0.023800 0.000000 0.000000 0.000000 0.023800 0.000000 0.000000 0.000000 0.012246 0.00000 0.00000 0.00000 Kiliszek, A. Kierzek, R. Krzyzosiak, W.J. Rypniewski, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.00 90.00 90.00 42.016 42.016 81.656 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 C11 H14 N5 O8 P 375.231 n [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE RNA linking O4 S -2 96.063 SULFATE ION non-polymer 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 N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N N N 20 N C N 21 N C N 22 N H 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 H N 36 N O N 37 N P N 38 N O N 39 N O N 40 N O N 41 N C N 42 R C N 43 N O N 44 S C N 45 N O N 46 R C N 47 N O N 48 R C Y 49 N N Y 50 N C Y 51 N N Y 52 N C N 53 N C N 54 N O N 55 N N N 56 N C N 57 N N N 58 N N Y 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 H N 76 N H N 77 N P N 78 N O N 79 N O N 80 N C N 81 S C N 82 N C Y 83 N N Y 84 N C Y 85 N C Y 86 N N Y 87 N C N 88 N C N 89 R C N 90 N O N 91 R C N 92 R C N 93 N C N 94 N N N 95 N O N 96 N O N 97 N N N 98 N N N 99 N O N 100 N O N 101 N O 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 H N 114 N H N 115 N H N 116 N S N 117 N O N 118 N O N 119 N O N 120 N O 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 N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N doub N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub 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 N 60 N sing Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing N 66 N sing Y 67 N doub 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 sing N 79 N doub 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 Y 95 N sing Y 96 N sing N 97 N sing Y 98 N doub N 99 N sing Y 100 N doub N 101 N sing Y 102 N sing N 103 N sing N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N doub 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 doub N 122 N doub N 123 N sing N 124 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 40 8155 8162 10.1093/nar/gks557 22718980 Crystallographic characterization of CCG repeats. 2012 10.2210/pdb4e58/pdb pdb_00004e58 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 2011-03-19 MARMOSAIC 225 mm CCD Si SINGLE WAVELENGTH M x-ray 1 0.9148 1.0 14.1 BESSY 0.9148 SYNCHROTRON BESSY BEAMLINE 14.1 2528.579 RNA duplex containing CCG repeats 3 syn polymer 96.063 SULFATE ION 2 syn non-polymer 18.015 water 14 nat water no yes GCC(LCG)CCGC GCCGCCGC C,E,D polyribonucleotide n n n n n n n n 1 2.38 48.22 VAPOR DIFFUSION, SITTING DROP 5.6 MES, MgCl2 and Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K 292.0 -16.776 1 19 C 3 D 7 -5.868 C_C3:G7_D 1 -1.190 0.060 0.234 -0.100 0.000 1 19 C 4 D 6 -1.510 C_LCG4:C6_D 2 -14.025 -0.304 0.389 -0.286 -13.016 C 5 D 5 -22.282 C_C5:C5_D 3 -20.467 2.379 0.252 -0.959 -11.228 1 19 C 6 D 4 -0.632 