data_1YRJ # _entry.id 1YRJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1YRJ pdb_00001yrj 10.2210/pdb1yrj/pdb NDB DR0011 ? ? RCSB RCSB031848 ? ? WWPDB D_1000031848 ? ? # _pdbx_database_related.db_name NDB _pdbx_database_related.db_id DR0008 _pdbx_database_related.details 'The same rna complexed with Geneticin' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YRJ _pdbx_database_status.recvd_initial_deposition_date 2005-02-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry N _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_ _audit_author.name _audit_author.pdbx_ordinal 'Han, Q.' 1 'Zhao, Q.' 2 'Fish, S.' 3 'Simonsen, K.B.' 4 'Vourloumis, D.' 5 'Froelich, J.M.' 6 'Wall, D.' 7 'Hermann, T.' 8 # _citation.id primary _citation.title 'Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 44 _citation.page_first 2694 _citation.page_last 2700 _citation.year 2005 _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 15849690 _citation.pdbx_database_id_DOI 10.1002/anie.200500028 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Han, Q.' 1 ? primary 'Zhao, Q.' 2 ? primary 'Fish, S.' 3 ? primary 'Simonsen, K.B.' 4 ? primary 'Vourloumis, D.' 5 ? primary 'Froelich, J.M.' 6 ? primary 'Wall, D.' 7 ? primary 'Hermann, T.' 8 ? # _cell.entry_id 1YRJ _cell.length_a 92.250 _cell.length_b 30.900 _cell.length_c 45.810 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 1YRJ _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? # 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 'Bacterial 16 S Ribosomal RNA A Site Oligonucleotide' 7355.409 2 ? ? ? ? 2 non-polymer syn APRAMYCIN 539.577 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 5 water nat water 18.015 65 ? ? ? ? # _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 UUGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 A n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 U n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1YRJ _struct_ref.pdbx_db_accession 1YRJ _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1YRJ A 1 ? 23 ? 1YRJ 1 ? 23 ? 1 23 2 1 1YRJ B 1 ? 23 ? 1YRJ 24 ? 46 ? 24 46 # 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 AM2 non-polymer . APRAMYCIN ;NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE ; 'C21 H41 N5 O11' 539.577 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 1YRJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.57 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'MPD, sodium cacodylate, NaCl, KCl, MgSO4, pH 6.5, EVAPORATION, temperature 310K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 1 NaCl ? ? ? 1 4 1 KCl ? ? ? 1 5 1 MgSO4 ? ? ? 1 6 1 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2004-10-30 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator MIRRORS _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.127 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.127 # _reflns.entry_id 1YRJ _reflns.observed_criterion_sigma_F 1.5 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.7 _reflns.d_resolution_low 8 _reflns.number_all ? _reflns.number_obs 3802 _reflns.percent_possible_obs 99.0 _reflns.pdbx_Rmerge_I_obs 0.073 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 43 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.5 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.7 _reflns_shell.d_res_low 2.79 _reflns_shell.percent_possible_all 99.0 _reflns_shell.Rmerge_I_obs 0.17 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 6.