ID code: '2ZNA' 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' --------------------------------------------------------------------------------- 11 C1' C A 1 beta 7 12 10 41 C1' G A 2 beta 37 42 40 74 C1' C A 3 beta 70 75 73 104 C1' G A 4 beta 100 105 103 137 C1' C A 5 beta 133 138 136 167 C1' G A 6 beta 163 168 166 200 C1' C A 7 beta 196 201 199 230 C1' G A 8 beta 226 231 229 263 C1' C A 9 beta 259 264 262 293 C1' G A 10 beta 289 294 292 326 C1' C A 11 beta 322 327 325 356 C1' G A 12 beta 352 357 355 390 C1' C B 1 beta 386 391 389 420 C1' G B 2 beta 416 421 419 453 C1' C B 3 beta 449 454 452 483 C1' G B 4 beta 479 484 482 516 C1' C B 5 beta 512 517 515 546 C1' G B 6 beta 542 547 545 579 C1' C B 7 beta 575 580 578 609 C1' G B 8 beta 605 610 608 642 C1' C B 9 beta 638 643 641 672 C1' G B 10 beta 668 673 671 705 C1' C B 11 beta 701 706 704 735 C1' G B 12 beta 731 736 734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 1 11 8 40 C2' G A 2 41 38 73 C2' C A 3 74 71 103 C2' G A 4 104 101 136 C2' C A 5 137 134 166 C2' G A 6 167 164 199 C2' C A 7 200 197 229 C2' G A 8 230 227 262 C2' C A 9 263 260 292 C2' G A 10 293 290 325 C2' C A 11 326 323 355 C2' G A 12 356 353 389 C2' C B 1 390 387 419 C2' G B 2 420 417 452 C2' C B 3 453 450 482 C2' G B 4 483 480 515 C2' C B 5 516 513 545 C2' G B 6 546 543 578 C2' C B 7 579 576 608 C2' G B 8 609 606 641 C2' C B 9 642 639 671 C2' G B 10 672 669 704 C2' C B 11 705 702 734 C2' G B 12 735 732 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 1 OK 6 9 10 38 C3' G A 2 OK 36 39 40 71 C3' C A 3 OK 69 72 73 101 C3' G A 4 OK 99 102 103 134 C3' C A 5 OK 132 135 136 164 C3' G A 6 OK 162 165 166 197 C3' C A 7 OK 195 198 199 227 C3' G A 8 OK 225 228 229 260 C3' C A 9 OK 258 261 262 290 C3' G A 10 OK 288 291 292 323 C3' C A 11 OK 321 324 325 353 C3' G A 12 OK 351 354 355 387 C3' C B 1 OK 385 388 389 417 C3' G B 2 OK 415 418 419 450 C3' C B 3 OK 448 451 452 480 C3' G B 4 OK 478 481 482 513 C3' C B 5 OK 511 514 515 543 C3' G B 6 OK 541 544 545 576 C3' C B 7 OK 574 577 578 606 C3' G B 8 OK 604 607 608 639 C3' C B 9 OK 637 640 641 669 C3' G B 10 OK 667 670 671 702 C3' C B 11 OK 700 703 704 732 C3' G B 12 OK 730 733 734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 1 OK 8 5 7 36 C4' G A 2 OK 38 35 37 69 C4' C A 3 OK 71 68 70 99 C4' G A 4 OK 101 98 100 132 C4' C A 5 OK 134 131 133 162 C4' G A 6 OK 164 161 163 195 C4' C A 7 OK 197 194 196 225 C4' G A 8 OK 227 224 226 258 C4' C A 9 OK 260 257 259 288 C4' G A 10 OK 290 287 289 321 C4' C A 11 OK 323 320 322 351 C4' G A 12 OK 353 350 352 385 C4' C B 1 OK 387 384 386 415 C4' G B 2 OK 417 414 416 448 C4' C B 3 OK 450 447 449 478 C4' G B 4 OK 480 477 479 511 C4' C B 5 OK 513 510 512 541 C4' G B 6 OK 543 540 542 574 C4' C B 7 OK 576 573 575 604 C4' G B 8 OK 606 603 605 637 C4' C B 9 OK 639 636 638 667 C4' G B 10 OK 669 666 668 700 C4' C B 11 OK 702 699 701 730 C4' G B 12 OK 732 729 731 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 1 4 6 35 C5' G A 2 34 36 68 C5' C A 3 67 69 98 C5' G A 4 97 99 131 C5' C A 5 130 132 161 C5' G A 6 160 162 194 C5' C A 7 193 195 224 C5' G A 8 223 225 257 C5' C A 9 256 258 287 C5' G A 10 286 288 320 C5' C A 11 319 321 350 C5' G A 12 349 351 384 C5' C B 1 383 385 414 C5' G B 2 413 415 447 C5' C B 3 446 448 477 C5' G B 4 476 478 510 C5' C B 5 509 511 540 C5' G B 6 539 541 573 C5' C B 7 572 574 603 C5' G B 8 602 604 636 C5' C B 9 635 637 666 C5' G B 10 665 667 699 C5' C B 11 698 700 729 C5' G B 12 728 730 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 1 OK OK 2 3 4 31 P G A 2 distorted distorted 9 32 33 34 64 P C A 3 distorted distorted 39 65 66 67 94 P G A 4 distorted distorted 72 95 96 97 127 P C A 5 distorted distorted 102 128 129 130 157 P G A 6 distorted distorted 135 158 159 160 190 P C A 7 distorted distorted 165 191 192 193 220 P G A 8 distorted distorted 198 221 222 223 253 P C A 9 distorted distorted 228 254 255 256 283 P G A 10 distorted distorted 261 284 285 286 316 P C A 11 distorted distorted 291 317 318 319 346 P G A 12 distorted distorted 324 347 348 349 380 P C B 1 OK OK 381 382 383 410 P G B 2 distorted distorted 388 411 412 413 443 P C B 3 distorted distorted 418 444 445 446 473 P G B 4 distorted distorted 451 474 475 476 506 P C B 5 distorted distorted 481 507 508 509 536 P G B 6 distorted distorted 514 537 538 539 569 P C B 7 distorted distorted 544 570 571 572 599 P G B 8 distorted distorted 577 600 601 602 632 P C B 9 distorted distorted 607 633 634 635 662 P G B 10 distorted distorted 640 663 664 665 695 P C B 11 distorted distorted 670 696 697 698 725 P G B 12 distorted distorted 703 726 727 728 ---------------------------------------------------------------------------------