C_C6:LCG4_D 4 -13.816 -0.228 0.871 -0.227 23.169 1 19 C 7 D 3 -0.042 C_G7:C3_D 5 2.798 -0.315 0.313 -0.089 13.131 1 19 E 1 D 2 -0.643 E_G1:C2_D 6 -9.890 -0.174 0.582 -0.239 0.797 1 19 E 2 D 1 -1.178 E_C2:G1_D 7 -13.851 0.422 0.208 -0.207 1.708 32.281 C C 3 4 28.098 D D 7 6 2.683 15.046 0.854 -1.455 CC_C3LCG4:C6G7_DD 1 -0.600 1.120 28.637 -4.524 -1.612 3.402 44.880 C C 4 5 8.310 D D 6 5 3.647 6.325 -0.863 -1.628 CC_LCG4C5:C5C6_DD 2 -0.337 0.443 44.454 -2.753 1.098 2.556 25.370 C C 5 6 12.237 D D 5 4 2.945 5.329 1.070 -1.963 CC_C5C6:LCG4C5_DD 3 2.217 -5.091 24.715 -5.781 -1.891 1.022 17.493 C C 6 7 36.074 D D 4 3 2.329 10.259 -0.761 -1.356 CC_C6G7:C3LCG4_DD 4 1.547 -5.440 14.104 -8.015 3.040 3.575 48.133 C E 7 1 7.747 D D 3 2 3.456 6.276 -1.423 -0.276 CE_G7G1:C2C3_DD 5 -7.934 9.793 47.120 -0.874 1.068 3.357 43.165 E E 1 2 1.486 D D 2 1 3.403 1.092 0.141 -1.943 EE_G1C2:G1C2_DD 6 2.926 -3.980 43.057 -2.752 0.105 pdbx_entity_src_syn software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Refinement description Source and taxonomy Data collection Database references Derived calculations Refinement description 1 0 2012-12-12 1 1 2017-11-15 1 2 2023-09-13 _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.organism_scientific _software.name _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 RCSB Y RCSB 2012-03-14 REL REL SO4 SULFATE ION HOH water Similar sequences occur in mRNA in humans 9606 Homo sapiens sample 3GLP PDB ENTRY 3GLP PDB experimental model SO4 1 2 SO4 SO4 101 C SO4 2 2 SO4 SO4 101 D HOH 3 3 HOH HOH 201 C HOH 6 3 HOH HOH 202 C HOH 11 3 HOH HOH 203 C HOH 13 3 HOH HOH 204 C HOH 2 3 HOH HOH 101 E HOH 7 3 HOH HOH 102 E HOH 10 3 HOH HOH 103 E HOH 16 3 HOH HOH 104 E HOH 17 3 HOH HOH 105 E HOH 18 3 HOH HOH 106 E HOH 19 3 HOH HOH 107 E HOH 8 3 HOH HOH 201 D HOH 9 3 HOH HOH 202 D HOH 15 3 HOH HOH 203 D G 1 n 1 G 1 C C 2 n 2 C 2 C C 3 n 3 C 3 C LCG 4 n 4 LCG 4 C C 5 n 5 C 5 C C 6 n 6 C 6 C G 7 n 7 G 7 C C 8 n 8 C 8 C G 1 n 1 G 1 E C 2 n 2 C 2 E C 3 n 3 C 3 E LCG 4 n 4 LCG 4 E C 5 n 5 C 5 E C 6 n 6 C 6 E G 7 n 7 G 7 E C 8 n 8 C 8 E G 1 n 1 G 1 D C 2 n 2 C 2 D C 3 n 3 C 3 D LCG 4 n 4 LCG 4 D C 5 n 5 C 5 D C 6 n 6 C 6 D G 7 n 7 G 7 D C 8 n 8 C 8 D author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric 2380 -27 2840 1750 6 2820 C LCG 4 A LCG 4 DG E LCG 4 B LCG 4 DG D LCG 4 C LCG 4 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z+1/4 crystal symmetry operation 0.0000000000 0.0000000000 20.4140000000 1 D HOH 203 H HOH 1 E C4' C 8 B C4' C 8 1 Y 1 E O4' C 8 B O4' C 8 1 Y 1 E C3' C 8 B C3' C 8 1 Y 1 E O3' C 8 B O3' C 8 1 Y 1 E C2' C 8 B C2' C 8 1 Y 1 E O2' C 8 B O2' C 8 1 Y 1 E C1' C 8 B C1' C 8 1 Y 1 E N1 C 8 B N1 C 8 1 Y 1 E C2 C 8 B C2 C 8 1 Y 1 E O2 C 8 B O2 C 8 1 Y 1 E N3 C 8 B N3 C 8 1 Y 1 E C4 C 8 B C4 C 8 1 Y 1 E N4 C 8 B N4 C 8 1 Y 1 E C5 C 8 B C5 C 8 1 Y 1 E C6 C 8 B C6 C 8 1 Y 49.43 6.3525 -0.0000 