0.022058 0.012735 0.000000 0.000000 0.025470 0.000000 0.000000 0.000000 0.010512 0.00000 0.00000 0.00000 Lima, S. Hildenbrand, J. Korostelev, A. Hattman, S. Li, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 45.336 45.336 95.129 C9 H12 Br N2 O9 P 403.077 n 5-BROMO-URIDINE-5'-MONOPHOSPHATE RNA linking 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 C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N P N 2 N O 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 N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N O N 20 N C N 21 N C N 22 N BR N 23 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 R C N 46 N O N 47 R C Y 48 N N Y 49 N C Y 50 N N Y 51 N C Y 52 N C N 53 N N Y 54 N N Y 55 N C Y 56 N N Y 57 N C N 58 N H 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 O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 R C N 83 N O 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 O N 146 N H N 147 N H N 148 N O N 149 N P N 150 N O N 151 N O N 152 N O N 153 N C N 154 R C N 155 N O N 156 S C N 157 N O N 158 R C N 159 N O N 160 R C N 161 N N N 162 N C N 163 N O N 164 N N N 165 N C N 166 N O N 167 N C N 168 N C N 169 N H N 170 N H N 171 N H N 172 N H 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 1 N doub N 2 N sing N 3 N sing 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 N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing 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 Y 60 N sing Y 61 N sing Y 62 N doub N 63 N sing Y 64 N sing Y 65 N sing Y 66 N doub N 67 N sing Y 68 N doub N 69 N sing N 70 N sing Y 71 N sing Y 72 N doub N 73 N sing Y 74 N sing N 75 N sing N 76 N sing N 77 N doub N 78 N sing 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 sing N 152 N sing N 153 N sing N 154 N sing N 155 N doub 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 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 doub N 180 N sing N 181 N sing N 182 N sing N 183 N doub N 184 N sing N 185 N doub N 186 N sing N 187 N sing UK RNA RNARFU 2122 1355-8382 8 924 932 10.1017/S1355838202028893 12166647 Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution. 2002 10.2210/pdb1kfo/pdb pdb_00001kfo 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 x-ray 1 1.0 6131.561 5'-R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3' 1 syn polymer 18.015 water 38 nat water no yes GAAUGCCUGCGAGCA(5BU)CCC GAAUGCCUGCGAGCAUCCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n 2.30 46.55 -8.259 1 19 A 1 A 18 -0.741 A_G1:C18_A 1 -10.553 -0.475 -0.181 -0.350 6.121 1 A 2 A 17 11.318 A_A2:C17_A 2 -15.481 -2.067 0.326 -0.541 1.367 1 20 A 3 A 16 1.511 A_A3:5BU16_A 3 -17.615 -0.007 -0.021 -0.197 2.640 1 20 A 4 A 15 6.252 A_U4:A15_A 4 -14.016 -0.048 0.109 -0.099 -0.543 1 19 A 5 A 14 2.008 A_G5:C14_A 5 -10.029 -0.170 -0.003 -0.194 1.484 1 19 A 6 A 13 -0.181 A_C6:G13_A 6 -12.541 0.227 -0.079 -0.215 -0.534 1 