data_2A04 # _entry.id 2A04 # _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 2A04 pdb_00002a04 10.2210/pdb2a04/pdb NDB DR0014 ? ? RCSB RCSB033325 ? ? WWPDB D_1000033325 ? ? # 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 2005-09-20 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' '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_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 19 4 'Structure model' '_struct_conn.pdbx_dist_value' 20 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 4 'Structure model' '_struct_conn.ptnr1_symmetry' 28 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 30 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 33 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_symmetry' 36 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 37 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 38 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2A04 _pdbx_database_status.recvd_initial_deposition_date 2005-06-15 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1ZX7 . unspecified PDB 1ZZ5 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhao, Q.' 1 'Zhao, F.' 2 'Blount, K.F.' 3 'Han, Q.' 4 'Tor, Y.' 5 'Hermann, T.' 6 # _citation.id primary _citation.title 'Molecular recognition of RNA by neomycin and a restricted neomycin derivative' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 44 _citation.page_first 5329 _citation.page_last 5334 _citation.year 2005 _citation.journal_id_ASTM ACIEAY _citation.country GE _citation.journal_id_ISSN 0570-0833 _citation.journal_id_CSD 0179 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16037995 _citation.pdbx_database_id_DOI 10.1002/anie.200500903 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhao, F.' 1 ? primary 'Zhao, Q.' 2 ? primary 'Blount, K.F.' 3 ? primary 'Han, Q.' 4 ? primary 'Tor, Y.' 5 ? primary 'Hermann, T.' 6 ? # 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'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'" 4903.961 2 ? ? 'Ribosomal RNA A-site' ? 2 polymer syn "5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'" 4380.691 2 ? ? 'Ribosomal RNA A-site' ? 3 non-polymer syn NEOMYCIN 614.644 4 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 water nat water 18.015 20 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GUGGUGAAGUCGCGG GUGGUGAAGUCGCGG A,C ? 2 polyribonucleotide no no CGCGUCACACCACC CGCGUCACACCACC B,D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 NEOMYCIN NMY 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 U n 1 3 G n 1 4 G n 1 5 U n 1 6 G n 1 7 A n 1 8 A n 1 9 G n 1 10 U n 1 11 C n 1 12 G n 1 13 C n 1 14 G n 1 15 G n 2 1 C n 2 2 G n 2 3 C n 2 4 G n 2 5 U n 2 6 C n 2 7 A n 2 8 C n 2 9 A n 2 10 C n 2 11 C n 2 12 A n 2 13 C n 2 14 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? ;This sequence occurs naturally in ESCHERICHIA COLI (bacteria) except one residue was removed near 3' terminal ; 2 1 sample ? ? ? ? ? ;This sequence occurs naturally in ESCHERICHIA COLI (bacteria) except one residue was removed near 5' terminal ; # 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NMY non-polymer . NEOMYCIN 'MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN' 'C23 H46 N6 O13' 614.644 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 G 1 2 2 G GUA A . n A 1 2 U 2 3 3 U URI A . n A 1 3 G 3 4 4 G GUA A . n A 1 4 G 4 5 5 G GUA A . n A 1 5 U 5 6 6 U URI A . n A 1 6 G 6 7 7 G GUA A . n A 1 7 A 7 8 8 A ADE A . n A 1 8 A 8 9 9 A ADE A . n A 1 9 G 9 10 10 G GUA A . n A 1 10 U 10 11 11 U URI A . n A 1 11 C 11 12 12 C CYT A . n A 1 12 G 12 13 13 G GUA A . n A 1 13 C 13 14 14 C CYT A . n A 1 14 G 14 15 15 G GUA A . n A 1 15 G 15 16 16 G GUA A . n B 2 1 C 1 21 21 C CYT B . n B 2 2 G 2 22 22 G GUA B . n B 2 3 C 3 23 23 C CYT B . n B 2 4 G 4 24 24 G GUA B . n B 2 5 U 5 25 25 U URI B . n B 2 6 C 6 26 26 C CYT B . n B 2 7 A 7 27 27 A ADE B . n B 2 8 C 8 28 28 C CYT B . n B 2 9 A 9 29 29 A ADE B . n B 2 10 C 10 30 30 C CYT B . n B 2 11 C 11 31 31 C CYT B . n B 2 12 A 12 32 32 A ADE B . n B 2 13 C 13 33 33 C CYT B . n B 2 14 C 14 34 34 C CYT B . n C 1 1 G 1 2 2 G GUA C . n C 1 2 U 2 3 3 U URI C . n C 1 3 G 3 4 4 G GUA C . n C 1 4 G 4 5 5 G GUA C . n C 1 5 U 5 6 6 U URI C . n C 1 6 G 6 7 7 G GUA C . n C 1 7 A 7 8 8 A ADE C . n C 1 8 A 8 9 9 A ADE C . n C 1 9 G 9 10 10 G GUA C . n C 1 10 U 10 11 11 U URI C . n C 1 11 C 11 12 12 C CYT C . n C 1 12 G 12 13 13 G GUA C . n C 1 13 C 13 14 14 C CYT C . n C 1 14 G 14 15 15 G GUA C . n C 1 15 G 15 16 16 G GUA C . n D 2 1 C 1 21 21 C CYT D . n D 2 2 G 2 22 22 G GUA D . n D 2 3 C 3 23 23 C CYT D . n D 2 4 G 4 24 24 G GUA D . n D 2 5 U 5 25 25 U URI D . n D 2 6 C 6 26 26 C CYT D . n D 2 7 A 7 27 27 A ADE D . n D 2 8 C 8 28 28 C CYT D . n D 2 9 A 9 29 29 A ADE D . n D 2 10 C 10 30 30 C CYT D . n D 2 11 C 11 31 31 C CYT D . n D 2 12 A 12 32 32 A ADE D . n D 2 13 C 13 33 33 C CYT D . n D 2 14 C 14 34 34 C CYT D . 