0.019944 0.000000 0.008286 0.000000 0.014609 0.000000 0.000000 0.000000 0.017982 0.00000 0.00000 0.00000 Scott, W.G. Schultz, E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 112.56 90.00 50.140 68.450 60.220 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 C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C10 H15 N5 O11 P2 443.201 n GUANOSINE-5'-DIPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C10 H16 N3 O8 P 337.223 n O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE RNA linking 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 N C N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 92 N C N 93 N H N 94 N H N 95 N H N 96 N H 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 O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 R C N 118 N O N 119 R C Y 120 N N Y 121 N C Y 122 N N Y 123 N C N 124 N C N 125 N O N 126 N N N 127 N C N 128 N N N 129 N N Y 130 N C N 131 N H N 132 N H 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 P N 146 N O N 147 N O N 148 N O N 149 N O N 150 N P N 151 N O N 152 N O N 153 N O N 154 N C N 155 R C N 156 N O N 157 S C N 158 N O N 159 R C N 160 N O N 161 R C Y 162 N N Y 163 N C Y 164 N N Y 165 N C N 166 N C N 167 N O N 168 N N N 169 N C N 170 N N N 171 N N Y 172 N C N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N O N 189 N H N 190 N H N 191 N N N 192 N C N 193 N N N 194 N C N 195 N C N 196 N C N 197 N O N 198 N N N 199 R C N 200 R C N 201 N O N 202 N C N 203 R C N 204 R C N 205 N O N 206 N O N 207 N C N 208 N O N 209 N P N 210 N O N 211 N O N 212 N O N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N O N 230 N P N 231 N O N 232 N O N 233 N O N 234 N C N 235 R C N 236 N O N 237 S C N 238 N O N 239 R C N 240 N O N 241 R C N 242 N N N 243 N C N 244 N O N 245 N N N 246 N C N 247 N O N 248 N C N 249 N C N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 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 N 100 N sing N 101 N doub N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub 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 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 Y 135 N sing Y 136 N sing Y 137 N doub N 138 N sing Y 139 N sing N 140 N sing Y 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N doub 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 doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing Y 180 N sing Y 181 N sing Y 182 N doub N 183 N sing Y 184 N sing N 185 N sing Y 186 N doub N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N doub N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N doub N 203 N doub N 204 N sing N 205 N sing N 206 N doub N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N doub N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N doub N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N doub N 264 N sing N 265 N sing N 266 N sing N 267 N doub N 268 N sing N 269 N doub N 270 N sing N 271 N sing DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 70 2256 10.1107/S1399004714010608 25195740 Structural and Catalytic Effects of an Invariant Purine Substitution in the Hammerhead Ribozyme: Implications for the Mechanism of Acid-Base Catalysis. 