data_4JIY # _entry.id 4JIY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4JIY pdb_00004jiy 10.2210/pdb4jiy/pdb NDB NA2298 ? ? RCSB RCSB078104 ? ? WWPDB D_1000078104 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-09-04 2 'Structure model' 1 1 2013-10-02 3 'Structure model' 1 2 2013-11-06 4 'Structure model' 1 3 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.value' 12 4 'Structure model' '_struct_conn.pdbx_dist_value' 13 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 14 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 15 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 16 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 19 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 20 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4JIY _pdbx_database_status.recvd_initial_deposition_date 2013-03-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2ET0 'The structure of a three-way DNA junction in complex with a metallo-supramolecular helicate reveals a new target for drugs' unspecified PDB 3FX8 ;Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate') ; unspecified PDB 3I1D ;Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate') ; unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sigel, R.K.O.' 1 'Schnabl, J.A.' 2 'Freisinger, E.' 3 'Spingler, B.' 4 'Hannon, M.J.' 5 # _citation.id primary _citation.title 'Binding of a designed anti-cancer drug to the central cavity of an RNA three-way junction.' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 52 _citation.page_first 11513 _citation.page_last 11516 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24039102 _citation.pdbx_database_id_DOI 10.1002/anie.201305079 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Phongtongpasuk, S.' 1 ? primary 'Paulus, S.' 2 ? primary 'Schnabl, J.' 3 ? primary 'Sigel, R.K.' 4 ? primary 'Spingler, B.' 5 ? primary 'Hannon, M.J.' 6 ? primary 'Freisinger, E.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-(CGUACG)-3'" 1891.189 1 ? ? ? ? 2 non-polymer syn 'N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE' 376.453 2 ? ? ? ? 3 non-polymer syn 'FE (II) ION' 55.845 4 ? ? ? ? 4 water nat water 18.015 39 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CGUACG _entity_poly.pdbx_seq_one_letter_code_can CGUACG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE' NPM 3 'FE (II) ION' FE2 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 U n 1 4 A n 1 5 C n 1 6 G n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 FE2 non-polymer . 'FE (II) ION' ? 'Fe 2' 55.845 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NPM non-polymer . 'N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE' '1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE' 'C25 H20 N4' 376.453 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 A 4 4 4 A A A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NPM 1 101 21 NPM NPM A . C 3 FE2 1 102 22 FE2 FE2 A . D 3 FE2 1 103 23 FE2 FE2 A . E 2 NPM 1 104 41 NPM NPM A . F 3 FE2 1 105 42 FE2 FE2 A . G 3 FE2 1 106 43 FE2 FE2 A . H 4 HOH 1 201 101 HOH HOH A . H 4 HOH 2 202 102 HOH HOH A . H 4 HOH 3 203 103 HOH HOH A . H 4 HOH 4 204 104 HOH HOH A . H 4 HOH 5 205 105 HOH HOH A . H 4 HOH 6 206 108 HOH HOH A . H 4 HOH 7 207 110 HOH HOH A . H 4 HOH 8 208 111 HOH HOH A . H 4 HOH 