.033147 .000000 .005108 .000000 .015997 .000000 .000000 .000000 .019865 .00000 .00000 .00000 Szep, S. Wang, J. Moore, P.B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 98.76 90.00 30.169 62.510 50.933 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking Br -1 79.904 BROMIDE ION non-polymer 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 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 BR N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 R C N 50 N O N 51 R C N 52 N N N 53 N C N 54 N O N 55 N N N 56 N C N 57 N N N 58 N C N 59 N C 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 H N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 R C N 85 N O N 86 R C Y 87 N N Y 88 N C Y 89 N N Y 90 N C N 91 N C N 92 N O N 93 N N N 94 N C N 95 N N N 96 N N Y 97 N C 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 H N 112 N O N 113 N H N 114 N H 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 RNA RNARFU 2122 1355-8382 9 44 51 10.1261/rna.2107303 12554875 The crystal structure of a 26-nucleotide RNA containing a hook-turn 2003 10.2210/pdb1mhk/pdb pdb_00001mhk 1.000000 .000000 .000000 .000000 1.000000 .000000 .000000 .000000 1.000000 .00000 .00000 .00000 193 1 193 1 focusing mirrors IMAGE PLATE 2001-01-31 RIGAKU RAXIS IIC CCD 2001-04-13 CUSTOM-MADE focusing mirrors SINGLE WAVELENGTH M x-ray 1 double crystal SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 0.91939 1.0 1.5418 ROTATING ANODE RIGAKU RU200 X25 NSLS 0.91939 SYNCHROTRON NSLS BEAMLINE X25 Short strand 3810.352 RNA 12-mer BCh12 fragment of 5S rRNA Loop E 1 syn polymer Long strand 4479.691 RNA 14-mer BCh12 fragment of 5S rRNA Loop E 1 syn polymer 79.904 BROMIDE ION 1 syn non-polymer 18.015 water 21 nat water no no CCAUGCGAACCG CCAUGCGAACCG S polyribonucleotide no no CGAUCCUAGUGUGG CGAUCCUAGUGUGG L 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 1 2.86 57.04 VAPOR DIFFUSION, SITTING DROP 7.5 ammonium sulfate, magnesium chloride, spermidine, tris-hydrogen chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 292K 292 (NH4)2SO4 1 MgCl2 1 spermidine 1 tris-HCl 1 (NH4)2SO4 2 MgCl2 2 tris-HCl 2 5.486 1 19 S 1 L 14 3.598 S_C1:G14_L 1 -5.863 0.230 0.061 0.037 3.710 1 19 S 2 L 13 1.946 S_C2:G13_L 2 -10.321 0.193 -0.033 0.052 -2.348 1 20 S 3 L 12 4.085 S_A3:U12_L 3 -16.880 0.417 -0.096 0.010 4.210 28 S 4 L 11 -2.437 S_U4:G11_L 4 -12.366 2.236 0.040 -0.603 -4.426 28 S 5 L 10 -0.544 S_G5:U10_L 5 -7.544 -2.519 -0.262 -0.508 3.108 1 19 S 6 L 9 -1.325 S_C6:G9_L 6 -12.388 0.077 -0.013 -0.208 3.994 10 11 S 7 L 8 -4.493 S_G7:A8_L 7 -15.825 6.664 -0.049 -4.470 -1.972 S 8 L 7 -110.074 S_A8:U7_L 8 -6.488 -4.632 0.290 -1.210 -14.178 L 1 L 6 18.219 L_C1:C6_L 9 -15.231 -2.404 0.721 -1.722 -4.003 1 19 L 2 L 5 8.094 L_G2:C5_L 10 -5.311 -1.200 0.042 -0.072 1.334 1 20 L 3 L 4 2.595 L_A3:U4_L 11 -8.800 -0.217 0.364 -0.220 -1.334 1 20 L 4 L 3 2.595 L_U4:A3_L 12 -8.800 0.217 0.364 -0.220 4.003 