ID code: '1NZ1' 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 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' U A 3 alpha beta 72 92 78 75 107 C1' U A 4 alpha beta 102 122 108 105 137 C1' C A 5 alpha beta 132 152 138 135 168 C1' C A 6 alpha beta 163 183 169 166 199 C1' C A 7 alpha beta 194 214 200 197 230 C1' C A 8 alpha beta 225 245 231 228 261 C1' U A 9 alpha beta 256 276 262 259 291 C1' G A 10 alpha beta 286 309 292 289 325 C1' C A 11 alpha beta 320 340 326 323 356 C1' A A 12 alpha beta 351 373 357 354 389 C1' U A 13 alpha beta 384 404 390 387 419 C1' A A 14 alpha beta 414 436 420 417 452 C1' A A 15 alpha beta 447 469 453 450 485 C1' G A 16 alpha beta 480 503 486 483 519 C1' G A 17 alpha beta 514 537 520 517 553 C1' A A 18 alpha beta 548 570 554 551 577 C1' SSU A 19 alpha beta 578 597 587 576 616 C1' G A 20 alpha beta 611 634 617 614 650 C1' A A 21 alpha beta 645 667 651 648 683 C1' A A 22 alpha beta 678 700 684 681 716 C1' C A 23 alpha beta 711 731 717 714 747 C1' C A 24 alpha beta 742 763 748 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' G A 2 OK OK 43 39 59 42 75 C2' U A 3 OK OK 77 73 90 76 105 C2' U A 4 OK OK 107 103 120 106 135 C2' C A 5 OK OK 137 133 150 136 166 C2' C A 6 OK OK 168 164 181 167 197 C2' C A 7 OK OK 199 195 212 198 228 C2' C A 8 OK OK 230 226 243 229 259 C2' U A 9 OK OK 261 257 274 260 289 C2' G A 10 OK OK 291 287 307 290 323 C2' C A 11 OK OK 325 321 338 324 354 C2' A A 12 OK OK 356 352 371 355 387 C2' U A 13 OK OK 389 385 402 388 417 C2' A A 14 OK OK 419 415 434 418 450 C2' A A 15 OK OK 452 448 467 451 483 C2' G A 16 OK OK 485 481 501 484 517 C2' G A 17 OK OK 519 515 535 518 551 C2' A A 18 OK OK 553 549 568 552 576 C2' SSU A 19 OK OK 577 585 596 575 614 C2' G A 20 OK OK 616 612 632 615 648 C2' A A 21 OK OK 650 646 665 649 681 C2' A A 22 OK OK 683 679 698 682 714 C2' C A 23 OK OK 716 712 729 715 745 C2' C A 24 OK OK 747 743 761 746 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' U A 3 OK OK 71 89 74 75 103 C3' U A 4 OK OK 101 119 104 105 133 C3' C A 5 OK OK 131 149 134 135 164 C3' C A 6 OK OK 162 180 165 166 195 C3' C A 7 OK OK 193 211 196 197 226 C3' C A 8 OK OK 224 242 227 228 257 C3' U A 9 OK OK 255 273 258 259 287 C3' G A 10 OK OK 285 306 288 289 321 C3' C A 11 OK OK 319 337 322 323 352 C3' A A 12 OK OK 350 370 353 354 385 C3' U A 13 OK OK 383 401 386 387 415 C3' A A 14 OK OK 413 433 416 417 448 C3' A A 15 OK OK 446 466 449 450 481 C3' G A 16 OK OK 479 500 482 483 515 C3' G A 17 OK OK 513 534 516 517 549 C3' A A 18 OK OK 547 567 550 551 585 C3' SSU A 19 OK OK 579 601 586 576 612 C3' G A 20 OK OK 610 631 613 614 646 C3' A A 21 OK OK 644 664 647 648 679 C3' A A 22 OK OK 677 697 680 681 712 C3' C A 23 OK OK 710 728 713 714 743 C3' C A 24 OK OK 741 759 744 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' U A 3 OK OK 73 