9 209 112 HOH HOH A . H 4 HOH 10 210 113 HOH HOH A . H 4 HOH 11 211 114 HOH HOH A . H 4 HOH 12 212 115 HOH HOH A . H 4 HOH 13 213 116 HOH HOH A . H 4 HOH 14 214 117 HOH HOH A . H 4 HOH 15 215 118 HOH HOH A . H 4 HOH 16 216 119 HOH HOH A . H 4 HOH 17 217 120 HOH HOH A . H 4 HOH 18 218 121 HOH HOH A . H 4 HOH 19 219 122 HOH HOH A . H 4 HOH 20 220 123 HOH HOH A . H 4 HOH 21 221 124 HOH HOH A . H 4 HOH 22 222 125 HOH HOH A . H 4 HOH 23 223 126 HOH HOH A . H 4 HOH 24 224 127 HOH HOH A . H 4 HOH 25 225 128 HOH HOH A . H 4 HOH 26 226 129 HOH HOH A . H 4 HOH 27 227 130 HOH HOH A . H 4 HOH 28 228 132 HOH HOH A . H 4 HOH 29 229 133 HOH HOH A . H 4 HOH 30 230 134 HOH HOH A . H 4 HOH 31 231 135 HOH HOH A . H 4 HOH 32 232 136 HOH HOH A . H 4 HOH 33 233 138 HOH HOH A . H 4 HOH 34 234 139 HOH HOH A . H 4 HOH 35 235 140 HOH HOH A . H 4 HOH 36 236 141 HOH HOH A . H 4 HOH 37 237 142 HOH HOH A . H 4 HOH 38 238 143 HOH HOH A . H 4 HOH 39 239 145 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal RemDAq 'data collection' . ? 1 SHELXD phasing . ? 2 SHELXL-97 refinement . ? 3 XDS 'data reduction' . ? 4 XPREP 'data reduction' . ? 5 # _cell.entry_id 4JIY _cell.length_a 45.745 _cell.length_b 45.745 _cell.length_c 45.745 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4JIY _symmetry.space_group_name_H-M 'P 21 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4JIY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # loop_ _exptl_crystal.id _exptl_crystal.density_meas _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 ? 4.22 70.84 'THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.' ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.temp _exptl_crystal_grow.temp_details _exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_details _exptl_crystal_grow.pdbx_pH_range 1 'VAPOR DIFFUSION, SITTING DROP' 293.15 ? 8.5 ;20% PEG 400, 0.18M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K. 15% PEG 400, 0.165M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K ; ? 2 'VAPOR DIFFUSION, SITTING DROP' 293.15 ? 8.5 '15% PEG 400, 0.165M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K' ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 2 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'MARMOSAIC 225 mm CCD' 2009-12-10 'MIRROR, BARTELS MONOCHROMATOR, DUAL CHANNEL CUT CRYSTALS, TOROIDAL MIRROR' 2 CCD 'MARMOSAIC 225 mm CCD' 2009-09-12 'MIRROR, BARTELS MONOCHROMATOR, DUAL CHANNEL CUT CRYSTALS, TOROIDAL MIRROR' # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'BARTELS MONOCHROMATOR' 'SINGLE WAVELENGTH' x-ray 2 1 M 'BARTELS MONOCHROMATOR' MAD x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9999 _diffrn_radiation_wavelength.wt 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'SLS BEAMLINE X06DA' SLS X06DA 0.9999 0.9999 2 SYNCHROTRON 'SLS BEAMLINE X06DA' SLS X06DA ? 