0.038850 -0.000000 0.000000 0.000000 0.009383 0.000000 0.000000 0.000000 0.033047 0.00000 0.00000 0.00000 Shi, K. Pan, B. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 25.740 106.580 30.260 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 H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION 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 O N 112 N H N 113 N H N 114 N NA N 115 N O N 116 N P N 117 N O N 118 N O N 119 N O N 120 N C N 121 R C N 122 N O N 123 S C N 124 N O N 125 R C N 126 N O N 127 R C N 128 N N N 129 N C N 130 N O N 131 N N N 132 N C N 133 N O N 134 N C N 135 N C N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 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 N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N doub N 151 N sing N 152 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 1392 1397 10.1093/nar/gkg226 12595546 The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs 2003 10.2210/pdb1l3z/pdb pdb_00001l3z 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293 1 IMAGE PLATE RIGAKU SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 2205.379 5'-R(*GP*UP*AP*UP*AP*CP*A)-3' 2 syn polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 39 nat water no no GUAUACA GUAUACA A,B polyribonucleotide n n n n n n n 1 2.35 47.72 7.0 MPD, CaCl2, Cacodylate buffer, pH7.0 MPD 1 CaCl2 1 Cacodylate buffer 1 -5.969 1 19 B 8 B 13 -0.483 B_G8:C13_B 1 -11.701 -0.203 0.112 -0.138 -2.264 1 20 B 9 B 12 0.967 B_U9:A12_B 2 -11.661 -0.223 0.271 -0.130 1.192 1 20 B 10 B 11 6.990 B_A10:U11_B 3 -15.805 -0.059 0.260 -0.119 -1.192 1 20 B 11 B 10 6.990 B_U11:A10_B 4 -15.805 0.059 0.260 -0.119 2.264 1 20 B 12 B 9 0.967 B_A12:U9_B 5 -11.661 0.223 0.271 -0.130 5.969 1 19 B 13 B 8 -0.483 B_C13:G8_B 6 -11.701 0.203 0.112 -0.138 2.769 32.045 B B 8 9 13.922 B B 13 12 3.186 7.603 -0.116 -1.405 BB_G8U9:A12C13_BB 1 -3.294 6.032 30.983 -3.814 -0.340 2.258 34.365 B B 9 10 23.663 B B 12 11 3.072 13.619 0.115 -1.490 BB_U9A10:U11A12_BB 2 0.179 -0.310 31.626 -4.335 -0.171 2.664 34.009 B B 10 11 21.796 B B 11 10 3.300 12.467 0.000 -1.173 BB_A10U11:A10U11_BB 3 0.000 0.000 31.704 -3.888 0.000 2.258 34.365 B B 11 12 23.663 B B 10 9 3.072 13.619 -0.115 -1.490 BB_U11A12:U9A10_BB 4 -0.179 0.310 31.626 -4.335 0.171 2.769 32.045 B B 12 13 13.922 B B 9 8 3.186 7.603 0.116 -1.405 BB_A12C13:G8U9_BB 5 3.294 -6.032 30.983 -3.814 0.340 software diffrn_source chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Data collection Database references Derived calculations 1 0 2003-02-25 1 1 2008-04-28 1 2 2011-07-13 1 3 2017-10-11 1 4 2018-03-07 1 5 2024-02-14 _diffrn_source.source _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-03-04 REL REL NA SODIUM ION HOH water NA 301 2 NA NA 301 A WAT 101 3 HOH HOH 101 A WAT 102 3 HOH HOH 102 A WAT 104 3 HOH HOH 104 A WAT 105 3 HOH HOH 105 A WAT 106 3 HOH HOH 106 A WAT 107 3 HOH HOH 107 A WAT 108 3 HOH HOH 108 A WAT 119 3 HOH HOH 119 A WAT 120 3 HOH HOH 120 A WAT 121 3 HOH HOH 121 A WAT 122 3 HOH HOH 