1 19 L 5 L 2 8.094 L_C5:G2_L 13 -5.311 1.200 0.042 -0.072 14.178 L 6 L 1 18.219 L_C6:C1_L 14 -15.231 2.404 0.721 -1.722 3.038 29.977 S S 1 2 8.266 L L 14 13 3.332 4.261 -0.370 -1.958 SS_C1C2:G13G14_LL 1 -0.931 1.807 29.665 -4.646 0.528 2.800 32.907 S S 2 3 19.182 L L 13 12 3.433 10.679 -0.331 -1.423 SS_C2A3:U12G13_LL 2 0.631 -1.134 31.165 -4.300 0.691 2.768 37.818 S S 3 4 12.724 L L 12 11 3.059 8.186 -0.430 -1.105 SS_A3U4:G11U12_LL 3 -0.777 1.208 36.945 -2.655 0.573 1.125 18.095 S S 4 5 36.472 L L 11 10 3.347 10.726 0.439 -2.689 SS_U4G5:U10G11_LL 4 0.316 -1.074 14.590 -13.189 -1.258 3.088 42.240 S S 5 6 1.538 L L 10 9 3.124 1.108 -0.069 -1.452 SS_G5C6:G9U10_LL 5 -1.359 1.886 42.206 -2.123 -0.036 3.563 57.005 S S 6 7 2.453 L L 9 8 3.594 2.341 -0.830 -0.390 SS_C6G7:A8G9_LL 6 0.964 -1.010 56.954 -0.550 0.927 -0.964 -17.335 S S 7 8 -14.354 L L 8 7 3.289 3.968 -5.680 -0.199 SS_G7A8:U7A8_LL 7 -10.705 -38.728 -13.066 -0.342 -21.549 2.766 30.884 L L 1 2 7.492 L L 6 5 3.021 3.966 -0.376 -1.189 LL_C1G2:C5C6_LL 8 4.414 -8.337 30.322 -2.920 1.471 2.754 35.391 L L 2 3 7.877 L L 5 4 2.985 4.774 0.020 -1.552 LL_G2A3:U4C5_LL 9 -1.179 1.945 35.059 -3.172 -0.185 3.095 36.784 L L 3 4 4.892 L L 4 3 3.211 3.084 0.000 -1.305 LL_A3U4:A3U4_LL 10 0.000 0.000 36.659 -2.473 0.000 2.754 35.391 L L 4 5 7.877 L L 3 2 2.985 4.774 -0.020 -1.552 LL_U4C5:G2A3_LL 11 1.179 -1.945 35.059 -3.172 0.185 2.766 30.884 L L 5 6 7.492 L L 2 1 3.021 3.966 0.376 -1.189 LL_C5C6:C1G2_LL 12 -4.414 8.337 30.322 -2.920 -1.471 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2002-09-06 1 1 2007-10-16 1 2 2011-07-13 1 3 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id NDB Y RCSB 2002-08-20 REL BR BROMIDE ION HOH water 5S rRNA Loop E region, sequence from Chromatium minutissimum sample 5S rRNA Loop E region, sequence from Chromatium minutissimum sample 6MER 6mer A-form RNA helix PDB experimental model BRO 4 3 BR BR 13 S HOH 1 4 HOH HOH 14 S HOH 2 4 HOH HOH 15 S HOH 3 4 HOH HOH 16 S HOH 4 4 HOH HOH 17 S HOH 5 4 HOH HOH 18 S HOH 9 4 HOH HOH 19 S HOH 22 4 HOH HOH 20 S HOH 24 4 HOH HOH 21 S HOH 28 4 HOH HOH 22 S HOH 34 4 HOH HOH 23 S HOH 35 4 HOH HOH 24 S HOH 6 4 HOH HOH 15 L HOH 11 4 HOH HOH 16 L HOH 12 4 HOH HOH 17 L HOH 14 4 HOH HOH 18 L HOH 15 4 HOH HOH 19 L HOH 25 4 HOH HOH 20 L HOH 27 4 HOH HOH 21 L HOH 29 4 HOH HOH 22 L HOH 30 4 HOH HOH 23 L HOH 32 4 HOH HOH 24 L C 1 n 1 C 1 S C 2 n 2 C 2 S A 3 n 3 A 3 S U 4 n 4 U 4 S G 5 n 5 G 5 S C 6 n 6 C 6 S G 7 n 7 G 7 S A 8 n 8 A 8 S A 9 n 9 A 9 S C 10 n 10 C 10 S C 11 n 11 C 11 S G 12 n 12 G 12 S C 1 n 1 C 1 L G 2 n 2 G 2 L A 3 n 3 A 3 L U 4 n 4 U 4 L C 5 n 5 C 5 L C 6 n 6 C 6 L U 7 n 7 U 7 L A 8 n 8 A 8 L G 9 n 9 G 9 L U 10 n 10 U 10 L G 11 n 11 G 11 L U 12 n 12 U 12 L G 13 n 13 G 13 L G 14 n 14 G 14 L author_defined_assembly 2 dimeric 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 S HOH 16 D HOH 1 L HOH 19 E HOH DNA-RNA_REP-BR2.PARAM DNA-RNA-BR2.TOP WATER.PARAM WATER.TOP ION.PARAM ION.TOP 55.8 6.17 0.00 20.29 5.29 0.00 -11.46 0.27 0.017 0.2391 0.243 2.50 15.0 252 3217 3011 8.4 93.6 RANDOM 1 RESTRAINED THROUGHOUT 2.0 MOLECULAR REPLACEMENT 6mer A-form RNA helix CNS standard parameter files:dna_rnarep.param FLAT MODEL 54.1757 0.402743 0.49 0.42 5.00 0.57 0.59 2.50 15.0 21 570 1 548 0 0.006 1.08 14.0 1.46 0.335 0.060 0.404 2.66 31 359 6 7.4 78.8 57.5 2.50 15.0 1MHK 3220 1. 