0.027812 0.000000 0.000000 0.000000 0.027812 0.000000 0.000000 0.000000 0.026285 0.00000 0.00000 0.00000 Pan, B.C. Xiong, Y. Shi, K. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 35.956 35.956 38.045 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C10 H13 Br N5 O7 P 426.117 n 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION non-polymer Co H18 N6 3 161.116 COBALT HEXAMMINE(III) 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 P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 R C Y 46 N N Y 47 N C Y 48 N N Y 49 N C Y 50 N C N 51 N N N 52 N C N 53 N N N 54 N N N 55 N C N 56 N O N 57 N C N 58 S C N 59 N O N 60 N O N 61 N BR 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 H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 R C N 86 N O N 87 R C Y 88 N N Y 89 N C Y 90 N N Y 91 N C N 92 N C N 93 N O N 94 N N N 95 N C N 96 N N N 97 N N Y 98 N C 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 H N 113 N O N 114 N H N 115 N H N 116 N NA N 117 N CO N 118 N N N 119 N N N 120 N N N 121 N N N 122 N N N 123 N N N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H 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 O N 143 N P N 144 N O N 145 N O N 146 N O N 147 N C N 148 R C N 149 N O N 150 S C N 151 N O N 152 R C N 153 N O N 154 R C N 155 N N N 156 N C N 157 N O N 158 N N N 159 N C N 160 N O N 161 N C N 162 N C N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H 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 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 doub 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 Y 56 N sing Y 57 N sing Y 58 N doub N 59 N sing Y 60 N sing Y 61 N doub N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N doub 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 sing N 102 N sing Y 103 N sing Y 104 N sing Y 105 N doub N 106 N sing Y 107 N sing N 108 N sing Y 109 N doub N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 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 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 sing 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 doub N 172 N sing N 173 N sing N 174 N sing N 175 N doub N 176 N sing N 177 N doub N 178 N sing N 179 N sing UK Structure STRUE6 2005 0969-2126 11 825 831 10.1016/S0969-2126(03)00108-4 12842045 An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction 2003 10.2210/pdb1mdg/pdb pdb_00001mdg 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 105 1 mirrors CCD 2001-05-31 ENRAF-NONIUS graphite MAD M x-ray 1 0.9195 1.0 0.9192 1.0 0.800 1.0 14-BM-D APS 0.9195, 0.9192, 0.800 SYNCHROTRON APS BEAMLINE 14-BM-D 1995.093 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3' 1 syn polymer 22.990 SODIUM ION 5 syn non-polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer 18.015 water 16 nat water no yes U(BGM)AGGU UGAGGU A polyribonucleotide n n n n n n 1 1.54 20.17 VAPOR DIFFUSION, HANGING DROP 6.6 MPD, MgCl2, Cobalt(III)hexammine, ethidine bromide, sodium cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 MPD 1 MgCl2 1 Cobalt(III)hexammine 1 ethidine bromide 1 sodium cacodylate 1 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations 1 0 2003-08-12 1 1 2008-04-28 1 2 2011-07-13 1 3 2011-09-28 1 4 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-08-07 REL REL NA SODIUM ION NCO COBALT HEXAMMINE(III) HOH water NA1 101 2 NA NA 101 A NA1 102 2 NA NA 102 A NA1 103 2 NA NA 103 A NA1 104 2 NA NA 104 A NA1 105 2 NA NA 105 A COB 201 3 NCO NCO 201 A WAT 301 4 HOH HOH 301 A WAT 302 4 HOH HOH 302 A WAT 303 4 HOH HOH 303 A WAT 304 4 HOH HOH 304 A WAT 305 4 HOH HOH 305 A WAT 316 4 HOH HOH 306 A WAT 307 4 HOH HOH 307 A WAT 308 4 HOH HOH 308 A WAT 309 4 HOH HOH 309 A WAT 310 4 HOH HOH 310 A WAT 312 4 HOH HOH 312 A WAT 313 4 HOH HOH 313 A WAT 314 4 HOH HOH 314 A WAT 315 4 HOH HOH 315 A WAT 317 4 HOH HOH 316 A WAT 411 4 HOH HOH 411 A URI 1 n 1 U 1 A GUA 2 n 2 BGM 2 A ADE 3 n 3 A 3 A GUA 4 n 4 G 4 A GUA 5 n 5 G 5 A URI 6 n 6 U 6 A author_defined_assembly 4 tetrameric A G 4 A O6 G 4 1_555 A NA 104 E NA NA 1_555 A G 5 A O6 G 5 1_555 71.8 A G 5 A O6 G 5 1_555 A NA 105 F NA NA 1_555 A U 6 A O4 U 6 1_555 69.7 A BGM 2 A BGM 2 DG 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 2_555 -x,-y,z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_555 -y,x,z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_555 y,-x,z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A NA 101 B NA 1 A NA 102 C NA 1 A NA 103 D NA 1 A NA 104 E NA 1 A NA 105 F NA 1 A NCO 201 G NCO 1 A HOH 305 H HOH 1 A HOH 315 H HOH 1 A G 4 0.064 SIDE CHAIN 1 29.06 1.60 113.70 142.76 A A A C2' C3' O3' U U U 6 6 6 N 1 -10.37 1.00 105.80 95.43 A A A O4' C1' C2' U U U 6 6 6 N 1 -31.93 1.10 112.00 80.07 A A A N1 C1' C2' U U U 6 6 6 N 1 22.72 3.00 110.60 133.32 A A A C1' C2' O2' U U U 6 6 6 N 1 -30.86 2.90 113.30 82.44 A A A C3' C2' O2' U U U 6 6 6 N 0.194 0.172 1.50 30.0 381 3821 3763 98.5 random 1 isotropic 2.0 MAD Engh & Huber 1.50 30.0 16 156 12 128 0 1.5 30.0 1MDG 3807 3800 2.0 2.0 0.056 1 41.7 99.8 1.50 1.55 364 0.309 1 98.6 data reduction DENZO data scaling SCALEPACK refinement CNS phasing CNS An Alternating Antiparallel Octaplex in an RNA Crystal Structure 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 4 N N The three strands of the tetraplex is generated by the four fold axis covale 1.592 both A U 1 A O3' U 1 1_555 A BGM 2 A P BGM 2 1_555 covale 1.633 both A BGM 2 A O3' BGM 2 1_555 A A 3 A P A 3 1_555 metalc 2.865 A BGM 2 A O6 BGM 2 1_555 A NA 101 B NA NA 1_555 metalc 2.823 A BGM 2 A O6 BGM 2 1_555 A NA 102 C NA NA 1_555 metalc 2.995 A G 