0.10 0.421 4.039 -2.933 A P DA 1 ATOM A P DA 1 1 1.00 1 P 0.16 0.818 5.069 -3.901 A OP1 DA 1 ATOM A OP1 DA 1 1 1.00 1 O 0.12 0.311 4.338 -1.509 A OP2 DA 1 ATOM A OP2 DA 1 1 1.00 1 O 0.11 1.400 2.800 -2.997 A O5' DA 1 ATOM A O5' DA 1 1 1.00 1 O 0.13 1.801 2.311 -4.251 A C5' DA 1 ATOM A C5' DA 1 1 1.00 1 C 0.08 2.995 1.329 -4.062 A C4' DA 1 ATOM A C4' DA 1 1 1.00 1 C 0.08 4.119 2.107 -3.636 A O4' DA 1 ATOM A O4' DA 1 1 1.00 1 O 0.07 2.825 0.234 -2.994 A C3' DA 1 ATOM A C3' DA 1 1 1.00 1 C 0.09 3.486 -0.903 -3.541 A O3' DA 1 ATOM A O3' DA 1 1 1.00 1 O 0.09 3.512 0.802 -1.757 A C2' DA 1 ATOM A C2' DA 1 1 1.00 1 C 0.09 4.621 1.636 -2.392 A C1' DA 1 ATOM A C1' DA 1 1 1.00 1 C 0.08 5.017 2.794 -1.636 A N9 DA 1 ATOM A N9 DA 1 1 1.00 1 N 0.10 4.355 3.964 -1.571 A C8 DA 1 ATOM A C8 DA 1 1 1.00 1 C 0.10 4.943 4.873 -0.817 A N7 DA 1 ATOM A N7 DA 1 1 1.00 1 N 0.08 6.031 4.196 -0.300 A C5 DA 1 ATOM A C5 DA 1 1 1.00 1 C 0.07 7.094 4.570 0.542 A C6 DA 1 ATOM A C6 DA 1 1 1.00 1 C 0.08 7.194 5.794 1.058 A N6 DA 1 ATOM A N6 DA 1 1 1.00 1 N 0.09 8.004 3.701 0.819 A N1 DA 1 ATOM A N1 DA 1 1 1.00 1 N 0.10 7.926 2.564 0.285 A C2 DA 1 ATOM A C2 DA 1 1 1.00 1 C 0.10 6.983 2.026 -0.522 A N3 DA 1 ATOM A N3 DA 1 1 1.00 1 N 0.07 6.068 2.946 -0.788 A C4 DA 1 ATOM A C4 DA 1 1 1.00 1 C 0.09 14.944 9.099 5.933 B P DA 2 ATOM B P DA 1 1 1.00 1 P 0.15 15.269 9.154 4.483 B OP1 DA 2 ATOM B OP1 DA 1 1 1.00 1 O 0.13 15.672 9.976 6.862 B OP2 DA 2 ATOM B OP2 DA 1 1 1.00 1 O 0.10 13.348 9.362 5.980 B O5' DA 2 ATOM B O5' DA 1 1 1.00 1 O 0.12 12.696 9.433 7.234 B C5' DA 2 ATOM B C5' DA 1 1 1.00 1 C 0.10 11.318 9.990 7.024 B C4' DA 2 ATOM B C4' DA 1 1 1.00 1 C 0.11 11.421 11.354 6.614 B O4' DA 2 ATOM B O4' DA 1 1 1.00 1 O 0.10 10.430 9.273 5.987 B C3' DA 2 ATOM B C3' DA 1 1 1.00 1 C 0.08 9.132 9.324 6.513 B O3' DA 2 ATOM B O3' DA 1 1 1.00 1 O 0.09 10.633 10.186 4.785 B C2' DA 2 ATOM B C2' DA 1 1 1.00 1 C 0.09 10.804 11.562 5.401 B C1' DA 2 ATOM B C1' DA 1 1 1.00 1 C 0.09 11.568 12.473 4.612 B N9 DA 2 ATOM B N9 DA 1 1 1.00 1 N 0.15 12.900 12.477 4.536 B C8 DA 2 ATOM B C8 DA 1 1 1.00 1 C 0.12 13.380 13.505 3.788 B N7 DA 2 ATOM B N7 DA 1 1 1.00 1 N 0.10 12.238 14.069 3.280 B C5 DA 2 ATOM B C5 DA 1 1 1.00 1 C 0.12 12.104 15.166 2.454 B C6 DA 2 ATOM B C6 DA 1 1 1.00 1 C 0.14 13.096 15.851 1.925 B N6 DA 2 ATOM B N6 DA 1 1 1.00 1 N 0.11 10.788 15.546 2.175 B N1 DA 2 ATOM B N1 DA 1 1 1.00 1 N 0.13 9.927 14.827 2.742 B C2 DA 2 ATOM B C2 DA 1 1 1.00 1 C 0.11 9.928 13.794 3.511 B N3 DA 2 ATOM B N3 DA 1 1 1.00 1 N 0.10 11.185 13.473 3.789 B C4 DA 2 ATOM B C4 DA 1 1 1.00 1 C 0.17 0.000 0.000 -0.975 A O HOH 4 HETATM C O HOH 2 0.33 1 O 0.18 11.665 6.734 3.904 A O HOH 5 HETATM C O HOH 2 0.33 1 O 0.19 0.000 0.000 3.307 A O HOH 6 HETATM C O HOH 2 0.33 1 O 0.11 0.890 2.325 0.214 A O HOH 7 HETATM C O HOH 2 1.00 1 O 0.10 9.230 7.154 2.752 A O HOH 8 HETATM C O HOH 2 1.00 1 O 0.22 0.020 5.012 3.134 A O HOH 9 HETATM C O HOH 2 1.00 1 O 0.13 10.807 4.273 0.669 A O HOH 10 HETATM C O HOH 2 1.00 1 O 0.14 -0.877 2.489 2.321 A O HOH 11 HETATM C O HOH 2 1.00 1 O 0.21 11.664 6.735 -0.303 A O HOH 12 HETATM C O HOH 2 0.33 1 O 0.17 0.146 6.831 1.878 A O HOH 13 HETATM C O HOH 2 1.00 1 O 0.24 1.701 5.931 0.657 A O HOH 14 HETATM C O HOH 2 1.00 1 O 0.28 -1.182 6.653 9.847 A O HOH 15 HETATM C O HOH 2 1.00 1 O 0.29 11.619 1.752 9.559 B O HOH 9 HETATM D O HOH 2 1.00 1 O 0.042867 0.024749 0.000000 0.000000 0.049498 0.000000 0.000000 0.000000 0.103306 0.00000 0.00000 0.00000 Gao, Y.G. Robinson, H. Guan, Y. Liaw, Y.C. van Boom, J.H. van der Marel, G.A. Wang, A.