0.128 1,2 10.35 17.69 98.6 2.50 2.55 307 0.342 4.59 98.7 data reduction DENZO data scaling SCALEPACK refinement CNS phasing CNS Crystal Structure Analysis of a 26mer RNA molecule, representing a new RNA motif, the hook-turn 1 N N 2 N N 3 N N 4 N N 4 N N covale 1.875 one S U 4 A C5 U 4 1_555 S BR 13 C BR BR 1_555 hydrog WATSON-CRICK S C 1 A N3 C 1 1_555 L G 14 B N1 G 14 1_555 hydrog WATSON-CRICK S C 1 A N4 C 1 1_555 L G 14 B O6 G 14 1_555 hydrog WATSON-CRICK S C 1 A O2 C 1 1_555 L G 14 B N2 G 14 1_555 hydrog WATSON-CRICK S C 2 A N3 C 2 1_555 L G 13 B N1 G 13 1_555 hydrog WATSON-CRICK S C 2 A N4 C 2 1_555 L G 13 B O6 G 13 1_555 hydrog WATSON-CRICK S C 2 A O2 C 2 1_555 L G 13 B N2 G 13 1_555 hydrog WATSON-CRICK S A 3 A N1 A 3 1_555 L U 12 B N3 U 12 1_555 hydrog WATSON-CRICK S A 3 A N6 A 3 1_555 L U 12 B O4 U 12 1_555 hydrog TYPE_28_PAIR S U 4 A N3 U 4 1_555 L G 11 B O6 G 11 1_555 hydrog TYPE_28_PAIR S U 4 A O2 U 4 1_555 L G 11 B N1 G 11 1_555 hydrog TYPE_28_PAIR S G 5 A N1 G 5 1_555 L U 10 B O2 U 10 1_555 hydrog TYPE_28_PAIR S G 5 A O6 G 5 1_555 L U 10 B N3 U 10 1_555 hydrog WATSON-CRICK S C 6 A N3 C 6 1_555 L G 9 B N1 G 9 1_555 hydrog WATSON-CRICK S C 6 A N4 C 6 1_555 L G 9 B O6 G 9 1_555 hydrog WATSON-CRICK S C 6 A O2 C 6 1_555 L G 9 B N2 G 9 1_555 hydrog TYPE_11_PAIR S G 7 A N2 G 7 1_555 L A 8 B N7 A 8 1_555 hydrog TYPE_11_PAIR S G 7 A N3 G 7 1_555 L A 8 B N6 A 8 1_555 hydrog A-U PAIR S A 8 A N7 A 8 1_555 L U 7 B N3 U 7 1_555 hydrog A-G MISPAIR S A 9 A N3 A 9 1_555 L G 9 B N2 G 9 1_555 hydrog C-C MISPAIR L C 1 B N4 C 1 1_555 L C 6 B N3 C 6 2_556 hydrog WATSON-CRICK L G 2 B N1 G 2 1_555 L C 5 B N3 C 5 2_556 hydrog WATSON-CRICK L G 2 B N2 G 2 1_555 L C 5 B O2 C 5 2_556 hydrog WATSON-CRICK L G 2 B O6 G 2 1_555 L C 5 B N4 C 5 2_556 hydrog WATSON-CRICK L A 3 B N1 A 3 1_555 L U 4 B N3 U 4 2_556 hydrog WATSON-CRICK L A 3 B N6 A 3 1_555 L U 4 B O4 U 4 2_556 hydrog WATSON-CRICK L U 4 B N3 U 4 1_555 L A 3 B N1 A 3 2_556 hydrog WATSON-CRICK L U 4 B O4 U 4 1_555 L A 3 B N6 A 3 2_556 hydrog WATSON-CRICK L C 5 B N3 C 5 1_555 L G 2 B N1 G 2 2_556 hydrog WATSON-CRICK L C 5 B N4 C 5 1_555 L G 2 B O6 G 2 2_556 hydrog WATSON-CRICK L C 5 B O2 C 5 1_555 L G 2 B N2 G 2 2_556 hydrog C-C MISPAIR L C 6 B N3 C 6 1_555 L C 1 B N4 C 1 2_556 RNA helix, 180 degree turn, RNA 1MHK PDB 1 1MHK 1MHK PDB 2 1MHK 1 12 1MHK 1 12 1MHK S 1 1 12 1 14 1MHK 1 14 1MHK L 2 1 14 BINDING SITE FOR RESIDUE BR S 13 S BR 13 Software 2 S A 3 A A 3 2 1_555 S U 4 A U 4 2 1_555 5 monoclinic C 1 2 1