0.022032 0.000000 0.000000 0.000000 0.022032 0.000000 0.000000 0.000000 0.019418 0.000000 0.000000 0.000000 Kacer, V. Scaringe, S.A. Scarsdale, J.N. Rife, J.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 45.388 45.388 51.499 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 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 O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 R C N 125 N O N 126 R C N 127 N N N 128 N C N 129 N O N 130 N N N 131 N C N 132 N O N 133 N C N 134 N C 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 146 N H N 147 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 59 423 432 10.1107/S0907444902021911 12595698 Crystal structures of r(GGUCACAGCCC)2. 2003 10.2210/pdb1kd5/pdb pdb_00001kd5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 98 1 CCD 2000-08-20 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 1.000 1.0 X8C NSLS 1.000 SYNCHROTRON NSLS BEAMLINE X8C 3481.146 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3' 2 syn polymer 18.015 water 127 nat water no no GGUCACAGCCC GGUCACAGCCC A,B polyribonucleotide n n n n n n n n n n n 1 3.23 61.6 VAPOR DIFFUSION, HANGING DROP 6.4 50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K 293 tris HCl 1 (NH4)2SO4 1 MgCl2 1 spermine 1 neomycin B 1 tris HCl 2 (NH4)2SO4 2 MgCl2 2 spermine 2 -9.606 1 19 A 1 B 10 0.061 A_G1:C10_B 1 -7.684 -0.202 -0.348 0.050 -12.963 1 19 A 2 B 9 -0.210 A_G2:C9_B 2 -11.629 -0.243 -0.259 -0.001 -9.446 28 A 3 B 8 -4.030 A_U3:G8_B 3 -3.829 2.396 0.137 -0.484 -9.748 6 A 4 B 7 -9.293 A_C4:A7_B 4 7.287 7.095 0.444 -4.159 -2.824 4 25 A 5 B 6 -97.780 A_A5:C6_B 5 -11.622 -3.187 -0.185 0.056 3.771 4 25 A 6 B 5 -96.196 A_C6:A5_B 6 -9.922 3.103 -0.089 0.024 10.141 6 A 7 B 4 -9.472 A_A7:C4_B 7 8.747 -7.126 0.455 -4.218 8.327 28 A 8 B 3 -3.801 A_G8:U3_B 8 -2.648 -2.377 0.081 -0.485 13.895 1 19 A 9 B 2 -0.129 A_C9:G2_B 9 -12.247 0.239 -0.248 0.052 8.637 1 19 A 10 B 1 -0.064 A_C10:G1_B 10 -5.644 0.197 -0.280 0.025 3.122 31.436 A A 1 2 9.585 B B 10 9 3.495 5.169 0.040 -2.034 AA_G1G2:C9C10_BB 1 1.262 -2.340 30.994 -4.740 0.167 3.107 42.097 A A 2 3 5.780 B B 9 8 3.246 4.146 0.087 -1.313 AA_G2U3:G8C9_BB 2 -0.248 0.346 41.901 -2.245 -0.146 3.327 58.380 A A 3 4 6.785 B B 8 7 3.456 6.592 0.345 -1.227 AA_U3C4:A7G8_BB 3 7.304 -7.518 57.617 -1.618 0.047 4.161 -12.152 A A 4 5 7.873 B B 7 6 2.983 -1.642 -5.470 -1.011 AA_C4A5:C6A7_BB 4 3.231 15.498 -11.601 7.100 -21.266 3.436 66.250 A A 5 6 -3.890 B B 6 5 3.228 -4.249 0.001 -3.751 AA_A5C6:A5C6_BB 5 -0.297 0.272 66.128 -3.258 -0.013 4.021 -12.121 A A 6 7 12.067 B B 5 4 2.978 -2.500 5.442 -1.008 AA_C6A7:C4A5_BB 6 -3.171 -15.305 -11.432 8.279 21.325 3.344 59.252 A A 7 8 7.010 B B 4 3 3.474 6.903 -0.354 -1.208 AA_A7G8:U3C4_BB 7 -7.299 7.412 58.470 -1.590 -0.031 3.076 41.359 A A 8 9 5.495 B B 3 2 3.207 3.876 -0.086 -1.322 AA_G8C9:G2U3_BB 8 -0.048 0.068 41.185 -2.271 0.117 3.148 31.753 A A 9 10 9.829 B B 2 1 3.539 5.351 -0.053 -2.070 AA_C9C10:G1G2_BB 9 -1.719 3.157 31.265 -4.794 -0.228 