88 70 72 101 C4' U A 4 OK OK 103 118 100 102 131 C4' C A 5 OK OK 133 148 130 132 162 C4' C A 6 OK OK 164 179 161 163 193 C4' C A 7 OK OK 195 210 192 194 224 C4' C A 8 OK OK 226 241 223 225 255 C4' U A 9 OK OK 257 272 254 256 285 C4' G A 10 OK OK 287 305 284 286 319 C4' C A 11 OK OK 321 336 318 320 350 C4' A A 12 OK OK 352 369 349 351 383 C4' U A 13 OK OK 385 400 382 384 413 C4' A A 14 OK OK 415 432 412 414 446 C4' A A 15 OK OK 448 465 445 447 479 C4' G A 16 OK OK 481 499 478 480 513 C4' G A 17 OK OK 515 533 512 514 547 C4' A A 18 OK OK 549 566 546 548 579 C4' SSU A 19 OK OK 585 598 580 578 610 C4' G A 20 OK OK 612 630 609 611 644 C4' A A 21 OK OK 646 663 643 645 677 C4' A A 22 OK OK 679 696 676 678 710 C4' C A 23 OK OK 712 727 709 711 741 C4' C A 24 OK OK 743 758 740 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' G A 2 OK OK 35 55 56 37 70 C5' U A 3 OK OK 69 86 87 71 100 C5' U A 4 OK OK 99 116 117 101 130 C5' C A 5 OK OK 129 146 147 131 161 C5' C A 6 OK OK 160 177 178 162 192 C5' C A 7 OK OK 191 208 209 193 223 C5' C A 8 OK OK 222 239 240 224 254 C5' U A 9 OK OK 253 270 271 255 284 C5' G A 10 OK OK 283 303 304 285 318 C5' C A 11 OK OK 317 334 335 319 349 C5' A A 12 OK OK 348 367 368 350 382 C5' U A 13 OK OK 381 398 399 383 412 C5' A A 14 OK OK 411 430 431 413 445 C5' A A 15 OK OK 444 463 464 446 478 C5' G A 16 OK OK 477 497 498 479 512 C5' G A 17 OK OK 511 531 532 513 546 C5' A A 18 OK OK 545 564 565 547 580 C5' SSU A 19 OK OK 581 599 600 579 609 C5' G A 20 OK OK 608 628 629 610 643 C5' A A 21 OK OK 642 661 662 644 676 C5' A A 22 OK OK 675 694 695 677 709 C5' C A 23 OK OK 708 725 726 710 740 C5' C A 24 OK OK 739 756 757 741 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P U A 3 distorted distorted 40 67 68 69 96 P U A 4 distorted distorted 74 97 98 99 126 P C A 5 distorted distorted 104 127 128 129 157 P C A 6 distorted distorted 134 158 159 160 188 P C A 7 distorted distorted 165 189 190 191 219 P C A 8 distorted distorted 196 220 221 222 250 P U A 9 distorted distorted 227 251 252 253 280 P G A 10 distorted distorted 258 281 282 283 314 P C A 11 distorted distorted 288 315 316 317 345 P A A 12 distorted distorted 322 346 347 348 378 P U A 13 distorted distorted 353 379 380 381 408 P A A 14 distorted distorted 386 409 410 411 441 P A A 15 distorted distorted 416 442 443 444 474 P G A 16 distorted distorted 449 475 476 477 508 P G A 17 distorted distorted 482 509 510 511 542 P A A 18 distorted distorted 516 543 544 545 582 P SSU A 19 550 584 581 605 P G A 20 distorted distorted 586 606 607 608 639 P A A 21 distorted distorted 613 640 641 642 672 P A A 22 distorted distorted 647 673 674 675 705 P C A 23 distorted distorted 680 706 707 708 736 P C A 24 distorted distorted 713 737 738 739 ---------------------------------------------------------------------------------