2014 10.2210/pdb3zd4/pdb pdb_00003zd4 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 ADSC QUANTUM 315r SINGLE WAVELENGTH M x-ray 1 1.097173 1.0 BL7-1 SSRL 1.097173 SYNCHROTRON SSRL BEAMLINE BL7-1 13925.326 HAMMERHEAD RIBOZYME, ENZYME STRAND 1 syn polymer 6333.816 HAMMERHEAD RIBOZYME, SUBSTRATE STRAND 1 syn polymer 18.015 water 31 nat water no yes (GDP)GAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC A polyribonucleotide no yes GGCGU(OMC)CUGGUAUCCAAUC(DC) GGCGUCCUGGUAUCCAAUCC B 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 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 2.35 47.74 G12A MUTATED AND MODELED IN COOT -6.475 1 19 A 1 B 20 5.134 A_GDP1:DC20_B 1 -3.555 -0.706 -0.057 -0.181 -10.413 1 19 A 2 B 19 1.604 A_G2:C19_B 2 -9.392 -0.502 -0.291 -0.258 -7.328 1 20 A 3 B 18 1.491 A_A3:U18_B 3 -7.186 0.128 0.092 -0.152 -4.307 A 4 B 15 -34.434 A_U4:C15_B 4 -5.425 -1.071 -0.880 -0.017 0.587 1 19 A 5 B 14 -0.212 A_G5:C14_B 5 -14.824 -0.218 0.398 -0.145 -12.525 4 24 A 6 A 28 -94.910 A_U6:A28_A 6 -5.701 4.045 -0.438 -2.263 -12.123 4 24 A 31 B 13 -94.586 A_A31:U13_B 7 -0.153 -4.098 -0.598 -2.150 7.568 1 20 A 9 B 12 4.412 A_U9:A12_B 8 -9.175 -0.219 0.598 -0.088 16.077 1 20 A 10 B 11 6.065 A_A10:U11_B 9 -16.561 -0.009 0.158 -0.067 7.468 1 19 A 11 B 10 4.938 A_C11:G10_B 10 -20.708 0.434 0.035 -0.208 -5.529 1 19 A 12 B 9 4.010 A_C12:G9_B 11 -9.579 0.078 0.253 -0.144 -7.696 1 20 A 13 B 8 2.084 A_A13:U8_B 12 -12.764 0.147 -0.016 -0.217 4.165 1 19 A 14 B 7 0.281 A_G14:C7_B 13 -16.341 0.060 0.475 -0.148 10.147 1 19 A 15 A 20 -2.747 A_C15:G20_A 14 1.399 0.361 -0.492 -0.197 11.301 2 15 A 8 A 26 179.121 A_C8:C26_A 15 5.773 1.949 -0.211 1.895 -0.336 1 19 A 32 A 25 0.271 A_G32:C25_A 16 -6.680 -0.259 0.208 -0.153 -6.564 1 19 A 33 A 24 5.620 A_G33:C24_A 17 -13.656 -0.536 0.101 -0.122 -6.196 1 20 A 34 A 23 -0.211 A_A34:U23_A 18 -10.360 0.010 -0.075 -0.191 -5.279 1 19 A 35 A 22 0.239 A_C35:G22_A 19 -4.847 0.240 0.556 -0.215 -2.557 10 A 36 A 21 -18.004 A_A36:A21_A 20 -13.939 6.430 0.508 -3.797 -20.898 A 37 B 6 -37.287 A_A37:OMC6_B 21 -13.423 -6.116 -1.615 -2.852 29.841 A 38 A 17 83.249 A_A38:G17_A 22 -44.817 -3.879 0.231 3.475 -0.049 1 20 A 39 B 5 3.155 A_A39:U5_B 23 -3.112 -0.383 0.440 0.025 5.528 1 19 A 40 B 4 1.137 A_C40:G4_B 24 -15.948 0.298 0.136 -0.236 -2.075 1 19 A 41 B 3 0.464 A_G41:C3_B 25 -17.244 -0.624 0.094 -0.252 -6.142 1 19 A 42 