0.9999 # _reflns.entry_id 4JIY _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F 4 _reflns.d_resolution_low 45.745 _reflns.d_resolution_high 1.910 _reflns.number_obs 4030 _reflns.number_all 4826 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.02040 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 27.0600 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.500 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # _reflns_shell.d_res_high 1.91 _reflns_shell.d_res_low 2.01 _reflns_shell.percent_possible_all 98.7 _reflns_shell.Rmerge_I_obs 0.38470 _reflns_shell.pdbx_Rsym_value 0.38470 _reflns_shell.meanI_over_sigI_obs 2.670 _reflns_shell.pdbx_redundancy 0.99 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 703 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2 # _refine.entry_id 4JIY _refine.ls_number_reflns_obs 4030 _refine.ls_number_reflns_all 4814 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 4.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 26.41 _refine.ls_d_res_high 1.91 _refine.ls_percent_reflns_obs 83.7 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.224 _refine.ls_R_factor_R_free 0.2709 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 242 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 51.2 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'KLOSTERMAN & SINE' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1,2 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 125 _refine_hist.pdbx_number_atoms_ligand 62 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 226 _refine_hist.d_res_high 1.91 _refine_hist.d_res_low 26.41 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.009 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.027 ? ? ? ? 'X-RAY DIFFRACTION' s_from_restr_planes 0.040 ? ? ? ? 'X-RAY DIFFRACTION' s_non_zero_chiral_vol 0.008 ? ? ? ? 'X-RAY DIFFRACTION' s_anti_bump_dis_restr 0.004 ? ? ? ? 'X-RAY DIFFRACTION' SIMU 0.164 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4JIY _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.234 _pdbx_refine.free_R_factor_no_cutoff 0.282 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.000 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 242 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.224 _pdbx_refine.free_R_factor_4sig_cutoff 0.271 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 211 _pdbx_refine.number_reflns_obs_4sig_cutoff 4030 # _database_PDB_matrix.entry_id 4JIY _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 4JIY _struct.title 'RNA three-way junction stabilized by a supramolecular di-iron(II) cylinder drug' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4JIY _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, THREE-WAY JUNCTION, DRUG-RNA COMPLEX, RNA STRUCTURE RECOGNITION, CYLINDER, SUPRAMOLECULE' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 2 ? F N N 3 ? G N N 3 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4JIY _struct_ref.pdbx_db_accession 4JIY _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGUACG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4JIY _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4JIY _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4090 ? 1 MORE -67 ? 1 'SSA (A^2)' 3040 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 5_555 z,x,y 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 3 'crystal symmetry operation' 9_555 y,z,x 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ;BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: THE RNA THREE-WAY JUNCTION IS GENERATED FROM THE ASYMMETRIC UNIT BY THE OPERATIONS. THE TERMINAL 1/3 CYLINDER LIGANDS ARE PART OF THE INFINITE CRYSTAL LATTICE. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 3870 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 BIOMOLECULE: 2 AUTHOR DETERMINED BIOLOGICAL UNIT: NONAMERIC APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -1.000000 0.000000 0.000000 68.61750 BIOMT2 2 0.000000 -1.000000 0.000000 91.49000 BIOMT3 2 0.000000 0.000000 1.000000 22.87250 BIOMT1 3 -1.000000 0.000000 0.000000 91.49000 BIOMT2 3 0.000000 1.000000 0.000000 -22.87250 BIOMT3 3 0.000000 0.000000 -1.000000 68.61750 BIOMT1 4 0.000000 0.000000 1.000000 0.00000 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 BIOMT3 4 0.000000 1.000000 0.000000 0.00000 BIOMT1 5 0.000000 0.000000 1.000000 22.87250 BIOMT2 5 -1.000000 0.000000 0.000000 68.61750 BIOMT3 5 0.000000 -1.000000 0.000000 91.49000 BIOMT1 6 0.000000 0.000000 -1.000000 68.61750 BIOMT2 6 -1.000000 0.000000 0.000000 91.49000 BIOMT3 6 0.000000 1.000000 0.000000 -22.87250 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 BIOMT2 7 0.000000 0.000000 1.000000 0.00000 BIOMT3 7 1.000000 0.000000 0.000000 0.00000 BIOMT1 8 0.000000 -1.000000 0.000000 91.49000 BIOMT2 8 0.000000 0.000000 1.000000 22.87250 BIOMT3 8 -1.000000 0.000000 0.000000 68.61750 BIOMT1 9 0.000000 1.000000 0.000000 -22.87250 BIOMT2 9 0.000000 0.000000 -1.000000 68.61750 BIOMT3 9 -1.000000 0.000000 0.000000 91.49000 ; # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? B NPM . N12 ? ? ? 1_555 C FE2 . FE ? ? A NPM 101 A FE2 102 1_555 ? ? ? ? ? ? ? 1.983 ? ? metalc2 metalc ? ? B NPM . N11 ? ? ? 1_555 C FE2 . FE ? ? A NPM 101 A FE2 102 1_555 ? ? ? ? ? ? ? 1.987 ? ? metalc3 metalc ? ? B NPM . N14 ? ? ? 1_555 D FE2 . FE ? ? A NPM 101 A FE2 103 1_555 ? ? ? ? ? ? ? 1.978 ? ? metalc4 metalc ? ? B NPM . N13 ? ? ? 1_555 D FE2 . FE ? ? A NPM 101 A FE2 103 1_555 ? ? ? ? ? ? ? 1.981 ? ? metalc5 metalc ? ? E NPM . N11 ? ? ? 1_555 F FE2 . FE ? ? A NPM 104 A FE2 105 1_555 ? ? ? ? ? ? ? 1.977 ? ? metalc6 metalc ? ? E NPM . N12 ? ? ? 1_555 F FE2 . FE ? ? A NPM 104 A FE2 105 1_555 ? ? ? ? ? ? ? 1.987 ? ? metalc7 metalc ? ? E NPM . N14 ? ? ? 1_555 G FE2 . FE ? ? A NPM 104 A FE2 106 1_555 ? ? ? ? ? ? ? 1.974 ? ? metalc8 metalc ? ? E NPM . N13 ? ? ? 1_555 G FE2 . FE ? ? A NPM 104 A FE2 106 1_555 ? ? ? ? ? ? ? 1.984 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 6 N1 ? ? A C 1 A G 6 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 6 O6 ? ? A C 1 A G 6 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 6 N2 ? ? A C 1 A G 6 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 5 N3 ? ? A G 2 A C 5 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 5 O2 ? ? A G 2 A C 5 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 5 N4 ? ? A G 2 A C 5 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 4 N1 ? ? A U 3 A A 4 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 4 N6 ? ? A U 3 A A 4 5_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N12 ? B NPM . ? A NPM 101 ? 1_555 FE ? C FE2 . ? A FE2 102 ? 1_555 N11 ? B NPM . ? A NPM 101 ? 1_555 79.1 ? 2 N14 ? B NPM . ? A NPM 101 ? 1_555 FE ? D FE2 . ? A FE2 103 ? 1_555 N13 ? B NPM . ? A NPM 101 ? 1_555 80.4 ? 3 N11 ? E NPM . ? A NPM 104 ? 1_555 FE ? F FE2 . ? A FE2 105 ? 1_555 N12 ? E NPM . ? A NPM 104 ? 1_555 79.2 ? 4 N14 ? E NPM . ? A NPM 104 ? 1_555 FE ? G FE2 . ? A FE2 106 ? 1_555 N13 ? E NPM . ? A NPM 104 ? 1_555 81.0 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NPM 101 ? 