1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Clore, G.M. Kuszewski, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C7 H8 N4 O2 180.164 THEOPHYLLINE non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking 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 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N C Y 112 N N Y 113 N C N 114 N O Y 115 N N N 116 N C Y 117 N C Y 118 N C Y 119 N C N 120 N O Y 121 N N Y 122 N C Y 123 N N N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N O N 133 N P N 134 N O N 135 N O N 136 N O N 137 N C N 138 R C N 139 N O N 140 S C N 141 N O N 142 R C N 143 N O N 144 R C N 145 N N N 146 N C N 147 N O N 148 N N N 149 N C N 150 N O N 151 N C N 152 N C N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 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 N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing Y 120 N sing Y 121 N sing N 122 N doub Y 123 N sing N 124 N sing Y 125 N sing N 126 N sing N 127 N sing N 128 N sing Y 129 N doub Y 130 N sing Y 131 N sing Y 132 N sing N 133 N doub Y 134 N sing N 135 N sing Y 136 N doub N 137 N sing N 138 N sing N 139 N sing N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N doub N 165 N sing N 166 N sing N 167 N sing N 168 N doub N 169 N sing N 170 N doub N 171 N sing N 172 N sing US J.Am.Chem.Soc. JACSAT 0004 0002-7863 125 1518 1525 10.1021/ja028383j 12568611 Improving the Accuracy of NMR Structures of RNA by Means of Conformational Database Potentials of Mean Force as Assessed by Complete Dipolar Coupling Cross-Validation 2003 US Nat.Struct.Biol. NSBIEW 2024 1072-8368 4 644 649 Interlocking Structural Motifs Mediate Molecular Discrimination by a Theophylline-Binding RNA 1997 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 12135 12146 10.1021/ja011646+ Refinement of Local and Long Range Structural Order in Theophylline-Binding RNA Using Using 13C-1H Residual Dipolar Couplings and Restrained Molecular Dynamics. 2001 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 3903 3918 10.1021/ja010033u Improving the Accuracy of NMR Structures of DNA by Means of a Database Potential of Mean Force Describing Base-Base Positional Interactions. 2001 10.2210/pdb1o15/pdb pdb_00001o15 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 CONSENSUS SEQUENCE OF THE THEOPHYLLINE BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP 10638.409 THEOPHYLLINE-BINDING RNA 1 syn polymer 180.164 THEOPHYLLINE 1 syn non-polymer no no GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 10.760 1 19 A 1 A 33 -2.593 A_G1:C33_A 1 6.865 -0.135 -0.046 -0.195 7.514 1 28 A 2 A 32 0.339 A_G2:U32_A 2 -23.022 -1.875 0.006 -0.375 8.696 1 19 A 3 A 31 0.300 A_C3:G31_A 3 -14.125 0.126 -0.255 -0.162 -5.936 1 19 A 4 A 30 0.541 A_G4:C30_A 4 -15.944 -0.137 -0.436 -0.182 -10.550 1 8 A 5 A 29 4.429 A_A5:G29_A 5 -17.722 0.256 -1.092 0.947 0.949 3 23 A 23 A 28 -74.340 A_U23:A28_A 6 -3.356 -0.326 -0.553 2.758 -5.644 1 19 A 8 A 26 -2.756 A_C8:G26_A 7 -1.843 0.011 0.014 -0.181 6.894 1 19 A 9 A 25 2.299 A_C9:G25_A 8 -21.686 0.244 -0.254 -0.219 9.162 1 19 A 11 A 20 -3.925 A_G11:C20_A 9 -21.229 -0.045 0.608 -0.238 2.951 1 19 A 12 A 19 1.049 A_C12:G19_A 10 -23.476 0.193 -0.088 -0.223 -1.623 1 19 A 13 A 18 -0.937 A_C13:G18_A 11 -4.383 0.172 -0.098 -0.196 18.272 A 14 A 17 -42.508 A_G14:A17_A 12 22.677 7.004 0.678 -5.448 3.001 23.322 A A 1 2 15.097 A A 33 32 3.621 6.034 0.132 -1.967 AA_G1G2:U32C33_AA 1 0.892 -2.232 22.521 -6.993 -0.011 2.850 40.486 A A 2 3 10.647 A A 32 31 3.114 7.328 -0.012 -1.232 AA_G2C3:G31U32_AA 2 -1.971 2.864 39.798 -2.535 -0.185 2.364 33.186 A A 3 4 28.042 A A 31 30 3.594 15.423 -0.118 -1.816 AA_C3G4:C30G31_AA 3 1.733 -3.152 29.424 -5.689 0.489 2.836 31.402 A A 4 5 17.755 A A 30 29 3.438 9.442 0.288 -1.560 AA_G4A5:G29C30_AA 4 3.989 -7.501 29.722 -4.632 0.206 1.767 -178.999 A A 5 23 -54.914 A A 29 28 1.955 109.794 -0.914 3.711 AA_A5U23:A28G29_AA 5 130.354 65.197 -167.971 -1.918 -0.383 1.244 39.592 A A 8 9 36.967 A A 26 25 2.674 23.501 0.376 -1.612 AA_C8C9:G25G26_AA 6 -0.612 0.962 32.085 -4.221 -0.602 3.188 35.941 A A 11 12 7.080 A A 20 19 3.394 4.354 0.173 -1.580 AA_G11C12:G19C20_AA 7 3.142 -5.110 35.550 -3.189 0.174 2.205 32.360 A A 12 13 25.144 A A 19 18 3.227 13.598 -0.178 -1.802 AA_C12C13:G18G19_AA 8 -0.936 1.730 29.420 -5.329 0.174 2.682 59.574 A A 13 14 8.579 A A 18 17 2.857 8.500 -2.867 -1.227 