B 2 0.724 A_C42:G2_B 26 -13.639 0.045 0.332 -0.231 4.489 1 19 A 43 B 1 -1.973 A_C43:G1_B 27 -3.015 0.564 0.091 -0.360 3.243 30.455 A A 1 2 5.671 B B 20 19 3.477 2.974 -0.268 -2.142 AA_GDP1G2:C19DC20_BB 1 1.284 -2.449 30.286 -4.690 0.774 2.938 36.195 A A 2 3 9.066 B B 19 18 3.188 5.610 -0.135 -1.444 AA_G2A3:U18C19_BB 2 -0.984 1.591 35.758 -3.067 0.087 3.749 67.233 A A 3 4 9.081 B B 18 15 4.213 10.016 3.174 -1.271 AA_A3U4:C15U18_BB 3 -5.896 5.345 66.337 -1.625 -3.148 1.863 36.600 A A 4 5 18.129 B B 15 14 3.187 11.030 1.766 -1.675 AA_U4G5:C14C15_BB 4 -11.440 18.802 33.078 -3.902 -4.093 3.453 83.486 A A 5 6 -1.623 B A 14 28 3.524 -2.160 -2.690 -1.998 AA_G5U6:A28C14_AB 5 4.165 -3.129 83.378 -1.445 2.127 4.430 -157.496 A A 6 31 35.221 A B 28 13 5.282 -68.809 3.272 -3.467 AA_U6A31:U13A28_BA 6 40.992 20.983 -150.465 2.126 1.881 2.526 77.439 A A 31 9 2.187 B B 13 12 2.861 2.723 1.563 -1.233 AA_A31U9:A12U13_BB 7 -15.049 12.086 76.148 -1.050 -1.607 2.167 34.683 A A 9 10 20.371 B B 12 11 2.791 11.909 -0.384 -1.349 AA_U9A10:U11A12_BB 8 1.077 -1.842 32.616 -3.694 0.773 3.193 36.513 A A 10 11 9.742 B B 11 10 3.452 6.077 0.317 -1.376 AA_A10C11:G10U11_BB 9 0.991 -1.588 36.008 -3.055 -0.366 2.427 30.670 A A 11 12 22.753 B B 10 9 3.407 11.705 -0.912 -2.197 AA_C11C12:G9G10_BB 10 -4.128 8.025 28.101 -6.304 0.965 2.261 40.260 A A 12 13 28.355 B B 9 8 3.072 18.790 -0.055 -1.024 AA_C12A13:U8G9_BB 11 3.518 -5.309 35.599 -3.341 0.427 2.436 27.267 A A 13 14 16.501 B B 8 7 2.919 7.675 0.802 -1.447 AA_A13G14:C7U8_BB 12 1.174 -2.523 26.158 -4.672 -1.455 3.226 39.072 A A 14 15 8.628 B A 7 20 3.288 5.664 0.304 0.217 AA_G14C15:G20C7_AB 13 12.046 -18.352 36.818 -0.376 1.036 1.349 178.804 A A 8 32 -77.408 A A 26 25 1.189 -154.566 -2.442 -2.108 AA_C8G32:C25C26_AA 14 87.002 -43.571 125.925 -0.788 1.371 2.909 32.334 A A 32 33 11.373 A A 25 24 3.258 6.279 0.736 -1.877 AA_G32G33:C24C25_AA 15 4.056 -7.347 31.480 -4.432 -0.636 2.821 36.522 A A 33 34 10.801 A A 24 23 3.147 6.733 -0.773 -1.546 AA_G33A34:U23C24_AA 16 -0.013 0.021 35.917 -3.323 1.232 2.701 32.979 A A 34 35 15.380 A A 23 22 3.198 8.622 0.415 -1.331 AA_A34C35:G22U23_AA 17 -3.166 5.649 31.708 -3.694 -1.227 3.186 56.372 A A 35 36 4.889 A A 22 21 3.287 4.608 0.252 -1.344 AA_C35A36:A21G22_AA 18 5.282 -5.604 55.970 -1.681 0.029 3.787 27.404 A A 36 37 12.921 A B 21 6 4.069 5.837 1.406 -1.758 AA_A36A37:OMC6A21_BA 19 12.846 -28.435 23.552 -5.581 1.149 3.646 -46.214 A A 37 38 -50.020 B A 6 17 1.858 31.941 0.201 -3.957 AA_A37A38:G17OMC6_AB 20 -27.072 -42.396 -20.016 1.717 -2.562 2.900 86.346 A A 38 39 -13.787 A B 17 5 3.423 -18.766 0.803 2.523 AA_A38A39:U5G17_BA 21 -3.045 2.237 84.632 2.254 -0.653 2.763 34.025 A A 39 40 16.526 B B 5 4 3.198 9.545 -0.261 -1.098 AA_A39C40:G4U5_BB 22 1.447 -2.505 32.666 -3.294 0.661 2.503 