8 'BINDING SITE FOR RESIDUE NPM A 101' AC2 Software A FE2 102 ? 3 'BINDING SITE FOR RESIDUE FE2 A 102' AC3 Software A FE2 103 ? 3 'BINDING SITE FOR RESIDUE FE2 A 103' AC4 Software A NPM 104 ? 9 'BINDING SITE FOR RESIDUE NPM A 104' AC5 Software A FE2 105 ? 3 'BINDING SITE FOR RESIDUE FE2 A 105' AC6 Software A FE2 106 ? 3 'BINDING SITE FOR RESIDUE FE2 A 106' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 8 C A 1 ? C A 1 . ? 10_756 ? 2 AC1 8 G A 6 ? G A 6 . ? 5_555 ? 3 AC1 8 FE2 C . ? FE2 A 102 . ? 10_756 ? 4 AC1 8 FE2 C . ? FE2 A 102 . ? 1_555 ? 5 AC1 8 FE2 C . ? FE2 A 102 . ? 7_674 ? 6 AC1 8 FE2 D . ? FE2 A 103 . ? 10_756 ? 7 AC1 8 FE2 D . ? FE2 A 103 . ? 7_674 ? 8 AC1 8 FE2 D . ? FE2 A 103 . ? 1_555 ? 9 AC2 3 NPM B . ? NPM A 101 . ? 1_555 ? 10 AC2 3 NPM B . ? NPM A 101 . ? 7_674 ? 11 AC2 3 NPM B . ? NPM A 101 . ? 10_756 ? 12 AC3 3 NPM B . ? NPM A 101 . ? 7_674 ? 13 AC3 3 NPM B . ? NPM A 101 . ? 10_756 ? 14 AC3 3 NPM B . ? NPM A 101 . ? 1_555 ? 15 AC4 9 U A 3 ? U A 3 . ? 5_555 ? 16 AC4 9 A A 4 ? A A 4 . ? 5_555 ? 17 AC4 9 A A 4 ? A A 4 . ? 9_555 ? 18 AC4 9 FE2 F . ? FE2 A 105 . ? 5_555 ? 19 AC4 9 FE2 F . ? FE2 A 105 . ? 9_555 ? 20 AC4 9 FE2 F . ? FE2 A 105 . ? 1_555 ? 21 AC4 9 FE2 G . ? FE2 A 106 . ? 9_555 ? 22 AC4 9 FE2 G . ? FE2 A 106 . ? 5_555 ? 23 AC4 9 FE2 G . ? FE2 A 106 . ? 1_555 ? 24 AC5 3 NPM E . ? NPM A 104 . ? 5_555 ? 25 AC5 3 NPM E . ? NPM A 104 . ? 1_555 ? 26 AC5 3 NPM E . ? NPM A 104 . ? 9_555 ? 27 AC6 3 NPM E . ? NPM A 104 . ? 5_555 ? 28 AC6 3 NPM E . ? NPM A 104 . ? 9_555 ? 29 AC6 3 NPM E . ? NPM A 104 . ? 1_555 ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text Intercalation # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A FE2 102 ? C FE2 . 2 1 A FE2 103 ? D FE2 . 3 1 A FE2 105 ? F FE2 . 4 1 A FE2 106 ? G FE2 . 5 1 A HOH 207 ? H HOH . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 FE2 FE FE N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 NPM N11 N Y N 115 NPM N12 N N N 116 NPM N13 N N N 117 NPM N14 N Y N 118 NPM C1A C Y N 119 NPM C1B C Y N 120 NPM C1C C Y N 121 NPM C1D C Y N 122 NPM C1E C Y N 123 NPM C1F C N N 124 NPM C1G C Y N 125 NPM C1H C Y N 126 NPM C1I C Y N 127 NPM C1J C Y N 128 NPM C1K C Y N 129 NPM C1L C Y N 130 NPM C1M C N N 131 NPM C1N C Y N 132 NPM C1O C Y N 133 NPM C1P C Y N 134 NPM C1Q C Y N 135 NPM C1R C Y N 136 NPM C1S C Y N 137 NPM C1T C N N 138 NPM C1U C Y N 139 NPM C1V C Y N 140 NPM C1W C Y N 141 NPM C1X C Y N 142 NPM C1Y C Y N 143 NPM H1A H N N 144 NPM H1B H N N 145 NPM H1C H N N 146 NPM H1D H N N 147 NPM H1F H N N 148 NPM H1H H N N 149 NPM H1I H N N 150 NPM H1K H N N 151 NPM H1L H N N 152 NPM H1M1 H N N 153 NPM H1M2 H N N 154 NPM H1O H N N 155 NPM H1P H N N 156 NPM H1R H N N 157 NPM H1S H N N 158 NPM H1T H N N 159 NPM H1V H N N 160 NPM H1W H N N 161 NPM H1X H N N 162 NPM H1Y H N N 163 U OP3 O N N 164 U P P N N 165 U OP1 O N N 166 U OP2 O N N 167 U "O5'" O N N 168 U "C5'" C N N 169 U "C4'" C N R 170 U "O4'" O N N 171 U "C3'" C N S 172 U "O3'" O N N 173 U "C2'" C N R 174 U "O2'" O N N 175 U "C1'" C N R 176 U N1 N N N 177 U C2 C N N 178 U O2 O N N 179 U N3 N N N 180 U C4 C N N 181 U O4 O N N 182 U C5 C N N 183 U C6 C N N 184 U HOP3 H N N 185 U HOP2 H N N 186 U "H5'" H N N 187 U "H5''" H N N 188 U "H4'" H N N 189 U "H3'" H N N 190 U "HO3'" H N N 191 U "H2'" H N N 192 U "HO2'" H