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 E 3 NMY 1 17 2 NMY NEO A . F 3 NMY 1 18 4 NMY NEO A . G 4 MG 1 41 21 MG MG2 A . H 3 NMY 1 1 1 NMY NEO C . I 3 NMY 1 17 3 NMY NEO C . J 4 MG 1 48 28 MG MG2 C . K 5 HOH 1 42 8 HOH TIP A . K 5 HOH 2 43 16 HOH TIP A . K 5 HOH 3 44 22 HOH TIP A . K 5 HOH 4 45 25 HOH TIP A . K 5 HOH 5 46 26 HOH TIP A . K 5 HOH 6 47 29 HOH TIP A . L 5 HOH 1 35 7 HOH TIP B . L 5 HOH 2 36 9 HOH TIP B . L 5 HOH 3 37 23 HOH TIP B . L 5 HOH 4 38 30 HOH TIP B . M 5 HOH 1 49 12 HOH TIP C . M 5 HOH 2 50 13 HOH TIP C . M 5 HOH 3 51 20 HOH TIP C . M 5 HOH 4 52 24 HOH TIP C . M 5 HOH 5 53 27 HOH TIP C . M 5 HOH 6 54 31 HOH TIP C . N 5 HOH 1 6 3 HOH TIP D . N 5 HOH 2 10 10 HOH TIP D . N 5 HOH 3 14 14 HOH TIP D . N 5 HOH 4 15 15 HOH TIP D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement 1.0 ? 4 # _cell.entry_id 2A04 _cell.length_a 49.800 _cell.length_b 49.900 _cell.length_c 144.600 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2A04 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2A04 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.5 _exptl_crystal.density_percent_sol 72.6 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'MPD, magnesium sulfate, potassium chloride, sodium chloride, cacodylate, pH 6.0, EVAPORATION, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 103 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2002-12-10 _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 2A04 _reflns.observed_criterion_sigma_F 3.0 _reflns.observed_criterion_sigma_I 3.0 _reflns.d_resolution_high 2.95 _reflns.d_resolution_low 28.5 _reflns.number_all ? _reflns.number_obs 7103 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.127 _reflns.pdbx_Rsym_value 0.127 _reflns.pdbx_netI_over_sigmaI 26.3 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.95 _reflns_shell.d_res_low 3.06 _reflns_shell.percent_possible_all 98.5 _reflns_shell.Rmerge_I_obs 0.535 _reflns_shell.pdbx_Rsym_value 0.535 _reflns_shell.meanI_over_sigI_obs 2.7 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 387 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2A04 _refine.ls_d_res_high 2.95 _refine.ls_d_res_low 8.0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_ls_sigma_I 0 _refine.ls_number_reflns_all 7599 _refine.ls_number_reflns_obs 6650 _refine.ls_number_reflns_R_free 723 _refine.ls_percent_reflns_obs 88.2 _refine.ls_R_factor_all 0.2976 _refine.ls_R_factor_obs 0.2976 _refine.ls_R_factor_R_work 0.2535 _refine.ls_R_factor_R_free 0.3183 _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 ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 75.7 _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_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2A04 _refine_analyze.Luzzati_coordinate_error_obs 0.46 _refine_analyze.Luzzati_sigma_a_obs 0.62 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.57 _refine_analyze.Luzzati_sigma_a_free 0.40 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 1228 _refine_hist.pdbx_number_atoms_ligand 170 _refine_hist.number_atoms_solvent 20 _refine_hist.number_atoms_total 1418 _refine_hist.d_res_high 2.95 _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 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 9.0 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.48 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.95 _refine_ls_shell.d_res_low 3.13 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.395 _refine_ls_shell.percent_reflns_obs 67.2 _refine_ls_shell.R_factor_R_free 0.412 _refine_ls_shell.R_factor_R_free_error 0.046 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 79 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2A04 _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 2A04 _struct.title 'Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2A04 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Ribosome, RNA, A-site. double helix, neomycin' # 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 1 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 3 ? I N N 3 ? J N N 4 ? K N N 5 ? L N N 5 ? M N N 5 ? N N N 5 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2A04 2A04 ? ? ? 