33.008 A A 40 41 22.216 B B 4 3 3.307 12.331 -0.031 -1.580 AA_C40G41:C3G4_BB 23 -0.509 0.917 30.673 -4.712 -0.026 2.844 38.680 A A 41 42 16.302 B B 3 2 3.301 10.667 0.323 -1.289 AA_G41C42:G2C3_BB 24 0.733 -1.121 37.227 -3.203 -0.401 2.681 28.091 A A 42 43 10.998 B B 2 1 2.958 5.269 1.169 -2.188 AA_C42C43:G1G2_BB 25 5.907 -12.331 26.975 -5.598 -1.185 atom_site atom_site_anisotrop database_2 pdbx_database_status pdbx_entity_src_syn struct_conn struct_ref chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Other Database references Database references Atomic model Database references Derived calculations Other Source and taxonomy Data collection Refinement description 1 0 2012-12-12 1 1 2013-03-06 1 2 2014-09-10 1 3 2014-09-17 2 0 2022-11-02 2 1 2024-01-31 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site.type_symbol _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[2][3] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.pdbx_auth_atom_id _atom_site_anisotrop.pdbx_label_atom_id _atom_site_anisotrop.type_symbol _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref.pdbx_align_begin HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME PDBE Y PDBE 2012-11-24 REL REL HOH water 32630 SYNTHETIC CONSTRUCT sample 1 43 32630 SYNTHETIC CONSTRUCT sample 1 20 2GOZ PDB ENTRY 2GOZ PDB experimental model HOH 2001 3 HOH HOH 2001 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2001 3 HOH HOH 2001 B HOH 2002 3 HOH HOH 2002 B HOH 2003 3 HOH HOH 2003 B HOH 2004 3 HOH HOH 2004 B HOH 2005 3 HOH HOH 2005 B HOH 2006 3 HOH HOH 2006 B HOH 2007 3 HOH HOH 2007 B HOH 2008 3 HOH HOH 2008 B HOH 2009 3 HOH HOH 2009 B HOH 2010 3 HOH HOH 2010 B GDP 1 n 1 GDP 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A A 7 n 7 A 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A C 11 n 11 C 11 A C 12 n 12 C 12 A A 13 n 13 A 13 A G 14 n 14 G 14 A C 15 n 15 C 15 A U 16 n 16 U 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A U 19 n 19 U 19 A G 20 n 20 G 20 A A 21 n 21 A 21 A G 22 n 22 G 22 A U 23 n 23 U 23 A C 24 n 24 C 24 A C 25 n 25 C 25 A C 26 n 26 C 26 A A 27 n 27 A 27 A A 28 n 28 A 28 A A 29 n 29 A 29 A U 30 n 30 U 30 A A 31 n 31 A 31 A G 32 n 32 G 32 A G 33 n 33 G 33 A A 34 n 34 A 34 A C 35 n 35 C 35 A A 36 n 36 A 36 A A 37 n 37 A 37 A A 38 n 38 A 38 A A 39 n 39 A 39 A C 40 n 40 C 40 A G 41 n 41 G 41 A C 42 n 42 C 42 A C 43 n 43 C 43 A G 1 n 1 G 1 B G 2 n 2 G 2 B C 3 n 3 C 3 B G 4 n 4 G 4 B U 5 n 5 U 5 B OMC 6 n 6 OMC 6 B C 7 n 7 C 7 B U 8 n 8 U 8 B G 9 n 9 G 9 B G 10 n 10 G 10 B U 11 n 11 U 11 B A 12 n 12 A 12 B U 13 n 13 U 13 B C 14 n 14 C 14 B C 15 n 15 C 15 B A 16 n 16 A 16 B A 17 n 17 A 17 B U 18 n 18 U 18 B C 19 n 19 C 19 B DC 20 n 20 DC 20 B 5.8229 1.9530 0.0423 2.1739 -0.4410 8.3154 0.3050 -0.1505 -0.3776 0.2587 -0.5892 -0.0871 1.4182 0.4680 0.3637 0.5997 0.0597 -0.0497 0.4442 0.0575 0.3273 refined -9.5342 18.6015 11.6618 X-RAY DIFFRACTION 0.5896 1.2146 0.9685 6.7655 1.8026 1.4247 -0.0108 -0.0107 -0.2627 -0.5724 0.2107 -0.9420 -0.1116 0.1653 -0.2598 0.3042 -0.0041 0.0582 0.3588 -0.0199 0.4791 refined -11.2177 7.3014 -8.4746 X-RAY DIFFRACTION 3.3811 0.4805 2.6882 5.2670 3.6670 4.1046 -0.6330 0.4047 0.2650 -0.7350 0.8563 -0.1389 -0.9638 0.5514 -0.2880 0.5547 -0.1595 0.0215 0.4813 0.0566 0.4111 refined -17.7545 10.0028 -21.1917 X-RAY DIFFRACTION 9.4704 -2.7584 -3.9634 8.7572 -0.2352 8.6600 -1.1293 -1.7006 0.3625 1.0332 -0.0925 0.6589 -0.2176 -0.9127 1.1960 0.4933 0.0280 -0.0638 0.7181 -0.1811 0.5702 refined -18.2220 15.6795 0.3312 X-RAY DIFFRACTION 7.1890 -3.6808 4.4502 8.6537 -1.6796 8.0079 0.0083 -0.3993 0.2379 -0.3373 -0.1489 0.5823 -0.5728 -1.6194 0.1746 0.4401 0.1070 -0.1613 0.6258 -0.0808 0.4785 refined -22.8271 14.1219 -9.8188 X-RAY DIFFRACTION 5.2889 3.6852 -1.4027 5.8918 -1.1376 0.3828 -1.4455 0.0748 1.0929 -0.5302 0.1727 -0.3188 -2.2335 -1.9499 1.0524 1.1338 0.2002 -0.3708 0.9593 -0.0864 0.6167 refined -23.5303 17.2769 -24.8286 X-RAY DIFFRACTION 2.9146 -2.6952 2.9942 5.7936 -1.3478 5.4784 0.3934 -0.0758 -0.0892 -0.5746 -0.2651 -0.0807 -0.7925 -0.0265 -0.1376 0.6271 0.0140 0.0163 0.4999 0.0282 0.3101 refined -31.3871 7.4091 -32.9070 X-RAY DIFFRACTION 3.9599 -1.3778 2.3283 1.0698 -0.1344 2.1025 -0.0626 -0.6905 -0.0826 0.2810 -0.0560 -0.0049 -0.3903 -0.6468 0.1255 0.6249 -0.0341 -0.0238 0.7158 0.1084 0.3262 refined -30.4950 12.5137 -25.5497 X-RAY DIFFRACTION 0.0526 -0.3828 -0.4311 5.1893 1.5050 3.0583 0.2296 -0.3693 -0.2889 0.7241 -0.2185 -0.6208 0.7800 -0.6640 -0.0468 0.4593 -0.0898 -0.0010 0.4172 0.0825 0.4521 refined -14.8169 2.4452 -3.7866 X-RAY DIFFRACTION 6.4416 2.3463 0.8041 4.0500 0.8010 9.8534 0.6212 -0.3305 -0.7250 -0.1020 -0.0247 -0.6883 -0.2298 -0.3106 -0.5422 0.3464 0.0749 -0.0350 0.3638 0.0217 0.4943 refined -0.3432 22.0699 9.4899 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 (CHAIN A AND RESID 1:4) X-RAY DIFFRACTION 2 (CHAIN A AND RESID 5:14) X-RAY DIFFRACTION 3 (CHAIN A AND RESID 15:25) X-RAY DIFFRACTION 4 (CHAIN A AND RESID 26:30) X-RAY DIFFRACTION 5 (CHAIN A AND RESID 31:34) X-RAY DIFFRACTION 6 (CHAIN A AND RESID 35:38) X-RAY DIFFRACTION 7 (CHAIN A AND RESID 39:43) X-RAY DIFFRACTION 8 (CHAIN B AND RESID 1:7) X-RAY DIFFRACTION 9 (CHAIN B AND RESID 8:15) X-RAY DIFFRACTION 10 (CHAIN B AND RESID 16:20) author_and_software_defined_assembly PISA 2 dimeric 3320 -7.2 10270 A GDP 1 GUANOSINE-5'-DIPHOSPHATE A GDP 1 G B OMC 6 O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE B OMC 6 C 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 A A OP1 O A HOH 29 2015 2.03 0.2360 0.1820 0.1876 2.200 20.216 907 9162 9.9 95.42 