122 A WAT 123 3 HOH HOH 123 A WAT 125 3 HOH HOH 125 A WAT 126 3 HOH HOH 126 A WAT 127 3 HOH HOH 127 A WAT 128 3 HOH HOH 128 A WAT 129 3 HOH HOH 129 A WAT 132 3 HOH HOH 132 A WAT 136 3 HOH HOH 136 A WAT 137 3 HOH HOH 137 A WAT 138 3 HOH HOH 138 A WAT 202 3 HOH HOH 202 A WAT 103 3 HOH HOH 103 B WAT 109 3 HOH HOH 109 B WAT 110 3 HOH HOH 110 B WAT 111 3 HOH HOH 111 B WAT 112 3 HOH HOH 112 B WAT 113 3 HOH HOH 113 B WAT 114 3 HOH HOH 114 B WAT 115 3 HOH HOH 115 B WAT 116 3 HOH HOH 116 B WAT 117 3 HOH HOH 117 B WAT 118 3 HOH HOH 118 B WAT 124 3 HOH HOH 124 B WAT 130 3 HOH HOH 130 B WAT 133 3 HOH HOH 133 B WAT 134 3 HOH HOH 134 B WAT 135 3 HOH HOH 135 B WAT 201 3 HOH HOH 201 B GUA 1 n 1 G 1 A URI 2 n 2 U 2 A ADE 3 n 3 A 3 A URI 4 n 4 U 4 A ADE 5 n 5 A 5 A CYT 6 n 6 C 6 A ADE 7 n 7 A 7 A GUA 8 n 1 G 8 B URI 9 n 2 U 9 B ADE 10 n 3 A 10 B URI 11 n 4 U 11 B ADE 12 n 5 A 12 B CYT 13 n 6 C 13 B ADE 14 n 7 A 14 B author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric A HOH 202 D O HOH 1_555 A NA 301 C NA NA 1_555 A HOH 202 D O HOH 6_555 1.5 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_556 -x,y,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 30.2600000000 1 A NA 301 C NA 1 A HOH 129 D HOH 1 A HOH 202 D HOH 1 B HOH 201 E HOH 30.5 3.28 0.00 0.00 -2.95 0.00 -0.34 0.225 0.014 0.18 0.18 2.01 20.00 259 2808 9.2 92.5 RANDOM 545644.27 1 RESTRAINED THROUGHOUT 2.0 0.24 0.21 5.00 0.24 0.23 2.01 20.00 39 332 1 292 0 0.003 0.8 10.5 1.33 1.52 1.50 2.12 2.00 1.33 2.00 1.85 2.50 0.289 0.049 0.245 2.13 35 329 6 9.6 74.0 18.1 2.01 50.0 1L3Z 22206 0 1 93.8 2.01 2.13 data scaling SCALEPACK phasing AMoRE refinement CNS Crystal Structure Analysis of an RNA Heptamer 1 N N 1 N N 2 N N 3 N N 3 N N metalc 2.347 A HOH 202 D O HOH 1_555 A NA 301 C NA NA 1_555 metalc 2.347 A HOH 202 D O HOH 6_555 A NA 301 C NA NA 1_555 hydrog WATSON-CRICK B G 8 B N1 G 1 1_555 B C 13 B N3 C 6 3_556 hydrog WATSON-CRICK B G 8 B N2 G 1 1_555 B C 13 B O2 C 6 3_556 hydrog WATSON-CRICK B G 8 B O6 G 1 1_555 B C 13 B N4 C 6 3_556 hydrog WATSON-CRICK B U 9 B N3 U 2 1_555 B A 12 B N1 A 5 3_556 hydrog WATSON-CRICK B U 9 B O4 U 2 1_555 B A 12 B N6 A 5 3_556 hydrog WATSON-CRICK B A 10 B N1 A 3 1_555 B U 11 B N3 U 4 3_556 hydrog WATSON-CRICK B A 10 B N6 A 3 1_555 B U 11 B O4 U 4 3_556 hydrog WATSON-CRICK B U 11 B N3 U 4 1_555 B A 10 B N1 A 3 3_556 hydrog WATSON-CRICK B U 11 B O4 U 4 1_555 B A 10 B N6 A 3 3_556 hydrog WATSON-CRICK B A 12 B N1 A 5 1_555 B U 9 B N3 U 2 3_556 hydrog WATSON-CRICK B A 12 B N6 A 5 1_555 B U 9 B O4 U 2 3_556 hydrog WATSON-CRICK B C 13 B N3 C 6 1_555 B G 8 B N1 G 1 3_556 hydrog WATSON-CRICK B C 13 B N4 C 6 1_555 B G 8 B O6 G 1 3_556 hydrog WATSON-CRICK B C 13 B O2 C 6 1_555 B G 8 B N2 G 1 3_556 RNA RNA 1L3Z PDB 1 1L3Z 1 7 1L3Z 1 7 1L3Z A 1 1 7 8 14 1L3Z 8 14 1L3Z B 1 1 7 BINDING SITE FOR RESIDUE NA A 301 A NA 301 Software 6 A HOH 125 D HOH 6 6_555 A HOH 125 D HOH 6 1_555 A HOH 127 D HOH 6 6_555 A HOH 127 D HOH 6 1_555 A HOH 202 D HOH 6 6_555 A HOH 202 D HOH 6 1_555 21 C 2 2 2