A 7 A 12 7.567 A_C7:A12_A 7 -8.005 2.480 0.194 -0.508 4.816 28 A 8 A 11 -3.237 A_U8:G11_A 8 -13.947 2.339 0.011 -0.643 -0.476 1 19 A 9 A 10 -0.086 A_G9:C10_A 9 -6.572 -0.162 0.047 -0.165 0.476 1 19 A 10 A 9 -0.086 A_C10:G9_A 10 -6.572 0.162 0.047 -0.165 -4.816 28 A 11 A 8 -3.237 A_G11:U8_A 11 -13.947 -2.339 0.011 -0.643 0.534 1 A 12 A 7 7.567 A_A12:C7_A 12 -8.005 -2.480 0.194 -0.508 -1.484 1 19 A 13 A 6 -0.181 A_G13:C6_A 13 -12.541 -0.227 -0.079 -0.215 0.543 1 19 A 14 A 5 2.008 A_C14:G5_A 14 -10.029 0.170 -0.003 -0.194 -2.640 1 20 A 15 A 4 6.252 A_A15:U4_A 15 -14.016 0.048 0.109 -0.099 -1.367 1 20 A 16 A 3 1.511 A_5BU16:A3_A 16 -17.615 0.007 -0.021 -0.197 -6.121 1 A 17 A 2 11.318 A_C17:A2_A 17 -15.481 2.067 0.326 -0.541 8.259 1 19 A 18 A 1 -0.741 A_C18:G1_A 18 -10.553 0.475 -0.181 -0.350 1.925 30.761 A A 1 2 18.553 A A 18 17 2.702 9.611 0.223 -1.770 AA_G1A2:C17C18_AA 1 -6.421 12.394 28.556 -4.720 -1.344 3.293 38.677 A A 2 3 10.076 A A 17 16 3.455 6.643 -0.358 -0.655 AA_A2A3:5BU16C17_AA 2 0.623 -0.945 38.119 -1.837 0.619 2.949 32.748 A A 3 4 11.039 A A 16 15 3.238 6.189 0.463 -1.290 AA_A3U4:A155BU16_AA 3 0.272 -0.485 32.172 -3.305 -0.777 2.612 32.741 A A 4 5 18.470 A A 15 14 3.221 10.245 -0.371 -1.511 AA_U4G5:C14A15_AA 4 -0.612 1.104 31.133 -4.297 0.561 2.901 33.397 A A 5 6 11.434 A A 14 13 3.246 6.530 -0.310 -1.534 AA_G5C6:G13C14_AA 5 -0.757 1.325 32.761 -3.695 0.420 3.088 39.600 A A 6 7 11.448 A A 13 12 3.396 7.709 0.180 -1.295 AA_C6C7:A12G13_AA 6 -1.091 1.620 38.857 -2.815 -0.393 2.392 34.504 A A 7 8 13.601 A A 12 11 2.985 7.941 -0.284 -1.765 AA_C7U8:G11A12_AA 7 7.233 -12.388 32.838 -4.014 1.424 1.528 19.403 A A 8 9 30.033 A A 11 10 3.243 9.674 0.138 -2.611 AA_U8G9:C10G11_AA 8 0.706 -2.191 16.824 -11.499 -0.136 3.105 32.592 A A 9 10 4.006 A A 10 9 3.267 2.246 0.000 -2.302 AA_G9C10:G9C10_AA 9 0.000 0.000 32.517 -4.482 0.000 1.528 19.403 A A 10 11 30.034 A A 9 8 3.243 9.674 -0.138 -2.611 AA_C10G11:U8G9_AA 10 -0.706 2.191 16.824 -11.499 0.136 2.392 34.504 A A 11 12 13.601 A A 8 7 2.985 7.941 0.284 -1.765 AA_G11A12:C7U8_AA 11 -7.233 12.388 32.838 -4.014 -1.424 3.088 39.600 A A 12 13 11.448 A A 7 6 3.396 7.709 -0.180 -1.295 AA_A12G13:C6C7_AA 12 1.091 -1.620 38.857 -2.815 0.393 2.901 33.397 A A 13 14 11.434 A A 6 5 3.246 6.530 0.310 -1.534 AA_G13C14:G5C6_AA 13 0.757 -1.325 32.761 -3.695 -0.420 2.612 32.741 A A 14 15 18.470 A A 5 4 3.221 10.245 0.371 -1.511 AA_C14A15:U4G5_AA 14 0.612 -1.104 31.133 -4.297 -0.561 2.949 32.748 A A 15 16 11.039 A A 4 3 3.238 6.189 -0.463 -1.290 AA_A155BU16:A3U4_AA 15 -0.272 0.485 32.172 -3.305 0.777 3.293 38.677 A A 16 17 10.076 A A 3 2 3.455 6.643 0.358 -0.655 AA_5BU16C17:A2A3_AA 16 -0.623 0.945 38.119 -1.837 -0.619 1.925 30.761 A A 17 18 18.553 A A 2 1 2.702 9.611 -0.223 -1.770 AA_C17C18:G1A2_AA 17 6.421 -12.394 28.556 -4.720 1.344 chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-12-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag Short contacts exhibited by residue 19 are due to the fact that residue 19 was not included in refinement and was left unrefined. RCSB Y RCSB 2001-11-21 REL HOH water TIP 1 2 HOH HOH 20 A TIP 2 2 HOH HOH 21 A TIP 3 2 HOH HOH 22 A TIP 4 2 HOH HOH 23 A TIP 5 2 HOH HOH 24 A TIP 6 2 HOH HOH 25 A TIP 7 2 HOH HOH 26 A TIP 8 2 HOH HOH 27 A TIP 9 2 HOH HOH 28 A TIP 10 2 HOH HOH 29 A TIP 11 2 HOH HOH 30 A TIP 12 2 HOH HOH 31 A TIP 13 2 HOH HOH 32 A TIP 14 2 HOH HOH 33 A TIP 15 2 HOH HOH 34 A TIP 16 2 HOH HOH 35 A TIP 17 2 HOH HOH 36 A TIP 18 2 HOH HOH 37 A TIP 19 2 HOH HOH 38 A TIP 20 2 HOH HOH 39 A TIP 21 2 HOH HOH 40 A TIP 22 2 HOH HOH 41 A TIP 23 2 HOH HOH 42 A TIP 24 2 HOH HOH 43 A TIP 25 2 HOH HOH 44 A TIP 26 2 HOH HOH 45 A TIP 27 2 HOH HOH 46 A TIP 28 2 HOH HOH 47 A TIP 29 2 HOH HOH 48 A TIP 30 2 HOH HOH 49 A TIP 31 2 HOH HOH 50 A TIP 32 2 HOH HOH 51 A TIP 33 2 HOH HOH 52 A TIP 34 2 HOH HOH 53 A TIP 35 2 HOH HOH 54 A TIP 36 2 HOH HOH 55 A TIP 37 2 HOH HOH 56 A TIP 38 2 HOH HOH 57 A G 1 n 1 G 1 A A 2 n 2 A 2 A A 3 n 3 A 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A C 7 n 7 C 7 A U 8 n 8 U 8 A G 9 n 9 G 9 A C 10 n 10 C 10 A G 11 n 11 G 11 A A 12 n 12 A 12 A G 13 n 13 G 13 A C 14 n 14 C 14 A A 15 n 15 A 15 A +U 16 n 16 5BU 16 A C 17 n 17 C 17 A C 18 n 18 C 18 A C 19 n 19 C 19 A author_defined_assembly 2 dimeric A 5BU 16 5-BROMO-URIDINE-5'-MONOPHOSPHATE A 5BU 16 U 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 8_555 x-y,-y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 4.34 0.70 108.50 112.84 A A A O4' C1' N9 G G G 11 11 11 N 1 -17.27 0.90 105.70 88.43 A A A O5' P OP2 C C C 19 19 19 N 1 A A P O5' C C 19 19 -0.125 0.010 1.593 1.468 N 1 A A O2' C4' A C 3 19 0.89 1_555 5_555 1 A A O2' C3' A C 3 19 1.05 1_555 5_555 1 A A C4' O2' A C 3 19 1.20 1_555 5_555 1 A A C3' O2' A C 3 19 1.36 1_555 5_555 1 A A O3' O2' A C 3 19 1.44 1_555 5_555 1 A A C2' O3' A C 3 19 1.55 1_555 5_555 1 A A O3' C2' A C 3 19 1.62 1_555 5_555 1 A A O2' O3' A C 3 19 1.64 1_555 5_555 1 A A O2' C5' A C 3 19 1.74 1_555 5_555 1 A A C2' C3' A C 3 19 1.90 1_555 5_555 1 A A C2' C4' A C 3 19 1.91 1_555 5_555 1 A A C5' O2' A C 3 19 1.92 1_555 5_555 1 A A O3' O3' A C 3 19 1.99 1_555 5_555 1 A A C3' O3' A C 3 19 2.04 1_555 5_555 1 A A O3' C3' A C 3 19 2.11 1_555 5_555 1 A A C3' C2' A C 3 19 2.13 1_555 5_555 1 A A C5' O3' U C 4 19 2.19 1_555 5_555 PROTEIN_REP.PARAM PROTEIN.TOP DNA-RNA_REP.PARAM WATER_REP.PARAM 28.8 2.94 1.92 0.00 2.94 0.00 -5.88 0.288 0.008 0.26 0.26 1.60 16.69 1346 13798 9.8 95.4 RANDOM 635784.22 0.000000 1 RESTRAINED THROUGHOUT 0.0 FLAT MODEL 42.3081 0.456314 0.29 0.25 5.00 0.10 0.07 1.60 16.69 38 439 1 400 0 0.008 1.2 6.0 1.25 0.317 0.022 0.286 1.70 215 1968 6 9.8 90.8 16.5 1KFO 1 refinement CNS 1.0 CRYSTAL STRUCTURE OF AN RNA HELIX RECOGNIZED BY A ZINC-FINGER PROTEIN: AN 18 BASE PAIR DUPLEX AT 1.6 RESOLUTION 