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _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 # _refine.entry_id 1YRJ _refine.ls_d_res_high 2.7 _refine.ls_d_res_low 8.0 _refine.pdbx_ls_sigma_F 1.5 _refine.pdbx_ls_sigma_I 1.5 _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 3712 _refine.ls_number_reflns_R_free ? _refine.ls_percent_reflns_obs 99.0 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.246 _refine.ls_R_factor_R_free 0.307 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free 10 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MIR _refine.pdbx_starting_model 'PDB entry 1LC4' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _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 952 _refine_hist.pdbx_number_atoms_ligand 76 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 1093 _refine_hist.d_res_high 2.7 _refine_hist.d_res_low 8.0 # 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_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.01 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.63 ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 1YRJ _struct.title 'Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YRJ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA complex, Apramycin-RNA Complex, Molecular Recognition, RNA' # 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 1 ? C N N 2 ? D N N 3 ? E N N 2 ? F N N 4 ? G N N 5 ? H N N 5 ? # _struct_biol.id 1 _struct_biol.details ? _struct_biol.pdbx_parent_biol_id ? # 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 ? ? A U 6 O2 ? ? ? 1_555 F K . K ? ? A U 6 B K 100 1_555 ? ? ? ? ? ? ? 2.851 ? ? metalc2 metalc ? ? A U 15 O4 ? ? ? 1_555 D MG . MG ? ? A U 15 A MG 101 1_555 ? ? ? ? ? ? ? 2.935 ? ? metalc3 metalc ? ? A G 16 O6 ? ? ? 1_555 D MG . MG ? ? A G 16 A MG 101 1_555 ? ? ? ? ? ? ? 2.482 ? ? metalc4 metalc ? ? A A 18 "O2'" ? ? ? 3_556 F K . K ? ? A A 18 B K 100 1_555 ? ? ? ? ? ? ? 2.375 ? ? metalc5 metalc ? ? A A 18 "O3'" ? ? ? 3_556 F K . K ? ? A A 18 B K 100 1_555 ? ? ? ? ? ? ? 2.847 ? ? metalc6 metalc ? ? A G 19 OP1 ? ? ? 3_556 F K . K ? ? A G 19 B K 100 1_555 ? ? ? ? ? ? ? 3.089 ? ? metalc7 metalc ? ? B C 21 "O4'" ? ? ? 1_555 F K . K ? ? B C 44 B K 100 1_555 ? ? ? ? ? ? ? 3.023 ? ? metalc8 metalc ? ? B C 21 N1 ? ? ? 1_555 F K . K ? ? B C 44 B K 100 1_555 ? ? ? ? ? ? ? 3.403 ? ? metalc9 metalc ? ? B C 21 O2 ? ? ? 1_555 F K . K ? ? B C 44 B K 100 1_555 ? ? ? ? ? ? ? 2.932 ? ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 N3 ? ? ? 1_555 B U 20 O2 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 6 O4 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 15 N3 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 15 O4 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 15 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 15 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O4 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog41 hydrog ? ? A U 20 O2 ? ? ? 1_555 B U 6 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog42 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 B AM2 150 ? 16 'BINDING SITE FOR RESIDUE AM2 B 150' AC2 Software A AM2 151 ? 12 'BINDING SITE FOR RESIDUE AM2 A 151' AC3 Software B K 100 ? 4 'BINDING SITE FOR RESIDUE K B 100' AC4 Software A MG 101 ? 2 'BINDING SITE FOR RESIDUE MG A 101' 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 16 C A 4 ? C A 4 . ? 1_555 ? 2 AC1 16 G A 5 ? G A 5 . ? 1_555 ? 3 AC1 16 A A 8 ? A A 8 . ? 1_555 ? 4 AC1 16 A A 10 ? A A 10 . ? 1_555 ? 5 AC1 16 HOH G . ? HOH A 152 . ? 1_555 ? 6 AC1 16 HOH G . ? HOH A 157 . ? 1_555 ? 7 AC1 16 G B 16 ? G B 39 . ? 2_655 ? 8 AC1 16 G B 16 ? G B 39 . ? 1_555 ? 9 AC1 16 A B 17 ? A B 40 . ? 2_655 ? 10 AC1 16 A B 17 ? A B 40 . ? 1_555 ? 11 AC1 16 A B 18 ? A B 41 . ? 1_555 ? 12 AC1 16 G B 19 ? G B 42 . ? 1_555 ? 13 AC1 16 U B 20 ? U B 43 . ? 1_555 ? 14 AC1 16 HOH H . ? HOH B 164 . ? 1_555 ? 15 AC1 16 HOH H . ? HOH B 169 . ? 1_555 ? 16 AC1 16 HOH H . ? HOH B 176 . ? 