0.0000 6.3525 -0.0000 -12.7050 0.3008 0.2580 0.2580 0.2580 1.952 18.790 562 5717 5717 100.00 99.46 0.36 RANDOM 1 Isotropic THROUGHOUT 0.00 MOLECULAR REPLACEMENT 31.83 0.49 0.80 PDB ENTRY 3GLP ML FLAT BULK SOLVENT MODEL 36.220 0.348 1.952 18.790 14 510 10 486 0 0.010 549 1.230 856 16.246 252 0.066 110 0.012 23 0.4417 0.3766 2.1486 129 179 1238 97.00 50.7 1.95 20.00 4E58 5762 5762 0 0 0.067 1 23.7 28.3 99.8 1.95 1.98 2.175 273 0.673 1 15.6 97.5 data collection MAR345 phasing PHASER refinement PHENIX (phenix.refine: 1.7_650) data reduction DENZO data scaling SCALEPACK Crystal structure of GCC(LCG)CCGC duplex containing LNA residue 1 N N 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N 3 N N covale 1.597 both C C 3 A O3' C 3 1_555 C LCG 4 A P LCG 4 1_555 covale 1.591 both C LCG 4 A O3' LCG 4 1_555 C C 5 A P C 5 1_555 covale 1.610 both E C 3 B O3' C 3 1_555 E LCG 4 B P LCG 4 1_555 covale 1.604 both E LCG 4 B O3' LCG 4 1_555 E C 5 B P C 5 1_555 covale 1.595 both D C 3 C O3' C 3 1_555 D LCG 4 C P LCG 4 1_555 covale 1.607 both D LCG 4 C O3' LCG 4 1_555 D C 5 C P C 5 1_555 hydrog WATSON-CRICK C C 3 A N3 C 3 1_555 D G 7 C N1 G 7 1_555 hydrog WATSON-CRICK C C 3 A N4 C 3 1_555 D G 7 C O6 G 7 1_555 hydrog WATSON-CRICK C C 3 A O2 C 3 1_555 D G 7 C N2 G 7 1_555 hydrog WATSON-CRICK C LCG 4 A N1 LCG 4 1_555 D C 6 C N3 C 6 1_555 hydrog WATSON-CRICK C LCG 4 A N2 LCG 4 1_555 D C 6 C O2 C 6 1_555 hydrog WATSON-CRICK C LCG 4 A O6 LCG 4 1_555 D C 6 C N4 C 6 1_555 hydrog C-LCG PAIR C C 5 A N4 C 5 1_555 D LCG 4 C O6 LCG 4 1_555 hydrog C-C MISPAIR C C 5 A N3 C 5 1_555 D C 5 C N4 C 5 1_555 hydrog WATSON-CRICK C C 6 A N3 C 6 1_555 D LCG 4 C N1 LCG 4 1_555 hydrog WATSON-CRICK C C 6 A N4 C 6 1_555 D LCG 4 C O6 LCG 4 1_555 hydrog WATSON-CRICK C C 6 A O2 C 6 1_555 D LCG 4 C N2 LCG 4 1_555 hydrog WATSON-CRICK C G 7 A N1 G 7 1_555 D C 3 C N3 C 3 1_555 hydrog WATSON-CRICK C G 7 A N2 G 7 1_555 D C 3 C O2 C 3 1_555 hydrog WATSON-CRICK C G 7 A O6 G 7 1_555 D C 3 C N4 C 3 1_555 hydrog WATSON-CRICK E G 1 B N1 G 1 1_555 D C 2 C N3 C 2 1_555 hydrog WATSON-CRICK E G 1 B N2 G 1 1_555 D C 2 C O2 C 2 1_555 hydrog WATSON-CRICK E G 1 B O6 G 1 1_555 D C 2 C N4 C 2 1_555 hydrog WATSON-CRICK E C 2 B N3 C 2 1_555 D G 1 C N1 G 1 1_555 hydrog WATSON-CRICK E C 2 B N4 C 2 1_555 D G 1 C O6 G 1 1_555 hydrog WATSON-CRICK E C 2 B O2 C 2 1_555 D G 1 C N2 G 1 1_555 RNA CCG repeats, 5' slippery duplexes, X-linked mental retardation, Huntington's disease, myotonic dystrophy type 1, LNA Guanosine, RNA 4E58 PDB 1 1 4E58 GCCGCCGC 1 8 4E58 1 8 4E58 C 1 1 8 1 8 4E58 1 8 4E58 E 1 1 8 1 8 4E58 1 8 4E58 D 1 1 8 BINDING SITE FOR RESIDUE SO4 C 101 C SO4 101 Software 3 BINDING SITE FOR RESIDUE SO4 D 101 D SO4 101 Software 4 C C 2 A C 2 3 1_555 C C 3 A C 3 3 1_555 C HOH 202 F HOH 3 1_555 C G 7 A G 7 4 1_555 C C 8 A C 8 4 1_555 D LCG 4 C LCG 4 4 1_555 D C 5 C C 5 4 1_555 95 P 43 2 2