0.023992 0.013852 0.000000 0.000000 0.027703 0.000000 0.000000 0.000000 0.016663 0.00000 0.00000 0.00000 Jiang, S. Sun, H. Gan, J. Huang, Z. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 18 90.00 90.00 120.00 41.681 41.681 60.014 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 Sr 2 87.620 STRONTIUM 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 SR N 112 N O N 113 N P N 114 N O N 115 N O N 116 N O N 117 N C N 118 R C N 119 N O N 120 S C N 121 N O N 122 R C N 123 N O N 124 R C N 125 N N N 126 N C N 127 N O N 128 N N N 129 N C N 130 N O N 131 N C N 132 N C N 133 N H N 134 N H N 135 N H 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 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 doub N 119 N sing N 120 N sing 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 doub N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing To be Published 0353 2-Se Uridine enhanced U/G Wobble Base Pair Discrimination 10.2210/pdb4jab/pdb pdb_00004jab 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2012-12-14 ADSC QUANTUM 315 Double crystal, Si(111) SINGLE WAVELENGTH M x-ray 1 0.97895 1.0 8.2.2 ALS 0.97895 SYNCHROTRON ALS BEAMLINE 8.2.2 2527.545 RNA (5'-R(*GP*UP*GP*UP*AP*UP*AP*C)-3') 2 syn polymer 87.620 STRONTIUM ION 5 syn non-polymer no no GUGUAUAC GUGUAUAC A,B polyribonucleotide n n n n n n n n 1 1.98 38.02 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP 4.107 1 A 1 B 16 -0.463 A_G1:C16_B 1 -13.157 0.133 0.944 0.373 5.236 1 20 A 2 B 15 -3.132 A_U2:A15_B 2 -22.484 0.356 0.361 -0.123 0.122 1 28 A 3 B 14 11.040 A_G3:U14_B 3 -16.955 -1.677 0.507 -0.112 -0.406 1 20 A 4 B 13 6.075 A_U4:A13_B 4 -15.915 -0.179 0.373 0.168 0.737 1 20 A 5 B 12 2.344 A_A5:U12_B 5 -19.878 0.133 0.440 -0.186 -1.655 1 28 A 6 B 11 2.342 A_U6:G11_B 6 -22.553 2.554 0.863 -0.504 4.436 1 20 A 7 B 10 2.080 A_A7:U10_B 7 -14.834 0.020 0.355 0.001 5.728 1 19 A 8 B 9 -4.456 A_C8:G9_B 8 -18.153 0.651 0.155 -0.093 2.638 35.901 A A 1 2 16.849 B B 16 15 3.174 10.235 -0.306 -1.335 AA_G1U2:A15C16_BB 1 3.424 -5.637 34.291 -3.499 0.943 2.398 29.901 A A 2 3 18.968 B B 15 14 2.962 9.618 1.268 -1.174 AA_U2G3:U14A15_BB 2 -0.998 1.968 28.328 -3.954 -2.633 2.993 35.281 A A 3 4 9.603 B B 14 13 3.213 5.794 -0.475 -1.220 AA_G3U4:A13U14_BB 3 -1.251 2.073 34.795 -2.833 0.606 2.847 36.775 A A 4 5 8.081 B B 13 12 3.050 5.083 -0.086 -1.326 AA_U4A5:U12A13_BB 4 -0.745 1.184 36.427 -2.729 0.045 2.817 43.802 A A 5 6 12.713 B B 12 11 3.133 9.417 -0.176 -1.213 AA_A5U6:G11U12_BB 5 0.202 -0.272 42.826 -2.451 0.253 1.667 30.825 A A 6 7 25.107 B B 11 10 2.610 12.885 -0.814 -1.313 AA_U6A7:U10G11_BB 6 5.226 -10.183 27.579 -4.210 2.237 2.892 35.984 A A 7 8 17.603 B B 10 9 3.267 10.703 0.474 -0.921 AA_A7C8:G9U10_BB 7 3.604 -5.928 34.222 -2.965 -0.271 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Data collection Database references Derived calculations Refinement description 1 0 2014-01-29 1 1 2023-09-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _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_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_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 2013-02-18 REL REL SR STRONTIUM ION 32630 synthetic construct sample 246D PDB ENTRY 246D PDB experimental model SR 1 2 SR SR 101 A SR 1 2 SR SR 102 A SR 1 2 SR SR 103 A SR 1 2 SR SR 104 A SR 1 2 SR SR 101 