1_555 ? 17 AC2 12 G A 16 ? G A 16 . ? 1_555 ? 18 AC2 12 A A 17 ? A A 17 . ? 1_555 ? 19 AC2 12 A A 18 ? A A 18 . ? 1_555 ? 20 AC2 12 G A 19 ? G A 19 . ? 1_555 ? 21 AC2 12 U A 20 ? U A 20 . ? 1_555 ? 22 AC2 12 HOH G . ? HOH A 169 . ? 1_555 ? 23 AC2 12 HOH G . ? HOH A 172 . ? 1_555 ? 24 AC2 12 HOH G . ? HOH A 180 . ? 1_555 ? 25 AC2 12 U B 2 ? U B 25 . ? 3_557 ? 26 AC2 12 A B 8 ? A B 31 . ? 1_555 ? 27 AC2 12 C B 9 ? C B 32 . ? 1_555 ? 28 AC2 12 A B 10 ? A B 33 . ? 1_555 ? 29 AC3 4 U A 6 ? U A 6 . ? 1_555 ? 30 AC3 4 A A 18 ? A A 18 . ? 3_556 ? 31 AC3 4 G A 19 ? G A 19 . ? 3_556 ? 32 AC3 4 C B 21 ? C B 44 . ? 1_555 ? 33 AC4 2 U A 15 ? U A 15 . ? 1_555 ? 34 AC4 2 G A 16 ? G A 16 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YRJ _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 # _atom_sites.entry_id 1YRJ _atom_sites.fract_transf_matrix[1][1] 0.010840 _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] 0.032362 _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] 0.021829 _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 K MG N O P # 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 U 1 1 1 U U A . n A 1 2 U 2 2 2 U U A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 U 15 15 15 U U A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n B 1 1 U 1 24 ? ? ? B . n B 1 2 U 2 25 25 U U B . n B 1 3 G 3 26 26 G G B . n B 1 4 C 4 27 27 C C B . n B 1 5 G 5 28 28 G G B . n B 1 6 U 6 29 29 U U B . n B 1 7 C 7 30 30 C C B . n B 1 8 A 8 31 31 A A B . n B 1 9 C 9 32 32 C C B . n B 1 10 A 10 33 33 A A B . n B 1 11 C 11 34 34 C C B . n B 1 12 C 12 35 35 C C B . n B 1 13 G 13 36 36 G G B . n B 1 14 G 14 37 37 G G B . n B 1 15 U 15 38 38 U U B . n B 1 16 G 16 39 39 G G B . n B 1 17 A 17 40 40 A A B . n B 1 18 A 18 41 41 A A B . n B 1 19 G 19 42 42 G G B . n B 1 20 U 20 43 43 U U B . n B 1 21 C 21 44 44 C C B . n B 1 22 G 22 45 45 G G B . n B 1 23 C 23 46 46 C C B . 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 C 2 AM2 1 151 151 AM2 AM2 A . D 3 MG 1 101 101 MG MG A . E 2 AM2 1 150 150 AM2 AM2 B . F 4 K 1 100 100 K K B . G 5 HOH 1 152 2 HOH HOH A . G 5 HOH 2 153 3 HOH HOH A . G 5 HOH 3 154 9 HOH HOH A . G 5 HOH 4 155 10 HOH HOH A . G 5 HOH 5 156 14 HOH HOH A . G 5 HOH 6 157 15 HOH HOH A . G 5 HOH 7 158 16 HOH HOH A . G 5 HOH 8 159 18 HOH HOH A . G 5 HOH 9 160 19 HOH HOH A . G 5 HOH 10 161 20 HOH HOH A . G 5 HOH 11 162 22 HOH HOH A . G 5 HOH 12 163 23 HOH HOH A . G 5 HOH 13 164 25 HOH HOH A . G 5 HOH 14 165 26 HOH HOH A . G 5 HOH 15 166 29 HOH HOH A . G 5 HOH 16 167 30 HOH HOH A . G 5 HOH 17 168 33 HOH HOH A . G 5 HOH 18 169 37 HOH HOH A . G 5 HOH 19 170 39 HOH HOH A . G 5 HOH 20 171 41 HOH HOH A . G 5 HOH 21 172 42 HOH HOH A . G 5 HOH 22 173 43 HOH HOH A . G 5 HOH 23 174 45 HOH HOH A . G 5 HOH 24 175 49 HOH HOH A . G 5 HOH 25 176 50 HOH HOH A . G 5 HOH 26 177 51 HOH HOH A . G 5 HOH 27 178 52 HOH HOH A . G 5 HOH 28 179 53 HOH HOH A . G 5 HOH 29 180 54 HOH HOH A . G 5 HOH 30 181 55 HOH HOH A . G 5 HOH 31 182 58 HOH HOH A . G 5 HOH 32 183 60 HOH HOH A . G 5 HOH 33 184 62 HOH HOH A . G 5 HOH 34 185 65 HOH HOH A . H 5 HOH 1 151 1 HOH HOH B . H 5 HOH 2 152 4 HOH HOH B . H 5 HOH 3 153 5 HOH HOH B . H 5 HOH 4 154 6 HOH HOH B . H 5 HOH 5 155 7 HOH HOH B . H 5 HOH 6 156 8 HOH HOH B . H 5 HOH 7 157 11 HOH HOH B . H 5 HOH 8 158 12 HOH HOH B . H 5 HOH 9 159 13 HOH HOH B . H 5 HOH 10 160 17 HOH HOH B . H 5 HOH 11 161 21 HOH HOH B . H 5 HOH 12 162 24 HOH HOH B . H 5 HOH 13 163 27 HOH HOH B . H 5 HOH 14 164 28 HOH HOH B . H 5 HOH 15 165 31 HOH HOH B . H 5 HOH 16 166 32 HOH HOH B . H 5 HOH 17 167 34 HOH HOH B . H 5 HOH 18 168 35 HOH HOH B . H 5 HOH 19 169 36 HOH HOH B . H 5 HOH 20 170 38 HOH HOH B . H 5 HOH 21 171 40 HOH HOH B . H 5 HOH 22 172 44 HOH HOH B . H 5 HOH 23 173 46 HOH HOH B . H 5 HOH 24 174 47 HOH HOH B . H 5 HOH 25 175 48 HOH HOH B . H 5 HOH 26 176 56 HOH HOH B . H 5 HOH 27 177 57 HOH HOH B . H 5 HOH 28 178 59 HOH HOH B . H 5 HOH 29 179 61 HOH HOH B . H 5 HOH 30 180 63 HOH HOH B . H 5 HOH 31 181 64 HOH HOH B . # _struct_site_keywords.site_id 1 _struct_site_keywords.text BIS-INTERCALATION # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 "O2'" ? A A 18 ? A A 18 ? 