0.33 1 1.44 MOLECULAR REPLACEMENT 30.80 0.90 1.11 PDB ENTRY 2GOZ ML FLAT BULK SOLVENT MODEL 2.200 20.216 31 1374 0 1343 0 0.005 1500 0.938 2331 14.735 746 0.040 311 0.007 63 0.3744 0.2845 2.3377 160 1396 98.00 0.3505 0.2933 2.5179 152 1408 98.00 0.3894 0.2840 2.7707 157 1388 98.00 0.3075 0.2330 3.1703 151 1410 97.00 0.1917 0.1487 3.9892 148 1384 96.00 0.1659 0.1283 20.2172 139 1269 86.00 53.23 2.20 38.35 3ZD4 9191 0.0 0.03 1 16.80 3.9 96.1 0.31 2.20 2.32 3.80 1 4.0 98.2 refinement PHENIX (PHENIX.REFINE) data reduction iMOSFLM data scaling SCALA phasing PHASER Full-Length Hammerhead Ribozyme with G12A substitution at the general base position 1 N N 2 N N 3 N N 3 N N covale 1.594 both A GDP 1 A O3' GDP 1 1_555 A G 2 A P G 2 1_555 covale 1.607 both B U 5 B O3' U 5 1_555 B OMC 6 B P OMC 6 1_555 covale 1.608 both B OMC 6 B O3' OMC 6 1_555 B C 7 B P C 7 1_555 covale 1.608 both B C 19 B O3' C 19 1_555 B DC 20 B P DC 20 1_555 hydrog WATSON-CRICK A GDP 1 A N1 GDP 1 1_555 B DC 20 B N3 DC 20 1_555 hydrog WATSON-CRICK A GDP 1 A N2 GDP 1 1_555 B DC 20 B O2 DC 20 1_555 hydrog WATSON-CRICK A GDP 1 A O6 GDP 1 1_555 B DC 20 B N4 DC 20 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 19 B N3 C 19 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 19 B O2 C 19 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 19 B N4 C 19 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 B U 18 B N3 U 18 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B U 18 B O4 U 18 1_555 hydrog U-C MISPAIR A U 4 A O4 U 4 1_555 B C 15 B N4 C 15 1_555 hydrog U-A PAIR A U 4 A O2 U 4 1_555 B A 17 B N6 A 17 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 B C 14 B N3 C 14 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 B C 14 B O2 C 14 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 B C 14 B N4 C 14 1_555 hydrog REVERSED HOOGSTEEN A U 6 A N3 U 6 1_555 A A 28 A N7 A 28 1_555 hydrog REVERSED HOOGSTEEN A U 6 A O2 U 6 1_555 A A 28 A N6 A 28 1_555 hydrog TYPE_15_PAIR A C 8 A N4 C 8 1_555 A C 26 A O2 C 26 1_555 hydrog TYPE_15_PAIR A C 8 A O2 C 8 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A U 9 A N3 U 9 1_555 B A 12 B N1 A 12 1_555 hydrog WATSON-CRICK A U 9 A O4 U 9 1_555 B A 12 B N6 A 12 1_555 hydrog WATSON-CRICK A A 10 A N1 A 10 1_555 B U 11 B N3 U 11 1_555 hydrog WATSON-CRICK A A 10 A N6 A 10 1_555 B U 11 B O4 U 11 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 B G 10 B N1 G 10 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 B G 10 B O6 G 10 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 B G 10 B N2 G 10 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 B G 9 B N1 G 9 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 B G 9 B O6 G 9 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 B G 9 B N2 G 9 1_555 hydrog