distorted distorted 267 294 295 296 327 P A A 11 distorted distorted 301 328 329 330 360 P G A 12 distorted distorted 335 361 362 363 394 P G A 13 distorted distorted 368 395 396 397 428 P C A 14 distorted distorted 402 429 430 431 459 P U A 15 distorted distorted 436 460 461 462 489 P C A 16 distorted distorted 467 490 491 492 521 P G B 17 distorted distorted 522 523 524 555 P C B 18 distorted distorted 529 556 557 558 586 P U B 19 distorted distorted 563 587 588 589 616 P G B 20 distorted distorted 594 617 618 619 650 P G B 21 distorted distorted 624 651 652 653 684 P U B 22 distorted distorted 658 685 686 687 714 P C B 23 distorted distorted 692 715 716 717 745 P C B 24 distorted distorted 722 746 747 748 776 P C B 25 distorted distorted 753 777 778 779 807 P A B 26 distorted distorted 784 808 809 810 840 P G B 27 distorted distorted 815 841 842 843 874 P A B 28 distorted distorted 848 875 876 877 907 P C B 29 distorted distorted 882 908 909 910 938 P A B 30 distorted distorted 915 939 940 941 971 P G B 31 distorted distorted 946 972 973 974 1005 P C B 32 distorted distorted 979 1006 1007 1008 ---------------------------------------------------------------------------------