3_556 55.4 ? 2 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 "O3'" ? A A 18 ? A A 18 ? 3_556 110.4 ? 3 "O2'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 "O3'" ? A A 18 ? A A 18 ? 3_556 56.9 ? 4 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 OP1 ? A G 19 ? A G 19 ? 3_556 137.8 ? 5 "O2'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 OP1 ? A G 19 ? A G 19 ? 3_556 100.7 ? 6 "O3'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 OP1 ? A G 19 ? A G 19 ? 3_556 48.2 ? 7 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 "O4'" ? B C 21 ? B C 44 ? 1_555 135.4 ? 8 "O2'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 "O4'" ? B C 21 ? B C 44 ? 1_555 129.6 ? 9 "O3'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 "O4'" ? B C 21 ? B C 44 ? 1_555 99.5 ? 10 OP1 ? A G 19 ? A G 19 ? 3_556 K ? F K . ? B K 100 ? 1_555 "O4'" ? B C 21 ? B C 44 ? 1_555 86.8 ? 11 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 N1 ? B C 21 ? B C 44 ? 1_555 93.2 ? 12 "O2'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 N1 ? B C 21 ? B C 44 ? 1_555 107.2 ? 13 "O3'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 N1 ? B C 21 ? B C 44 ? 1_555 120.1 ? 14 OP1 ? A G 19 ? A G 19 ? 3_556 K ? F K . ? B K 100 ? 1_555 N1 ? B C 21 ? B C 44 ? 1_555 128.6 ? 15 "O4'" ? B C 21 ? B C 44 ? 1_555 K ? F K . ? B K 100 ? 1_555 N1 ? B C 21 ? B C 44 ? 1_555 42.4 ? 16 O2 ? A U 6 ? A U 6 ? 1_555 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 56.5 ? 17 "O2'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 70.0 ? 18 "O3'" ? A A 18 ? A A 18 ? 3_556 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 111.4 ? 19 OP1 ? A G 19 ? A G 19 ? 3_556 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 154.8 ? 20 "O4'" ? B C 21 ? B C 44 ? 1_555 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 82.4 ? 21 N1 ? B C 21 ? B C 44 ? 1_555 K ? F K . ? B K 100 ? 1_555 O2 ? B C 21 ? B C 44 ? 1_555 41.8 ? 22 O4 ? A U 15 ? A U 15 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O6 ? A G 16 ? A G 16 ? 1_555 75.5 ? # 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 2005-06-07 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2016-11-30 5 'Structure model' 1 4 2023-08-23 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' Other 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Refinement description' 8 5 'Structure model' 'Structure summary' # 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 5 'Structure model' chem_comp 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_initial_refinement_model 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 5 '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 5 'Structure model' '_chem_comp.pdbx_synonyms' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 20 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 21 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 22 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 23 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 24 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 25 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 26 5 'Structure model' '_pdbx_struct_conn_angle.value' 27 5 'Structure model' '_struct_conn.pdbx_dist_value' 28 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 29 