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 23.328 23.328 9.680 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N H N 39 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 16 69 76 9745896 Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution. 1998 10.2210/pdb1o56/pdb pdb_00001o56 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.00 1 IMAGE PLATE 1997-12-29 RIGAKU SINGLE WAVELENGTH M x-ray 1 1.0 ROTATING ANODE RIGAKU RU200 894.663 DNA (5'-CD(*AP*AP*AP*)-3') 2 syn polymer 18.015 water 13 nat water no no (DA)(DA)(DA) AAA A,B polydeoxyribonucleotide n n n 1 1.41 42.0000 VAPOR DIFFUSION, HANGING DROP 4.50 pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K 298.00 MPD 1 GLYCINE 1 MGCL2 1 MPD 2 software chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Atomic model Refinement description Data collection Database references 1 0 2003-08-26 1 1 2008-04-26 1 2 2011-07-13 1 3 2011-11-16 1 4 2017-10-04 1 5 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession 2003-08-26 SPRSDE SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent molecules sits on the crystallographic 3-fold axis. Remark 350 provides the way to create cyclic D(*Ap*Ap*Ap) molecule. RCSB Y RCSB 2003-08-20 REL HOH water Synthetic sample HOH 3 2 HOH HOH 4 A HOH 4 2 HOH HOH 5 A HOH 5 2 HOH HOH 6 A HOH 6 2 HOH HOH 7 A HOH 7 2 HOH HOH 8 A HOH 8 2 HOH HOH 9 A HOH 10 2 HOH HOH 10 A HOH 11 2 HOH HOH 11 A HOH 12 2 HOH HOH 12 A HOH 13 2 HOH HOH 13 A HOH 14 2 HOH HOH 14 A HOH 15 2 HOH HOH 15 A HOH 9 2 HOH HOH 9 B A 1 n 1 DA 1 A n 2 2 A n 3 3 A A 2 n 1 DA 2 B n 2 3 B n 3 4 B 0.109 author_defined_assembly 3 trimeric author_defined_assembly 3 trimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_555 -y,x-y,z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_555 -x+y,-x,z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_655 -y+1,x-y,z crystal symmetry operation 23.3280000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_665 -x+y+1,-x+1,z crystal symmetry operation 11.6640000000 20.2026406195 0.0000000000 1 A HOH 4 C HOH 1 A HOH 5 C HOH 1 A HOH 6 C HOH 1 A HOH 12 C HOH 1 A DA 2 A DA 2 1 Y 1 A DA 3 A DA 3 1 Y 1 B DA 3 B DA 2 1 Y 1 B DA 4 B DA 3 1 Y 1 A A O O HOH HOH 13 14 2.17 1 1.80 0.30 108.30 110.10 B B B O4' C1' N9 DA DA DA 2 2 2 N 1 -5.06 0.60 118.60 113.54 B B B C6 N1 C2 DA DA DA 2 2 2 N 1 7.39 0.50 129.30 136.69 B B B N1 C2 N3 DA DA DA 2 2 2 N 1 4.01 0.50 117.00 121.01 B B B C4 C5 C6 DA DA DA 2 2 2 N 1 4.38 0.40 105.80 110.18 B B B N9 C4 C5 DA DA DA 2 2 2 N 1 A A C5' C4' DA DA 1 1 0.045 0.007 1.512 1.557 N 1 A A N1 C2 DA DA 1 1 -0.080 0.009 1.339 1.259 N 1 A A C6 N1 DA DA 1 1 -0.063 0.007 1.351 1.288 N 1 B B N1 C2 DA DA 2 2 -0.082 0.009 1.339 1.257 N 1 B B C4 C5 DA DA 2 2 -0.070 0.007 1.383 1.313 N 1 B B C6 N1 DA DA 2 2 0.047 0.007 1.351 1.398 N 1 B B N7 C8 DA DA 2 2 0.048 0.007 1.311 1.359 N 1 B B P O3' DA DA 2 2 1.59 1_555 3_665 1 A A P O3' DA DA 1 1 1.61 1_555 2_555 1 A A O O HOH HOH 13 15 2.17 1_555 1_554 0.109 0.900 10.000 3059 3059 1 3.000 0.900 10.000 13 55 0 42 0 0.032 0.900 10.000 1O56 3059 3.000 1 phasing SHELXS refinement SHELXL-97 MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION 1 N N 1 N N 2 N N 2 N N DNA CYCLIC TRINUCLEOTIDE, DNA 1O56 PDB 1 1O56 1 3 1O56 1 3 1O56 A 1 1 3 2 4 1O56 2 4 1O56 B 1 1 3 143 P 3