WATSON-CRICK A A 13 A N1 A 13 1_555 B U 8 B N3 U 8 1_555 hydrog WATSON-CRICK A A 13 A N6 A 13 1_555 B U 8 B O4 U 8 1_555 hydrog WATSON-CRICK A G 14 A N1 G 14 1_555 B C 7 B N3 C 7 1_555 hydrog WATSON-CRICK A G 14 A N2 G 14 1_555 B C 7 B O2 C 7 1_555 hydrog WATSON-CRICK A G 14 A O6 G 14 1_555 B C 7 B N4 C 7 1_555 hydrog WATSON-CRICK A C 15 A N3 C 15 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 15 A N4 C 15 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 15 A O2 C 15 1_555 A G 20 A N2 G 20 1_555 hydrog G-A MISPAIR A G 17 A N2 G 17 1_555 A A 38 A N1 A 38 1_555 hydrog A-A MISPAIR A A 21 A N6 A 21 1_555 A A 36 A N3 A 36 1_555 hydrog WATSON-CRICK A G 22 A N1 G 22 1_555 A C 35 A N3 C 35 1_555 hydrog WATSON-CRICK A G 22 A N2 G 22 1_555 A C 35 A O2 C 35 1_555 hydrog WATSON-CRICK A G 22 A O6 G 22 1_555 A C 35 A N4 C 35 1_555 hydrog WATSON-CRICK A U 23 A N3 U 23 1_555 A A 34 A N1 A 34 1_555 hydrog WATSON-CRICK A U 23 A O4 U 23 1_555 A A 34 A N6 A 34 1_555 hydrog WATSON-CRICK A C 24 A N3 C 24 1_555 A G 33 A N1 G 33 1_555 hydrog WATSON-CRICK A C 24 A N4 C 24 1_555 A G 33 A O6 G 33 1_555 hydrog WATSON-CRICK A C 24 A O2 C 24 1_555 A G 33 A N2 G 33 1_555 hydrog WATSON-CRICK A C 25 A N3 C 25 1_555 A G 32 A N1 G 32 1_555 hydrog WATSON-CRICK A C 25 A N4 C 25 1_555 A G 32 A O6 G 32 1_555 hydrog WATSON-CRICK A C 25 A O2 C 25 1_555 A G 32 A N2 G 32 1_555 hydrog A-U PAIR A A 28 A N3 A 28 1_555 A U 30 A N3 U 30 1_555 hydrog REVERSED HOOGSTEEN A A 31 A N6 A 31 1_555 B U 13 B O2 U 13 1_555 hydrog REVERSED HOOGSTEEN A A 31 A N7 A 31 1_555 B U 13 B N3 U 13 1_555 hydrog A-OMC MISPAIR A A 37 A N6 A 37 1_555 B OMC 6 B O2 OMC 6 1_555 hydrog A-OMC MISPAIR A A 38 A N6 A 38 1_555 B OMC 6 B O2 OMC 6 1_555 hydrog WATSON-CRICK A A 39 A N1 A 39 1_555 B U 5 B N3 U 5 1_555 hydrog WATSON-CRICK A A 39 A N6 A 39 1_555 B U 5 B O4 U 5 1_555 hydrog WATSON-CRICK A C 40 A N3 C 40 1_555 B G 4 B N1 G 4 1_555 hydrog WATSON-CRICK A C 40 A N4 C 40 1_555 B G 4 B O6 G 4 1_555 hydrog WATSON-CRICK A C 40 A O2 C 40 1_555 B G 4 B N2 G 4 1_555 hydrog WATSON-CRICK A G 41 A N1 G 41 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A G 41 A N2 G 41 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A G 41 A O6 G 41 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A C 42 A N3 C 42 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 42 A N4 C 42 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 42 A O2 C 42 1_555 B G 2 B N2 G 2 1_555 hydrog WATSON-CRICK A C 43 A N3 C 43 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 43 A N4 C 43 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 43 A O2 C 43 1_555 B G 1 B N2 G 1 1_555 RNA RNA, GENERAL BASE CATALYSIS 3ZD4 PDB 1 1 3ZD4 3ZD4 PDB 2 1 3ZD4 1 43 3ZD4 1 43 3ZD4 A 1 1 43 1 20 3ZD4 1 20 3ZD4 B 2 1 20 5 C 1 2 1