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 30 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 31 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 32 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 33 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 34 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 35 5 'Structure model' '_struct_conn.ptnr1_symmetry' 36 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 37 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 38 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 39 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 40 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 41 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 42 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 43 5 'Structure model' '_struct_conn.ptnr2_symmetry' 44 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 45 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 46 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 G _pdbx_validate_close_contact.auth_seq_id_1 22 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 167 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N1 A U 1 ? ? "C1'" A U 1 ? ? "C2'" A U 1 ? ? 123.03 114.00 9.03 1.30 N 2 1 N9 A A 17 ? ? "C1'" A A 17 ? ? "C2'" A A 17 ? ? 124.40 114.00 10.40 1.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 U A 1 ? ? 0.099 'SIDE CHAIN' 2 1 A A 17 ? ? 0.068 'SIDE CHAIN' 3 1 U A 20 ? ? 0.079 'SIDE CHAIN' 4 1 U B 38 ? ? 0.059 'SIDE CHAIN' 5 1 U B 43 ? ? 0.067 'SIDE CHAIN' 6 1 G B 45 ? ? 0.052 'SIDE CHAIN' # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B U 25 ? P ? B U 2 P 2 1 Y 1 B U 25 ? OP1 ? B U 2 OP1 3 1 Y 1 B U 25 ? OP2 ? B U 2 OP2 # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id B _pdbx_unobs_or_zero_occ_residues.auth_comp_id U _pdbx_unobs_or_zero_occ_residues.auth_seq_id 24 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id B _pdbx_unobs_or_zero_occ_residues.label_comp_id U _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # 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 AM2 CA1 C N S 38 AM2 CA2 C N R 39 AM2 CA3 C N N 40 AM2 CA4 C N S 41 AM2 CA5 C N R 42 AM2 CA6 C N R 43 AM2 CA7 C N S 44 AM2 CA8 C N R 45 AM2 CA9 C N N 46 AM2 OA4 O N N 47 AM2 OA5 O N N 48 AM2 NA2 N N N 49 AM2 NA7 N N N 50 AM2 OA6 O N N 51 AM2 OA8 O N N 52 AM2 OA1 O N N 53 AM2 CB1 C N R 54 AM2 CB2 C N R 55 AM2 CB3 C N S 56 AM2 CB4 C N S 57 AM2 CB5 C N S 58 AM2 CB6 C N N 59 AM2 OB1 O N N 60 AM2 NB4 N N N 61 AM2 OB2 O N N 62 AM2 OB3 O N N 63 AM2 OB6 O N N 64 AM2 CC1 C N R 65 AM2 CC2 C N R 66 AM2 CC3 C N S 67 AM2 CC4 C N R 68 AM2 CC5 C N N 69 AM2 CC6 C N S 70 AM2 NC4 N N N 71 AM2 NC6 N N N 72 AM2 OC2 O N N 73 AM2 OC3 O N N 74 AM2 HA1 H N N 75 AM2 HA2 H N N 76 AM2 HA31 H N N 77 AM2 HA32 H N N 78 AM2 HA4 H N N 79 AM2 HA5 H N N 80 AM2 HA6 H N N 81 AM2 HA7 H N N 82 AM2 HA8 H N N 83 AM2 HA91 H N N 84 AM2 HA92 H N N 85 AM2 HA93 H N N 86 AM2 HA21 H N N 87 AM2 HA22 H N N 88 AM2 H2 H N N 89 AM2 H1 H N N 90 AM2 HB1 H N N 91 AM2 HB2 H N N 92 AM2 HB3 H N N 93 AM2 HB4 H N N 94 AM2 HB5 H N N 95 AM2 HB61 H N N 96 AM2 HB62 H N N 97 AM2 HB41 H N N 98 AM2 HB42 H N N 99 AM2 H5 H N N 100 AM2 H6 H N N 101 AM2 HB6 H N N 102 AM2 HC1 H N N 103 AM2 HC2 H N N 104 AM2 HC3 H N N 105 AM2 HC4 H N N 106 AM2 HC51 H N N 107 AM2 HC52 H N N 108 AM2 HC6 H N N 109 AM2 HC41 H N N 110 AM2 HC42 H N N 111 AM2 HC61 H N N 112 AM2 HC62 H N N 113 AM2 H3 H N N 114 AM2 H4 H N N 115 C OP3 O N N 116 C P P N N 117 C OP1 O N N 118 C OP2 O N N 119 C "O5'" O N N 120 C "C5'" C N N 121 C "C4'" C N R 122 C "O4'" O N N 123 C "C3'" C N S 124 C "O3'" O N N 125 C "C2'" C N R 126 C "O2'" O N N 127 C "C1'" C N R 128 C N1 N N N 129 C C2 C N N 130 C O2 O N N 131 C N3 N N N 132 C