4 A O6 G 4 1_555 A NA 103 D NA NA 1_555 metalc 2.752 A G 4 A O6 G 4 1_555 A NA 104 E NA NA 1_555 metalc 2.749 A G 5 A O6 G 5 1_555 A NA 104 E NA NA 1_555 metalc 2.830 A G 5 A O6 G 5 1_555 A NA 105 F NA NA 1_555 metalc 2.703 A U 6 A O4 U 6 1_555 A NA 105 F NA NA 1_555 RNA tetraplex, base tetrads, base octads, RNA 1MDG PDB 1 1MDG 1 6 1MDG 1 6 1MDG A 1 1 6 BINDING SITE FOR RESIDUE NA A 101 A NA 101 Software 16 BINDING SITE FOR RESIDUE NA A 102 A NA 102 Software 20 BINDING SITE FOR RESIDUE NA A 103 A NA 103 Software 16 BINDING SITE FOR RESIDUE NA A 104 A NA 104 Software 16 BINDING SITE FOR RESIDUE NA A 105 A NA 105 Software 12 BINDING SITE FOR RESIDUE NCO A 201 A NCO 201 Software 12 A BGM 2 A BGM 2 16 3_555 A BGM 2 A BGM 2 16 6_556 A BGM 2 A BGM 2 16 7_556 A BGM 2 A BGM 2 16 1_555 A BGM 2 A BGM 2 16 4_555 A BGM 2 A BGM 2 16 5_556 A BGM 2 A BGM 2 16 2_555 A BGM 2 A BGM 2 16 8_556 A NA 102 C NA 16 4_555 A NA 102 C NA 16 5_556 A NA 102 C NA 16 6_556 A NA 102 C NA 16 7_556 A NA 102 C NA 16 8_556 A NA 102 C NA 16 3_555 A NA 102 C NA 16 2_555 A NA 102 C NA 16 1_555 A BGM 2 A BGM 2 20 3_555 A BGM 2 A BGM 2 20 1_555 A BGM 2 A BGM 2 20 2_555 A BGM 2 A BGM 2 20 4_555 A A 3 A A 3 20 3_555 A A 3 A A 3 20 2_555 A A 3 A A 3 20 1_555 A A 3 A A 3 20 4_555 A NA 101 B NA 20 4_555 A NA 101 B NA 20 3_555 A NA 101 B NA 20 1_555 A NA 101 B NA 20 2_555 A NA 101 B NA 20 5_556 A NA 101 B NA 20 6_556 A NA 101 B NA 20 7_556 A NA 101 B NA 20 8_556 A NA 103 D NA 20 4_555 A NA 103 D NA 20 3_555 A NA 103 D NA 20 2_555 A NA 103 D NA 20 1_555 A A 3 A A 3 16 3_555 A A 3 A A 3 16 1_555 A A 3 A A 3 16 2_555 A A 3 A A 3 16 4_555 A G 4 A G 4 16 4_555 A G 4 A G 4 16 1_555 A G 4 A G 4 16 2_555 A G 4 A G 4 16 3_555 A NA 102 C NA 16 3_555 A NA 102 C NA 16 1_555 A NA 102 C NA 16 2_555 A NA 102 C NA 16 4_555 A NA 104 E NA 16 4_555 A NA 104 E NA 16 3_555 A NA 104 E NA 16 2_555 A NA 104 E NA 16 1_555 A G 4 A G 4 16 2_555 A G 4 A G 4 16 4_555 A G 4 A G 4 16 1_555 A G 4 A G 4 16 3_555 A G 5 A G 5 16 2_555 A G 5 A G 5 16 4_555 A G 5 A G 5 16 1_555 A G 5 A G 5 16 3_555 A NA 103 D NA 16 1_555 A NA 103 D NA 16 2_555 A NA 103 D NA 16 3_555 A NA 103 D NA 16 4_555 A NA 105 F NA 16 4_555 A NA 105 F NA 16 3_555 A NA 105 F NA 16 2_555 A NA 105 F NA 16 1_555 A G 5 A G 5 12 2_555 A G 5 A G 5 12 3_555 A G 5 A G 5 12 1_555 A G 5 A G 5 12 4_555 A U 6 A U 6 12 2_555 A U 6 A U 6 12 1_555 A U 6 A U 6 12 3_555 A U 6 A U 6 12 4_555 A NA 104 E NA 12 4_555 A NA 104 E NA 12 3_555 A NA 104 E NA 12 2_555 A NA 104 E NA 12 1_555 A BGM 2 A BGM 2 12 1_555 A BGM 2 A BGM 2 12 8_556 A A 3 A A 3 12 8_556 A A 3 A A 3 12 1_555 A G 5 A G 5 12 14_455 A G 5 A G 5 12 12_455 A U 6 A U 6 12 12_455 A U 6 A U 6 12 14_455 A HOH 308 H HOH 12 8_556 A HOH 308 H HOH 12 1_555 A HOH 314 H HOH 12 14_455 A HOH 314 H HOH 12 12_455 97 I 4 2 2