B G 1 n 1 G 1 A U 2 n 2 U 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A A 5 n 5 A 5 A U 6 n 6 U 6 A A 7 n 7 A 7 A C 8 n 8 C 8 A G 9 n 1 G 9 B U 10 n 2 U 10 B G 11 n 3 G 11 B U 12 n 4 U 12 B A 13 n 5 A 13 B U 14 n 6 U 14 B A 15 n 7 A 15 B C 16 n 8 C 16 B author_and_software_defined_assembly PISA 2 dimeric 1630 -118 2830 A C 8 A O2' C 8 1_555 A SR 103 E SR SR 1_555 A C 8 A O3' C 8 1_555 64.8 A C 8 A O2' C 8 1_555 A SR 103 E SR SR 1_555 A C 8 A O3' C 8 1_555 64.8 A C 8 A O3' C 8 1_555 A SR 103 E SR SR 1_555 A C 8 A O3' C 8 1_555 0.0 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 -7.81 1.20 119.70 111.89 A A A C3' O3' P G G U 3 3 4 Y 1 -11.03 1.20 119.70 108.67 B B B C3' O3' P G G U 11 11 12 Y 32.957 -7.33 -0.00 -0.00 -7.33 -0.00 14.67 0.981 0.958 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 0.22898 0.15250 0.15648 2.23 30.93 73 1893 1650 4.2 91.02 22.870 0.222 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.051 0.80 0.80 1.20 PDB ENTRY 246D MAXIMUM LIKELIHOOD MASK 2.23 30.93 0 339 5 334 0 0.009 0.011 372 2.093 1.452 576 0.111 0.200 64 0.012 0.020 164 6.192 3.000 372 68.134 5.000 3 41.320 5.000 336 0.561 0.340 2.288 5 112 20 90.70 2.23 30.93 4JAB 1893 1723 2 -3 0.066 1 2.2 91.02 0.33 2.23 2.31 1 2 90.1 data collection HKL-2000 phasing PHASER refinement REFMAC 5.6.0117 data reduction HKL-2000 data scaling HKL-2000 U/G Wobble Base Pair in a RNA Duplex 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N metalc 2.741 A U 6 A O4 U 6 1_555 A SR 102 D SR SR 1_555 metalc 2.330 A C 8 A O2' C 8 1_555 A SR 103 E SR SR 1_555 metalc 2.609 A C 8 A O3' C 8 1_555 A SR 103 E SR SR 1_555 metalc 1.992 A C 8 A O3' C 8 1_555 A SR 103 E SR SR 2_545 metalc 2.467 B U 14 B O4 U 6 1_555 B SR 101 G SR SR 1_555 hydrog G-A MISPAIR A G 1 A O6 G 1 1_555 B A 15 B N6 A 7 1_555 hydrog G-C PAIR A G 1 A N1 G 1 1_555 B C 16 B N3 C 8 1_555 hydrog WATSON-CRICK A U 2 A N3 U 2 1_555 B A 15 B N1 A 7 1_555 hydrog WATSON-CRICK A U 2 A O4 U 2 1_555 B A 15 B N6 A 7 1_555 hydrog TYPE_28_PAIR A G 3 A N1 G 3 1_555 B U 14 B O2 U 6 1_555 hydrog TYPE_28_PAIR A G 3 A O6 G 3 1_555 B U 14 B N3 U 6 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 B A 13 B N1 A 5 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 B A 13 B N6 A 5 1_555 hydrog A-G MISPAIR A A 5 A N6 A 5 1_555 B G 11 B O6 G 3 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 B U 12 B N3 U 4 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 B U 12 B O4 U 4 1_555 hydrog TYPE_28_PAIR A U 6 A N3 U 6 1_555 B G 11 B O6 G 3 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 B G 11 B N1 G 3 1_555 hydrog WATSON-CRICK A A 7 A N1 A 7 1_555 B U 10 B N3 U 2 1_555 hydrog WATSON-CRICK A A 7 A N6 A 7 1_555 B U 10 B O4 U 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 9 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 9 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 9 B N2 G 1 1_555 RNA U/G wobble pair, RNA 4JAB PDB 1 4JAB 1 8 4JAB 1 8 4JAB A 1 1 8 9 16 4JAB 9 16 4JAB B 1 1 8 BINDING SITE FOR RESIDUE SR A 101 A SR 101 Software 1 BINDING SITE FOR RESIDUE SR A 102 A SR 102 Software 1 BINDING SITE FOR RESIDUE SR A 103 A SR 103 Software 3 BINDING SITE FOR RESIDUE SR B 101 B SR 101 Software 1 A U 4 A U 4 1 1_555 A U 6 A U 6 1 1_555 A C 8 A C 8 3 1_555 A C 8 A C 8 3 2_545 A C 8 A C 8 3 3_655 B U 14 B U 6 1 1_555 146 H 3