C4 C N N 133 C N4 N N N 134 C C5 C N N 135 C C6 C N N 136 C HOP3 H N N 137 C HOP2 H N N 138 C "H5'" H N N 139 C "H5''" H N N 140 C "H4'" H N N 141 C "H3'" H N N 142 C "HO3'" H N N 143 C "H2'" H N N 144 C "HO2'" H N N 145 C "H1'" H N N 146 C H41 H N N 147 C H42 H N N 148 C H5 H N N 149 C H6 H N N 150 G OP3 O N N 151 G P P N N 152 G OP1 O N N 153 G OP2 O N N 154 G "O5'" O N N 155 G "C5'" C N N 156 G "C4'" C N R 157 G "O4'" O N N 158 G "C3'" C N S 159 G "O3'" O N N 160 G "C2'" C N R 161 G "O2'" O N N 162 G "C1'" C N R 163 G N9 N Y N 164 G C8 C Y N 165 G N7 N Y N 166 G C5 C Y N 167 G C6 C N N 168 G O6 O N N 169 G N1 N N N 170 G C2 C N N 171 G N2 N N N 172 G N3 N N N 173 G C4 C Y N 174 G HOP3 H N N 175 G HOP2 H N N 176 G "H5'" H N N 177 G "H5''" H N N 178 G "H4'" H N N 179 G "H3'" H N N 180 G "HO3'" H N N 181 G "H2'" H N N 182 G "HO2'" H N N 183 G "H1'" H N N 184 G H8 H N N 185 G H1 H N N 186 G H21 H N N 187 G H22 H N N 188 HOH O O N N 189 HOH H1 H N N 190 HOH H2 H N N 191 K K K N N 192 MG MG MG N N 193 U OP3 O N N 194 U P P N N 195 U OP1 O N N 196 U OP2 O N N 197 U "O5'" O N N 198 U "C5'" C N N 199 U "C4'" C N R 200 U "O4'" O N N 201 U "C3'" C N S 202 U "O3'" O N N 203 U "C2'" C N R 204 U "O2'" O N N 205 U "C1'" C N R 206 U N1 N N N 207 U C2 C N N 208 U O2 O N N 209 U N3 N N N 210 U C4 C N N 211 U O4 O N N 212 U C5 C N N 213 U C6 C N N 214 U HOP3 H N N 215 U HOP2 H N N 216 U "H5'" H N N 217 U "H5''" H N N 218 U "H4'" H N N 219 U "H3'" H N N 220 U "HO3'" H N N 221 U "H2'" H N N 222 U "HO2'" H N N 223 U "H1'" H N N 224 U H3 H N N 225 U H5 H N N 226 U H6 H N N 227 # 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 AM2 CA1 CA2 sing N N 40 AM2 CA1 OA4 sing N N 41 AM2 CA1 OA1 sing N N 42 AM2 CA1 HA1 sing N N 43 AM2 CA2 CA3 sing N N 44 AM2 CA2 NA2 sing N N 45 AM2 CA2 HA2 sing N N 46 AM2 CA3 CA4 sing N N 47 AM2 CA3 HA31 sing N N 48 AM2 CA3 HA32 sing N N 49 AM2 CA4 CA5 sing N N 50 AM2 CA4 OA5 sing N N 51 AM2 CA4 HA4 sing N N 52 AM2 CA5 CA6 sing N N 53 AM2 CA5 OA4 sing N N 54 AM2 CA5 HA5 sing N N 55 AM2 CA6 CA7 sing N N 56 AM2 CA6 OA6 sing N N 57 AM2 CA6 HA6 sing N N 58 AM2 CA7 CA8 sing N N 59 AM2 CA7 NA7 sing N N 60 AM2 CA7 HA7 sing N N 61 AM2 CA8 OA5 sing N N 62 AM2 CA8 OA8 sing N N 63 AM2 CA8 HA8 sing N N 64 AM2 CA9 NA7 sing N N 65 AM2 CA9 HA91 sing N N 66 AM2 CA9 HA92 sing N N 67 AM2 CA9 HA93 sing N N 68 AM2 NA2 HA21 sing N N 69 AM2 NA2 HA22 sing N N 70 AM2 NA7 H2 sing N N 71 AM2 OA6 H1 sing N N 72 AM2 OA8 CB1 sing N N 73 AM2 OA1 CC1 sing N N 74 AM2 CB1 CB2 sing N N 75 AM2 CB1 OB1 sing N N 76 AM2 CB1 HB1 sing N N 77 AM2 CB2 CB3 sing N N 78 AM2 CB2 OB2 sing N N 79 AM2 CB2 HB2 sing N N 80 AM2 CB3 CB4 sing N N 81 AM2 CB3 OB3 sing N N 82 AM2 CB3 HB3 sing N N 83 AM2 CB4 CB5 sing N N 84 AM2 CB4 NB4 sing N N 85 AM2 CB4 HB4 sing N N 86 AM2 CB5 CB6 sing N N 87 AM2 CB5 OB1 sing N N 88 AM2 CB5 HB5 sing N N 89 AM2 CB6 OB6 sing N N 90 AM2 CB6 HB61 sing N N 91 AM2 CB6 HB62 sing N N 92 AM2 NB4 HB41 sing N N 93 AM2 NB4 HB42 sing N N 94 AM2 OB2 H5 sing N N 95 AM2 OB3 H6 sing N N 96 AM2 OB6 HB6 sing N N 97 AM2 CC1 CC2 sing N N 98 AM2 CC1 CC6 sing N N 99 AM2 CC1 HC1 sing N N 100 AM2 CC2 CC3 sing N N 101 AM2 CC2 OC2 sing N N 102 AM2 CC2 HC2 sing N N 103 AM2 CC3 CC4 sing N N 104 AM2 CC3 OC3 sing N N 105 AM2 CC3 HC3 sing N N 106 AM2 CC4 CC5 sing N N 107 AM2 CC4 NC4 sing N N 108 AM2 CC4 HC4 sing N N 109 AM2 CC5 CC6 sing N N 110 AM2 CC5 HC51 sing N N 111 AM2 CC5 HC52 sing N N 112 AM2 CC6 NC6 sing N N 113 AM2 CC6 HC6 sing N N 114 AM2 NC4 HC41 sing N N 115 AM2 NC4 HC42 sing N N 116 AM2 NC6 HC61 sing N N 117 AM2 NC6 HC62 sing N N 118 AM2 OC2 H3 sing N N 119 AM2 OC3 H4 sing N N 120 C OP3 P sing N N 121 C OP3 HOP3 sing N N 122 C P OP1 doub N N 123 C P OP2 sing N N 124 C P "O5'" sing