2 2 PDB 2A04 2A04 ? ? ? # 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 2A04 A 1 ? 15 ? 2A04 2 ? 16 ? 2 16 2 2 2A04 B 1 ? 14 ? 2A04 21 ? 34 ? 21 34 3 1 2A04 C 1 ? 15 ? 2A04 2 ? 16 ? 2 16 4 2 2A04 D 1 ? 14 ? 2A04 21 ? 34 ? 21 34 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G,K,L 2 1 C,D,H,I,J,M,N # _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_ _struct_biol.id _struct_biol.details _struct_biol.pdbx_parent_biol_id 1 ;The chains A and B, C and D form two double-helix RNA biological unit. The two units are related by non-crystallographic symmetry in the asymmetric unit. ; ? 2 ? ? # 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 G 1 N7 ? ? ? 1_555 G MG . MG ? ? A G 2 A MG 41 1_555 ? ? ? ? ? ? ? 2.994 ? ? metalc2 metalc ? ? F NMY . O20 ? ? ? 2_664 J MG . MG ? ? A NMY 18 C MG 48 1_555 ? ? ? ? ? ? ? 2.934 ? ? metalc3 metalc ? ? C G 1 N7 ? ? ? 1_555 J MG . MG ? ? C G 2 C MG 48 1_555 ? ? ? ? ? ? ? 2.708 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 2 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 2 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 2 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 12 N1 ? ? A U 3 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 12 N6 ? ? A U 3 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 4 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 4 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 4 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 5 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 5 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 5 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 6 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 6 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 10 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 11 B U 25 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 2 N1 ? ? A C 14 B G 22 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog28 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 14 N3 ? ? ? 1_555 C G 15 N1 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 14 N4 ? ? ? 1_555 C G 15 O6 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 14 O2 ? ? ? 1_555 C G 15 N2 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 13 N3 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 13 O2 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 13 N4 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C U 2 N3 ? ? ? 1_555 D A 12 N1 ? ? C U 3 D A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C U 2 O4 ? ? ? 1_555 D A 12 N6 ? ? C U 3 D A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 11 N3 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 11 O2 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 11 N4 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 10 N3 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 10 O2 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 10 N4 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C U 5 N3 ? ? ? 1_555 D A 9 N1 ? ? C U 6 D A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C U 5 O4 ? ? ? 1_555 D A 9 N6 ? ? C U 6 D A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 6 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 7 D C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 6 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 7 D C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 6 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 7 D C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C G 9 N1 ? ? ? 1_555 D C 6 N3 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C G 9 N2 ? ? ? 1_555 D C 6 O2 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C G 9 O6 ? ? ? 1_555 D C 6 N4 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 4 N1 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 4 O6 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 4 N2 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C G 12 N1 ? ? ? 1_555 D C 3 N3 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C G 12 N2 ? ? ? 1_555 D C 3 O2 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C G 12 O6 ? ? ? 