chem_comp_atom chem_comp_bond database_2 software repository Initial release Version format compliance Version format compliance Data collection Database references Refinement description 1 0 2003-03-04 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _software.name NDB Y RCSB 2001-11-12 REL REL HOH water HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 31 2 HOH HOH 31 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 37 2 HOH HOH 37 A HOH 38 2 HOH HOH 38 A HOH 41 2 HOH HOH 41 A HOH 42 2 HOH HOH 42 A HOH 46 2 HOH HOH 46 A HOH 47 2 HOH HOH 47 A HOH 51 2 HOH HOH 51 A HOH 53 2 HOH HOH 53 A HOH 54 2 HOH HOH 54 A HOH 56 2 HOH HOH 56 A HOH 59 2 HOH HOH 59 A HOH 60 2 HOH HOH 60 A HOH 63 2 HOH HOH 63 A HOH 64 2 HOH HOH 64 A HOH 65 2 HOH HOH 65 A HOH 67 2 HOH HOH 67 A HOH 71 2 HOH HOH 71 A HOH 73 2 HOH HOH 73 A HOH 75 2 HOH HOH 75 A HOH 78 2 HOH HOH 78 A HOH 79 2 HOH HOH 79 A HOH 82 2 HOH HOH 82 A HOH 87 2 HOH HOH 87 A HOH 88 2 HOH HOH 88 A HOH 92 2 HOH HOH 92 A HOH 94 2 HOH HOH 94 A HOH 95 2 HOH HOH 95 A HOH 96 2 HOH HOH 96 A HOH 97 2 HOH HOH 97 A HOH 98 2 HOH HOH 98 A HOH 102 2 HOH HOH 102 A HOH 104 2 HOH HOH 104 A HOH 105 2 HOH HOH 105 A HOH 107 2 HOH HOH 107 A HOH 108 2 HOH HOH 108 A HOH 110 2 HOH HOH 110 A HOH 112 2 HOH HOH 112 A HOH 118 2 HOH HOH 118 A HOH 120 2 HOH HOH 120 A HOH 121 2 HOH HOH 121 A HOH 122 2 HOH HOH 122 A HOH 124 2 HOH HOH 124 A HOH 126 2 HOH HOH 126 A HOH 131 2 HOH HOH 131 A HOH 132 2 HOH HOH 132 A HOH 133 2 HOH HOH 133 A HOH 136 2 HOH HOH 136 A HOH 137 2 HOH HOH 137 A HOH 138 2 HOH HOH 138 A HOH 139 2 HOH HOH 139 A HOH 141 2 HOH HOH 141 A HOH 144 2 HOH HOH 144 A HOH 145 2 HOH HOH 145 A HOH 146 2 HOH HOH 146 A HOH 150 2 HOH HOH 150 A HOH 152 2 HOH HOH 152 A HOH 155 2 HOH HOH 155 A HOH 156 2 HOH HOH 156 A HOH 26 2 HOH HOH 26 B HOH 29 2 HOH HOH 29 B HOH 30 2 HOH HOH 30 B HOH 32 2 HOH HOH 32 B HOH 33 2 HOH HOH 33 B HOH 39 2 HOH HOH 39 B HOH 40 2 HOH HOH 40 B HOH 43 2 HOH HOH 43 B HOH 44 2 HOH HOH 44 B HOH 45 2 HOH HOH 45 B HOH 48 2 HOH HOH 48 B HOH 49 2 HOH HOH 49 B HOH 50 2 HOH HOH 50 B HOH 52 2 HOH HOH 52 B HOH 55 2 HOH HOH 55 B HOH 57 2 HOH HOH 57 B HOH 58 2 HOH HOH 58 B HOH 61 2 HOH HOH 61 B HOH 62 2 HOH HOH 62 B HOH 66 2 HOH HOH 66 B HOH 68 2 HOH HOH 68 B HOH 69 2 HOH HOH 69 B HOH 70 2 HOH HOH 70 B HOH 72 2 HOH HOH 72 B HOH 74 2 HOH HOH 74 B HOH 76 2 HOH HOH 76 B HOH 77 2 HOH HOH 77 B HOH 80 2 HOH HOH 80 B HOH 81 2 HOH HOH 81 B HOH 83 2 HOH HOH 83 B HOH 84 2 HOH HOH 84 B HOH 85 2 HOH HOH 85 B HOH 86 2 HOH HOH 86 B HOH 89 2 HOH HOH 89 B HOH 90 2 HOH HOH 90 B HOH 91 2 HOH HOH 91 B HOH 93 2 HOH HOH 93 B HOH 99 2 HOH HOH 99 B HOH 100 2 HOH HOH 100 B HOH 101 2 HOH HOH 101 B HOH 103 2 HOH HOH 103 B HOH 106 2 HOH HOH 106 B HOH 109 2 HOH HOH 109 B HOH 111 2 HOH HOH 111 B HOH 113 2 HOH HOH 113 B HOH 114 2 HOH HOH 114 B HOH 116 2 HOH HOH 116 B HOH 117 2 HOH HOH 117 B HOH 119 2 HOH HOH 119 B HOH 123 2 HOH HOH 123 B HOH 125 2 HOH HOH 125 B HOH 127 2 HOH HOH 127 B HOH 128 2 HOH HOH 128 B HOH 129 2 HOH HOH 