ID code: '2N0J' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' G A 5 alpha beta 134 157 140 137 173 C1' C A 6 alpha beta 168 188 174 171 204 C1' U A 7 alpha beta 199 219 205 202 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' G A 9 alpha beta 259 282 265 262 298 C1' U A 10 alpha beta 293 313 299 296 328 C1' C A 11 alpha beta 323 343 329 326 359 C1' C A 12 alpha beta 354 374 360 357 390 C1' U A 13 alpha beta 385 405 391 388 420 C1' U A 14 alpha beta 415 435 421 418 450 C1' U A 15 alpha beta 445 465 451 448 480 C1' A A 16 alpha beta 475 497 481 478 513 C1' A A 17 alpha beta 508 530 514 511 546 C1' U A 18 alpha beta 541 561 547 544 576 C1' G A 19 alpha beta 571 594 577 574 610 C1' G A 20 alpha beta 605 628 611 608 644 C1' U A 21 alpha beta 639 659 645 642 674 C1' C A 22 alpha beta 669 689 675 672 705 C1' C A 23 alpha beta 700 720 706 703 736 C1' A A 24 alpha beta 731 753 737 734 769 C1' G A 25 alpha beta 764 787 770 767 803 C1' U A 26 alpha beta 798 818 804 801 833 C1' C A 27 alpha beta 828 849 834 831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' G A 5 OK OK 139 135 155 138 171 C2' C A 6 OK OK 173 169 186 172 202 C2' U A 7 OK OK 204 200 217 203 232 C2' U A 8 OK OK 234 230 247 233 262 C2' G A 9 OK OK 264 260 280 263 296 C2' U A 10 OK OK 298 294 311 297 326 C2' C A 11 OK OK 328 324 341 327 357 C2' C A 12 OK OK 359 355 372 358 388 C2' U A 13 OK OK 390 386 403 389 418 C2' U A 14 OK OK 420 416 433 419 448 C2' U A 15 OK OK 450 446 463 449 478 C2' A A 16 OK OK 480 476 495 479 511 C2' A A 17 OK OK 513 509 528 512 544 C2' U A 18 OK OK 546 542 559 545 574 C2' G A 19 OK OK 576 572 592 575 608 C2' G A 20 OK OK 610 606 626 609 642 C2' U A 21 OK OK 644 640 657 643 672 C2' C A 22 OK OK 674 670 687 673 703 C2' C A 23 OK OK 705 701 718 704 734 C2' A A 24 OK OK 736 732 751 735 767 C2' G A 25 OK OK 769 765 785 768 801 C2' U A 26 OK OK 803 799 816 802 831 C2' C A 27 OK OK 833 829 847 832 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' G A 5 OK OK 133 154 136 137 169 C3' C A 6 OK OK 167 185 170 171 200 C3' U A 7 OK OK 198 216 201 202 230 C3' U A 8 OK OK 228 246 231 232 260 C3' G A 9 OK OK 258 279 261 262 294 C3' U A 10 OK OK 292 310 295 296 324 C3' C A 11 OK OK 322 340 325 326 355 C3' C A 12 OK OK 353 371 356 357 386 C3' U A 13 OK OK 384 402 387 388 416 C3' U A 14 OK OK 414 432 417 418 446 C3' U A 15 OK OK 444 462 447 448 476 C3' A A 16 OK OK 474 494 477 478 509 C3' A A 17 OK OK 507 527 510 511 542 C3' U A 18 OK OK 540 558 543 544 572 C3' G A 19 OK OK 570 591 573 574 606 C3' G A 20 OK OK 604 625 607 608 640 C3' U A 21 OK OK 638 656 641 642 670 C3' C A 22 OK OK 668 686 671 672 701 C3' C A 23 OK OK 699 717 702 703 732 C3' A A 24 OK OK 730 750 733 734 765 C3' G A 25 OK OK 763 784 766 767 799 C3' U A 26 OK OK 797 815 800 801 829 C3' C A 27 OK OK 827 845 830 831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' G A 5 OK OK 135 153 132 134 167 C4' C A 6 OK OK 169 184 