1 N N 2 N N covale 1.615 both A A 15 A O3' A 15 1_555 A 5BU 16 A P 5BU 16 1_555 covale 1.611 both A 5BU 16 A O3' 5BU 16 1_555 A C 17 A P C 17 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 18 A N3 C 18 7_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 18 A O2 C 18 7_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 18 A N4 C 18 7_555 hydrog A-C MISPAIR A A 2 A N6 A 2 1_555 A C 17 A N3 C 17 7_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A 5BU 16 A N3 5BU 16 7_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A 5BU 16 A O4 5BU 16 7_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 15 A N1 A 15 7_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 15 A N6 A 15 7_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 14 A N3 C 14 7_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 14 A O2 C 14 7_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 14 A N4 C 14 7_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 13 A N1 G 13 7_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 13 A O6 G 13 7_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 13 A N2 G 13 7_555 hydrog C-A MISPAIR A C 7 A N3 C 7 1_555 A A 12 A N6 A 12 7_555 hydrog TYPE_28_PAIR A U 8 A N3 U 8 1_555 A G 11 A O6 G 11 7_555 hydrog TYPE_28_PAIR A U 8 A O2 U 8 1_555 A G 11 A N1 G 11 7_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 10 A N3 C 10 7_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 10 A O2 C 10 7_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 10 A N4 C 10 7_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 9 A N1 G 9 7_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 9 A O6 G 9 7_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 9 A N2 G 9 7_555 hydrog TYPE_28_PAIR A G 11 A N1 G 11 1_555 A U 8 A O2 U 8 7_555 hydrog TYPE_28_PAIR A G 11 A O6 G 11 1_555 A U 8 A N3 U 8 7_555 hydrog A-C MISPAIR A A 12 A N6 A 12 1_555 A C 7 A N3 C 7 7_555 hydrog WATSON-CRICK A G 13 A N1 G 13 1_555 A C 6 A N3 C 6 7_555 hydrog WATSON-CRICK A G 13 A N2 G 13 1_555 A C 6 A O2 C 6 7_555 hydrog WATSON-CRICK A G 13 A O6 G 13 1_555 A C 6 A N4 C 6 7_555 hydrog WATSON-CRICK A C 14 A N3 C 14 1_555 A G 5 A N1 G 5 7_555 hydrog WATSON-CRICK A C 14 A N4 C 14 1_555 A G 5 A O6 G 5 7_555 hydrog WATSON-CRICK A C 14 A O2 C 14 1_555 A G 5 A N2 G 5 7_555 hydrog WATSON-CRICK A A 15 A N1 A 15 1_555 A U 4 A N3 U 4 7_555 hydrog WATSON-CRICK A A 15 A N6 A 15 1_555 A U 4 A O4 U 4 7_555 hydrog WATSON-CRICK A 5BU 16 A N3 5BU 16 1_555 A A 3 A N1 A 3 7_555 hydrog WATSON-CRICK A 5BU 16 A O4 5BU 16 1_555 A A 3 A N6 A 3 7_555 hydrog C-A MISPAIR A C 17 A N3 C 17 1_555 A A 2 A N6 A 2 7_555 hydrog WATSON-CRICK A C 18 A N3 C 18 1_555 A G 1 A N1 G 1 7_555 hydrog WATSON-CRICK A C 18 A N4 C 18 1_555 A G 1 A O6 G 1 7_555 hydrog WATSON-CRICK A C 18 A O2 C 18 1_555 A G 1 A N2 G 1 7_555 RNA RNA 1KFO PDB 1 1KFO 1 19 1KFO 1 19 1KFO A 1 1 19 182 P 63 2 2