129 B HOH 130 2 HOH HOH 130 B HOH 134 2 HOH HOH 134 B HOH 135 2 HOH HOH 135 B HOH 140 2 HOH HOH 140 B HOH 142 2 HOH HOH 142 B HOH 143 2 HOH HOH 143 B HOH 147 2 HOH HOH 147 B HOH 148 2 HOH HOH 148 B HOH 149 2 HOH HOH 149 B G 1 n 1 G 1 A G 2 n 2 G 2 A U 3 n 3 U 3 A C 4 n 4 C 4 A A 5 n 5 A 5 A C 6 n 6 C 6 A A 7 n 7 A 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A C 10 n 10 C 10 A C 11 n 11 C 11 A G 1 n 1 G 1 B G 2 n 2 G 2 B U 3 n 3 U 3 B C 4 n 4 C 4 B A 5 n 5 A 5 B C 6 n 6 C 6 B A 7 n 7 A 7 B G 8 n 8 G 8 B C 9 n 9 C 9 B C 10 n 10 C 10 B C 11 n 11 C 11 B 0.1569 0.1714 0.1569 0.1714 0.226 0.226 1324 13.9 9475 12429 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 -2.46 0.40 120.30 117.84 A A A C6 N1 C2 C C C 4 4 4 N 1 5.33 0.70 108.50 113.83 A A A O4' C1' N9 A A A 5 5 5 N 1 3.81 0.50 111.90 115.71 A A A C2 N3 C4 G G G 8 8 8 N 1 -3.89 0.50 128.60 124.71 A A A N3 C4 C5 G G G 8 8 8 N 1 -3.15 0.40 120.30 117.15 A A A C6 N1 C2 C C C 10 10 10 N 1 3.66 0.50 111.90 115.56 B B B C2 N3 C4 G G G 8 8 8 N 1 -3.52 0.50 128.60 125.08 B B B N3 C4 C5 G G G 8 8 8 N 1 B B N7 C8 G G 2 2 0.037 0.006 1.305 1.342 N Preliminary refinement in CNS. Restrained Anisotropic B factors as implemented in SHELXL-96 0.226 0.1714 0.174 0.1714 1.58 5.00 5286 1324 13324 6608 9.93 96.4 random 1 Restrained Anisotropic B factors as implemented in SHELXL-96 THROUGHOUT 2.0 SIRAS MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-227 0.164 5.00 0 0.00 587.00 1.58 5.00 127 587 0 460 0 0.013 0.028 0.037 0.016 1.58 25 1KD5 14792 14143 -3 0.058 1 17.7 5.4 95.6 0.558 1.58 1.67 1.7 721 2.2 91.7 data reduction DENZO data scaling SCALEPACK phasing SHARP refinement SHELXL The Crystal Structure of r(GGUCACAGCCC)2 metal free form 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 10 B N3 C 10 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 10 B O2 C 10 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 10 B N4 C 10 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 9 B N3 C 9 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 9 B O2 C 9 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 9 B N4 C 9 1_555 hydrog TYPE_28_PAIR A U 3 A N3 U 3 1_555 B G 8 B O6 G 8 1_555 hydrog TYPE_28_PAIR A U 3 A O2 U 3 1_555 B G 8 B N1 G 8 1_555 hydrog C-A MISPAIR A C 4 A O2 C 4 1_555 B A 7 B N6 A 7 1_555 hydrog TYPE_25_PAIR A A 5 A N6 A 5 1_555 B C 6 B N3 C 6 1_555 hydrog TYPE_25_PAIR A A 5 A N7 A 5 1_555 B C 6 B N4 C 6 1_555 hydrog TYPE_25_PAIR A C 6 A N3 C 6 1_555 B A 5 B N6 A 5 1_555 hydrog TYPE_25_PAIR A C 6 A N4 C 6 1_555 B A 5 B N7 A 5 1_555 hydrog A-C MISPAIR A A 7 A N6 A 7 1_555 B C 4 B O2 C 4 1_555 hydrog TYPE_28_PAIR A G 8 A N1 G 8 1_555 B U 3 B O2 U 3 1_555 hydrog TYPE_28_PAIR A G 8 A O6 G 8 1_555 B U 3 B N3 U 3 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 2 B N2 G 2 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 B G 1 B N2 G 1 1_555 RNA RNA duplex, RNA 1KD5 PDB 1 1KD5 1 11 1KD5 1 11 1KD5 A 1 1 11 1 11 1KD5 1 11 1KD5 B 1 1 11 78 tetragonal P 43