N N 125 C OP2 HOP2 sing N N 126 C "O5'" "C5'" sing N N 127 C "C5'" "C4'" sing N N 128 C "C5'" "H5'" sing N N 129 C "C5'" "H5''" sing N N 130 C "C4'" "O4'" sing N N 131 C "C4'" "C3'" sing N N 132 C "C4'" "H4'" sing N N 133 C "O4'" "C1'" sing N N 134 C "C3'" "O3'" sing N N 135 C "C3'" "C2'" sing N N 136 C "C3'" "H3'" sing N N 137 C "O3'" "HO3'" sing N N 138 C "C2'" "O2'" sing N N 139 C "C2'" "C1'" sing N N 140 C "C2'" "H2'" sing N N 141 C "O2'" "HO2'" sing N N 142 C "C1'" N1 sing N N 143 C "C1'" "H1'" sing N N 144 C N1 C2 sing N N 145 C N1 C6 sing N N 146 C C2 O2 doub N N 147 C C2 N3 sing N N 148 C N3 C4 doub N N 149 C C4 N4 sing N N 150 C C4 C5 sing N N 151 C N4 H41 sing N N 152 C N4 H42 sing N N 153 C C5 C6 doub N N 154 C C5 H5 sing N N 155 C C6 H6 sing N N 156 G OP3 P sing N N 157 G OP3 HOP3 sing N N 158 G P OP1 doub N N 159 G P OP2 sing N N 160 G P "O5'" sing N N 161 G OP2 HOP2 sing N N 162 G "O5'" "C5'" sing N N 163 G "C5'" "C4'" sing N N 164 G "C5'" "H5'" sing N N 165 G "C5'" "H5''" sing N N 166 G "C4'" "O4'" sing N N 167 G "C4'" "C3'" sing N N 168 G "C4'" "H4'" sing N N 169 G "O4'" "C1'" sing N N 170 G "C3'" "O3'" sing N N 171 G "C3'" "C2'" sing N N 172 G "C3'" "H3'" sing N N 173 G "O3'" "HO3'" sing N N 174 G "C2'" "O2'" sing N N 175 G "C2'" "C1'" sing N N 176 G "C2'" "H2'" sing N N 177 G "O2'" "HO2'" sing N N 178 G "C1'" N9 sing N N 179 G "C1'" "H1'" sing N N 180 G N9 C8 sing Y N 181 G N9 C4 sing Y N 182 G C8 N7 doub Y N 183 G C8 H8 sing N N 184 G N7 C5 sing Y N 185 G C5 C6 sing N N 186 G C5 C4 doub Y N 187 G C6 O6 doub N N 188 G C6 N1 sing N N 189 G N1 C2 sing N N 190 G N1 H1 sing N N 191 G C2 N2 sing N N 192 G C2 N3 doub N N 193 G N2 H21 sing N N 194 G N2 H22 sing N N 195 G N3 C4 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 U OP3 P sing N N 199 U OP3 HOP3 sing N N 200 U P OP1 doub N N 201 U P OP2 sing N N 202 U P "O5'" sing N N 203 U OP2 HOP2 sing N N 204 U "O5'" "C5'" sing N N 205 U "C5'" "C4'" sing N N 206 U "C5'" "H5'" sing N N 207 U "C5'" "H5''" sing N N 208 U "C4'" "O4'" sing N N 209 U "C4'" "C3'" sing N N 210 U "C4'" "H4'" sing N N 211 U "O4'" "C1'" sing N N 212 U "C3'" "O3'" sing N N 213 U "C3'" "C2'" sing N N 214 U "C3'" "H3'" sing N N 215 U "O3'" "HO3'" sing N N 216 U "C2'" "O2'" sing N N 217 U "C2'" "C1'" sing N N 218 U "C2'" "H2'" sing N N 219 U "O2'" "HO2'" sing N N 220 U "C1'" N1 sing N N 221 U "C1'" "H1'" sing N N 222 U N1 C2 sing N N 223 U N1 C6 sing N N 224 U C2 O2 doub N N 225 U C2 N3 sing N N 226 U N3 C4 sing N N 227 U N3 H3 sing N N 228 U C4 O4 doub N N 229 U C4 C5 sing N N 230 U C5 C6 doub N N 231 U C5 H5 sing N N 232 U C6 H6 sing N N 233 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1YRJ 'double helix' 1YRJ 'a-form double helix' 1YRJ 'mismatched base pair' 1YRJ 'internal loop' # 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 G 3 1_555 B C 23 1_555 0.333 -0.348 0.408 -4.051 7.547 -6.749 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 0.969 -0.321 0.041 -4.987 -9.811 -5.458 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.664 -0.678 -1.030 -23.140 -9.398 1.696 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 6 1_555 B U 20 1_555 -2.689 -1.946 1.051 -5.222 -26.013 10.839 4 A_U6:U43_B A 6 ? B 43 ? 16 1 1 A C 7 1_555 B G 19 1_555 0.281 -0.058 0.547 -2.161 -21.371 9.132 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.454 -0.100 0.218 1.127 -0.146 7.873 6 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A A 10 1_555 B U 15 1_555 -0.457 0.106 0.152 3.060 -24.467 1.983 7 A_A10:U38_B A 10 ? B 38 ? 