N N 193 U "H1'" H N N 194 U H3 H N N 195 U H5 H N N 196 U H6 H N N 197 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 NPM N11 C1A doub Y N 118 NPM N11 C1E sing Y N 119 NPM N12 C1F doub N N 120 NPM N12 C1G sing N N 121 NPM N13 C1Q sing N N 122 NPM N13 C1T doub N N 123 NPM N14 C1U sing Y N 124 NPM N14 C1Y doub Y N 125 NPM C1A C1B sing Y N 126 NPM C1A H1A sing N N 127 NPM C1B C1C doub Y N 128 NPM C1B H1B sing N N 129 NPM C1C C1D sing Y N 130 NPM C1C H1C sing N N 131 NPM C1D C1E doub Y N 132 NPM C1D H1D sing N N 133 NPM C1E C1F sing N N 134 NPM C1F H1F sing N N 135 NPM C1G C1H sing Y N 136 NPM C1G C1L doub Y N 137 NPM C1H C1I doub Y N 138 NPM C1H H1H sing N N 139 NPM C1I C1J sing Y N 140 NPM C1I H1I sing N N 141 NPM C1J C1K doub Y N 142 NPM C1J C1M sing N N 143 NPM C1K C1L sing Y N 144 NPM C1K H1K sing N N 145 NPM C1L H1L sing N N 146 NPM C1M C1N sing N N 147 NPM C1M H1M1 sing N N 148 NPM C1M H1M2 sing N N 149 NPM C1N C1O doub Y N 150 NPM C1N C1S sing Y N 151 NPM C1O C1P sing Y N 152 NPM C1O H1O sing N N 153 NPM C1P C1Q doub Y N 154 NPM C1P H1P sing N N 155 NPM C1Q C1R sing Y N 156 NPM C1R C1S doub Y N 157 NPM C1R H1R sing N N 158 NPM C1S H1S sing N N 159 NPM C1T C1U sing N N 160 NPM C1T H1T sing N N 161 NPM C1U C1V doub Y N 162 NPM C1V C1W sing Y N 163 NPM C1V H1V sing N N 164 NPM C1W C1X doub Y N 165 NPM C1W H1W sing N N 166 NPM C1X C1Y sing Y N 167 NPM C1X H1X sing N N 168 NPM C1Y H1Y sing N N 169 U OP3 P sing N N 170 U OP3 HOP3 sing N N 171 U P OP1 doub N N 172 U P OP2 sing N N 173 U P "O5'" sing N N 174 U OP2 HOP2 sing N N 175 U "O5'" "C5'" sing N N 176 U "C5'" "C4'" sing N N 177 U "C5'" "H5'" sing N N 178 U "C5'" "H5''" sing N N 179 U "C4'" "O4'" sing N N 180 U "C4'" "C3'" sing N N 181 U "C4'" "H4'" sing N N 182 U "O4'" "C1'" sing N N 183 U "C3'" "O3'" sing N N 184 U "C3'" "C2'" sing N N 185 U "C3'" "H3'" sing N N 186 U "O3'" "HO3'" sing N N 187 U "C2'" "O2'" sing N N 188 U "C2'" "C1'" sing N N 189 U "C2'" "H2'" sing N N 190 U "O2'" "HO2'" sing N N 191 U "C1'" N1 sing N N 192 U "C1'" "H1'" sing N N 193 U N1 C2 sing N N 194 U N1 C6 sing N N 195 U C2 O2 doub N N 196 U C2 N3 sing N N 197 U N3 C4 sing N N 198 U N3 H3 sing N N 199 U C4 O4 doub N N 200 U C4 C5 sing N N 201 U C5 C6 doub N N 202 U C5 H5 sing N N 203 U C6 H6 sing N N 204 # _ndb_struct_conf_na.entry_id 4JIY _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 6 5_555 0.184 -0.195 0.189 -2.229 -7.943 -0.143 1 A_C1:G6_A A 1 ? A 6 ? 19 1 1 A G 2 1_555 A C 5 5_555 -0.452 -0.268 0.135 -4.570 -21.204 3.891 2 A_G2:C5_A A 2 ? A 5 ? 19 1 1 A U 3 1_555 A A 4 5_555 0.138 -0.275 0.279 -6.662 -15.620 3.883 3 A_U3:A4_A A 3 ? A 4 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 6 5_555 A G 2 1_555 A C 5 5_555 0.499 -1.739 3.123 0.890 11.302 29.730 -4.966 -0.770 2.336 21.086 -1.660 31.773 1 AA_C1G2:C5G6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A G 2 1_555 A C 5 5_555 A U 3 1_555 A A 4 5_555 0.035 -1.312 3.308 -0.824 5.320 36.717 -2.762 -0.163 3.093 8.390 1.300 37.096 2 AA_G2U3:A4C5_AA A 2 ? A 5 ? A 3 ? A 4 ? # _atom_sites.entry_id 4JIY _atom_sites.fract_transf_matrix[1][1] 0.021860 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.021860 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.021860 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C FE N O P # loop_