AA_C13G14:A17G18_AA 9 -0.194 0.195 59.019 -1.599 2.877 database_2 pdbx_database_remark pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations Data collection 1 0 2003-02-18 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-23 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_remark.text _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE ARE SUMMARIZED AS FOLLOWS: DISTANCE RESTRAINTS 30 INTRARESIDUE NOES 86 SEQUENTIAL NOES 17 MEDIUM RANGE (1 < |i-j|<5) NOES 90 LONG RANGE (|i-j|>=5) NOES 52 DISTANCES FOR 8 W-C BASE PAIRS and 1 G-U WOBBLE PAIR TOTAL: 223 LOOSE TORSION ANGLE RESTRAINTS 31 DELTA 33 CHI 9 ALPHA, 9 BETA, 10 GAMMA, 9 EPSILON AND 9 ZETA TOTAL: 110. 13C-1H DIPOLAR COUPLINGS 55 SUGAR 46 BASE TOTAL 101 RCSB Y RCSB 2002-10-21 REL TEP THEOPHYLLINE THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND PARTITIONED IN A RATIO OF 70% (WORKING) AND 30% (TEST). 25 SIMULATED ANNEALING STRUCTURES WERE CALCULATED FOR EACH PAIR, RESULTING IN A TOTAL OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN COORDINATES OF THE ENSEMBLE OF 250 INDIVIDUAL SIMULATED ANNEALING STRUCTURES CALCULATED WITH COMPLETE DIPOLAR COUPLING CROSS-VALIDATION. FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING DIPOLAR COUPLING R-FACTOR IS 8.6+/-0.5% AND THE FREE DIPOLAR COUPLING R-FACTOR IS 26.8+/-2.8%. RESTRAINED REGULARIZED MEAN STRUCTURE 250 1 THE STRUCTURE IS BASED ON A TOTAL OF 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. THE EXPERIMENTAL RESTRAINTS ARE ESSENTIALLY THE SAME AS THOSE LISTED IN N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE J.AM.CHEM.SOC. V 123, 12135 2001. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA refinement X-PLOR NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) THE 34 2 TEP TEP 34 A GUA 1 n 1 G 1 A GUA 2 n 2 G 2 A CYT 3 n 3 C 3 A GUA 4 n 4 G 4 A ADE 5 n 5 A 5 A URI 6 n 6 U 6 A ADE 7 n 7 A 7 A CYT 8 n 8 C 8 A CYT 9 n 9 C 9 A ADE 10 n 10 A 10 A GUA 11 n 11 G 11 A CYT 12 n 12 C 12 A CYT 13 n 13 C 13 A GUA 14 n 14 G 14 A ADE 15 n 15 A 15 A ADE 16 n 16 A 16 A ADE 17 n 17 A 17 A GUA 18 n 18 G 18 A GUA 19 n 19 G 19 A CYT 20 n 20 C 20 A CYT 21 n 21 C 21 A CYT 22 n 22 C 22 A URI 23 n 23 U 23 A URI 24 n 24 U 24 A GUA 25 n 25 G 25 A GUA 26 n 26 G 26 A CYT 27 n 27 C 27 A ADE 28 n 28 A 28 A GUA 29 n 29 G 29 A CYT 30 n 30 C 30 A GUA 31 n 31 G 31 A URI 32 n 32 U 32 A CYT 33 n 33 C 33 A author_defined_assembly 1 monomeric 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 1 4.11 0.40 120.30 124.41 A A A C6 N1 C2 C C C 27 27 27 N THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 33 A N3 C 33 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 33 A O2 C 33 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 33 A N4 C 33 1_555 hydrog TYPE_28_PAIR A G 2 A N1 G 2 1_555 A U 32 A O2 U 32 1_555 hydrog TYPE_28_PAIR A G 2 A O6 G 2 1_555 A U 32 A N3 U 32 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 31 A N1 G 31 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 31 A O6 G 31 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 31 A N2 G 31 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 30 A N4 C 30 1_555 hydrog TYPE_8_PAIR A A 5 A N1 A 5 1_555 A G 29 A N1 G 29 1_555 hydrog TYPE_8_PAIR A A 5 A N6 A 5 1_555 A G 29 A O6 G 29 1_555 hydrog U-U MISPAIR A U 6 A N3 U 6 1_555 A U 23 A O4 U 23 1_555 hydrog U-A PAIR A U 6 A O2 U 6 1_555 A A 28 A N6 A 28 1_555 hydrog A-C MISPAIR A A 7 A N3 A 7 1_555 A C 8 A N4 C 8 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 26 A N1 G 26 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 26 A O6 G 26 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 26 A N2 G 26 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 25 A N2 G 25 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 19 A N2 G 19 1_555 hydrog WATSON-CRICK A C 13 A N3 C 13 1_555 A G 18 A N1 G 18 1_555 hydrog WATSON-CRICK A C 13 A N4 C 13 1_555 A G 18 A O6 G 18 1_555 hydrog WATSON-CRICK A C 13 A O2 C 13 1_555 A G 18 A N2 G 18 1_555 hydrog G-A MISPAIR A G 14 A N2 G 14 1_555 A A 17 A N7 A 17 1_555 hydrog HOOGSTEEN A U 23 A N3 U 23 1_555 A A 28 A N7 A 28 1_555 hydrog HOOGSTEEN A U 23 A O4 U 23 1_555 A A 28 A N6 A 28 1_555 RNA RIBONUCLEIC ACID, RNA 1O15 PDB 1 1O15 1 33 1O15 1 33 1O15 A 1 1 33 BINDING SITE FOR RESIDUE TEP A 34 A TEP 34 Software 3 A A 7 A A 7 3 1_555 A C 22 A C 22 3 1_555 A U 24 A U 24 3 1_555 1 P 1