20 1 1 A C 11 1_555 B G 14 1_555 1.367 -0.529 -0.002 8.392 -10.985 5.405 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 12 1_555 B G 13 1_555 -0.555 -0.300 0.446 2.629 -11.704 5.890 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.071 -0.130 0.217 -3.981 -12.814 2.801 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 14 1_555 B C 11 1_555 -0.458 -0.761 -0.189 -2.585 -21.917 -0.771 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A U 15 1_555 B A 10 1_555 -0.800 -0.535 -0.211 3.873 -12.853 7.803 12 A_U15:A33_B A 15 ? B 33 ? 20 1 1 A G 16 1_555 B C 9 1_555 -0.238 0.183 0.468 4.616 -15.025 5.973 13 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 19 1_555 B C 7 1_555 0.616 -0.140 -0.102 4.008 -17.838 -5.288 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 1.647 -1.678 0.058 -0.702 -17.370 2.240 15 A_U20:U29_B A 20 ? B 29 ? 16 1 1 A C 21 1_555 B G 5 1_555 1.153 -0.637 0.515 -2.422 -14.550 6.160 16 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.285 -0.179 0.101 -0.993 -10.370 7.747 17 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.567 -0.051 0.124 2.537 -5.439 2.779 18 A_C23:G26_B A 23 ? B 26 ? 19 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 G 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 -0.859 -2.645 3.344 3.787 -2.906 31.201 -4.301 2.315 3.444 -5.364 -6.989 31.555 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 1.061 -2.016 3.909 8.621 6.218 20.686 -7.526 0.859 3.341 16.023 -22.215 23.230 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 0.569 -1.478 2.684 -15.842 1.350 24.873 -3.128 -3.706 1.906 2.798 32.842 29.453 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 0.025 -0.699 2.969 4.511 3.941 50.200 -1.070 0.258 2.902 4.626 -5.295 50.533 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 7 1_555 B G 19 1_555 A C 9 1_555 B G 16 1_555 1.930 -2.799 6.309 -10.960 17.523 84.819 -2.746 -1.849 5.536 12.827 8.023 86.835 5 AA_C7C9:G39G42_BB A 7 ? B 42 ? A 9 ? B 39 ? 1 A C 9 1_555 B G 16 1_555 A A 10 1_555 B U 15 1_555 -0.808 -1.413 3.162 -0.778 10.295 27.078 -4.864 1.462 2.491 21.042 1.590 28.945 6 AA_C9A10:U38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A A 10 1_555 B U 15 1_555 A C 11 1_555 B G 14 1_555 0.789 -1.500 3.147 0.577 5.738 39.124 -2.847 -1.103 2.918 8.512 -0.856 39.530 7 AA_A10C11:G37U38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 -0.083 -2.758 2.948 -4.371 12.976 17.865 -10.129 -0.816 0.785 35.741 12.040 22.475 8 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 -0.156 -1.396 3.170 3.211 8.912 36.270 -3.249 0.631 2.740 14.024 -5.052 37.446 9 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 -0.368 -2.066 3.257 3.999 8.045 28.700 -5.480 1.453 2.525 15.750 -7.830 30.045 10 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 14 1_555 B C 11 1_555 A U 15 1_555 B A 10 1_555 0.655 -1.323 3.030 0.336 4.871 27.242 -3.821 -1.298 2.763 10.238 -0.706 27.668 11 AA_G14U15:A33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A U 15 1_555 B A 10 1_555 A G 16 1_555 B C 9 1_555 0.094 -1.325 3.056 -2.683 8.882 35.404 -3.197 -0.478 2.644 14.304 4.320 36.562 12 AA_U15G16:C32A33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 -0.453 -1.772 3.496 1.179 1.226 37.715 -2.906 0.861 3.424 1.896 -1.822 37.752 13 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 -0.107 -1.621 3.216 -3.612 8.192 33.028 -3.958 -0.347 2.744 14.089 6.213 34.187 14 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 -0.304 -2.181 3.236 1.303 -2.400 20.323 -5.037 1.446 3.441 -6.762 -3.671 20.504 15 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 -0.375 -2.209 3.196 1.832 5.658 31.807 -4.883 0.970 2.747 10.212 -3.306 32.344 16 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 APRAMYCIN AM2 3 'MAGNESIUM ION' MG 4 'POTASSIUM ION' K 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1LC4 _pdbx_initial_refinement_model.details 'PDB entry 1LC4' #