166 168 198 C4' U A 7 OK OK 200 215 197 199 228 C4' U A 8 OK OK 230 245 227 229 258 C4' G A 9 OK OK 260 278 257 259 292 C4' U A 10 OK OK 294 309 291 293 322 C4' C A 11 OK OK 324 339 321 323 353 C4' C A 12 OK OK 355 370 352 354 384 C4' U A 13 OK OK 386 401 383 385 414 C4' U A 14 OK OK 416 431 413 415 444 C4' U A 15 OK OK 446 461 443 445 474 C4' A A 16 OK OK 476 493 473 475 507 C4' A A 17 OK OK 509 526 506 508 540 C4' U A 18 OK OK 542 557 539 541 570 C4' G A 19 OK OK 572 590 569 571 604 C4' G A 20 OK OK 606 624 603 605 638 C4' U A 21 OK OK 640 655 637 639 668 C4' C A 22 OK OK 670 685 667 669 699 C4' C A 23 OK OK 701 716 698 700 730 C4' A A 24 OK OK 732 749 729 731 763 C4' G A 25 OK OK 765 783 762 764 797 C4' U A 26 OK OK 799 814 796 798 827 C4' C A 27 OK OK 829 844 826 828 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' G A 5 OK OK 131 151 152 133 166 C5' C A 6 OK OK 165 182 183 167 197 C5' U A 7 OK OK 196 213 214 198 227 C5' U A 8 OK OK 226 243 244 228 257 C5' G A 9 OK OK 256 276 277 258 291 C5' U A 10 OK OK 290 307 308 292 321 C5' C A 11 OK OK 320 337 338 322 352 C5' C A 12 OK OK 351 368 369 353 383 C5' U A 13 OK OK 382 399 400 384 413 C5' U A 14 OK OK 412 429 430 414 443 C5' U A 15 OK OK 442 459 460 444 473 C5' A A 16 OK OK 472 491 492 474 506 C5' A A 17 OK OK 505 524 525 507 539 C5' U A 18 OK OK 538 555 556 540 569 C5' G A 19 OK OK 568 588 589 570 603 C5' G A 20 OK OK 602 622 623 604 637 C5' U A 21 OK OK 636 653 654 638 667 C5' C A 22 OK OK 666 683 684 668 698 C5' C A 23 OK OK 697 714 715 699 729 C5' A A 24 OK OK 728 747 748 730 762 C5' G A 25 OK OK 761 781 782 763 796 C5' U A 26 OK OK 795 812 813 797 826 C5' C A 27 OK OK 825 842 843 827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P G A 5 distorted distorted 106 129 130 131 162 P C A 6 distorted distorted 136 163 164 165 193 P U A 7 distorted distorted 170 194 195 196 223 P U A 8 distorted distorted 201 224 225 226 253 P G A 9 distorted distorted 231 254 255 256 287 P U A 10 distorted distorted 261 288 289 290 317 P C A 11 distorted distorted 295 318 319 320 348 P C A 12 distorted distorted 325 349 350 351 379 P U A 13 distorted distorted 356 380 381 382 409 P U A 14 distorted distorted 387 410 411 412 439 P U A 15 distorted distorted 417 440 441 442 469 P A A 16 distorted distorted 447 470 471 472 502 P A A 17 distorted distorted 477 503 504 505 535 P U A 18 distorted distorted 510 536 537 538 565 P G A 19 distorted distorted 543 566 567 568 599 P G A 20 distorted distorted 573 600 601 602 633 P U A 21 distorted distorted 607 634 635 636 663 P C A 22 distorted distorted 641 664 665 666 694 P C A 23 distorted distorted 671 695 696 697 725 P A A 24 distorted distorted 702 726 727 728 758 P G A 25 distorted distorted 733 759 760 761 792 P U A 26 distorted distorted 766 793 794 795 822 P C A 27 distorted distorted 800 823 824 825 ---------------------------------------------------------------------------------