1_555 D C 3 N4 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C G 14 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 15 D C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C G 14 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 15 D C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C G 14 O6 ? ? ? 1_555 D C 1 N4 ? ? C G 15 D C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id O20 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id F _pdbx_struct_conn_angle.ptnr1_label_comp_id NMY _pdbx_struct_conn_angle.ptnr1_label_seq_id . _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id NMY _pdbx_struct_conn_angle.ptnr1_auth_seq_id 18 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 2_664 _pdbx_struct_conn_angle.ptnr2_label_atom_id MG _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id J _pdbx_struct_conn_angle.ptnr2_label_comp_id MG _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id C _pdbx_struct_conn_angle.ptnr2_auth_comp_id MG _pdbx_struct_conn_angle.ptnr2_auth_seq_id 48 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id N7 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id C _pdbx_struct_conn_angle.ptnr3_label_comp_id G _pdbx_struct_conn_angle.ptnr3_label_seq_id 1 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id C _pdbx_struct_conn_angle.ptnr3_auth_comp_id G _pdbx_struct_conn_angle.ptnr3_auth_seq_id 2 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 60.6 _pdbx_struct_conn_angle.value_esd ? # 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 C NMY 1 ? 13 'BINDING SITE FOR RESIDUE NMY C 1' AC2 Software A NMY 17 ? 11 'BINDING SITE FOR RESIDUE NMY A 17' AC3 Software C NMY 17 ? 11 'BINDING SITE FOR RESIDUE NMY C 17' AC4 Software A NMY 18 ? 12 'BINDING SITE FOR RESIDUE NMY A 18' AC5 Software A MG 41 ? 1 'BINDING SITE FOR RESIDUE MG A 41' AC6 Software C MG 48 ? 2 'BINDING SITE FOR RESIDUE MG C 48' 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 13 U C 5 ? U C 6 . ? 1_555 ? 2 AC1 13 G C 6 ? G C 7 . ? 1_555 ? 3 AC1 13 A C 7 ? A C 8 . ? 1_555 ? 4 AC1 13 A C 8 ? A C 9 . ? 1_555 ? 5 AC1 13 G C 9 ? G C 10 . ? 1_555 ? 6 AC1 13 U C 10 ? U C 11 . ? 1_555 ? 7 AC1 13 HOH M . ? HOH C 50 . ? 1_555 ? 8 AC1 13 HOH M . ? HOH C 51 . ? 1_555 ? 9 AC1 13 G D 4 ? G D 24 . ? 1_555 ? 10 AC1 13 U D 5 ? U D 25 . ? 1_555 ? 11 AC1 13 C D 6 ? C D 26 . ? 1_555 ? 12 AC1 13 A D 7 ? A D 27 . ? 1_555 ? 13 AC1 13 C D 8 ? C D 28 . ? 1_555 ? 14 AC2 11 U A 5 ? U A 6 . ? 1_555 ? 15 AC2 11 G A 6 ? G A 7 . ? 1_555 ? 16 AC2 11 A A 7 ? A A 8 . ? 1_555 ? 17 AC2 11 A A 8 ? A A 9 . ? 1_555 ? 18 AC2 11 G A 9 ? G A 10 . ? 1_555 ? 19 AC2 11 U A 10 ? U A 11 . ? 1_555 ? 20 AC2 11 G B 4 ? G B 24 . ? 1_555 ? 21 AC2 11 U B 5 ? U B 25 . ? 1_555 ? 22 AC2 11 C B 6 ? C B 26 . ? 1_555 ? 23 AC2 11 A B 7 ? A B 27 . ? 1_555 ? 24 AC2 11 C B 8 ? C B 28 . ? 1_555 ? 25 AC3 11 G A 1 ? G A 2 . ? 1_555 ? 26 AC3 11 C B 13 ? C B 33 . ? 1_555 ? 27 AC3 11 C B 14 ? C B 34 . ? 1_555 ? 28 AC3 11 U C 10 ? U C 11 . ? 1_555 ? 29 AC3 11 C C 11 ? C C 12 . ? 1_555 ? 30 AC3 11 C C 13 ? C C 14 . ? 1_555 ? 31 AC3 11 G C 14 ? G C 15 . ? 1_555 ? 32 AC3 11 G C 15 ? G C 16 . ? 1_555 ? 33 AC3 11 A D 12 ? A D 32 . ? 4_465 ? 34 AC3 11 C D 13 ? C D 33 . ? 4_465 ? 35 AC3 11 C D 14 ? C D 34 . ? 4_465 ? 36 AC4 12 U A 10 ? U A 11 . ? 1_555 ? 37 AC4 12 C A 11 ? C A 12 . ? 1_555 ? 38 AC4 12 C A 13 ? C A 14 . ? 1_555 ? 39 AC4 12 G A 14 ? G A 15 . ? 1_555 ? 40 AC4 12 G A 15 ? G A 16 . ? 1_555 ? 41 AC4 12 A B 12 ? A B 32 . ? 3_645 ? 42 AC4 12 C B 13 ? C B 33 . ? 3_645 ? 43 AC4 12 C B 14 ? C B 34 . ? 3_645 ? 44 AC4 12 G C 1 ? G C 2 . ? 2_665 ? 45 AC4 12 MG J . ? MG C 48 . ? 2_665 ? 46 AC4 12 C D 13 ? C D 33 . ? 2_665 ? 47 AC4 12 C D 14 ? C D 34 . ? 2_665 ? 48 AC5 1 G A 1 ? G A 2 . ? 1_555 ? 49 AC6 2 NMY F . ? NMY A 18 . ? 2_664 ? 50 AC6 2 G C 1 ? G C 2 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 D _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 10 _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 D _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 14 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.08 # 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 3 ? ? 0.064 'SIDE CHAIN' 2 1 U D 25 ? ? 0.074 'SIDE CHAIN' 3 1 A D 29 ? ? 0.055 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text bisintercalation # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 NMY C1 C N R 115 NMY O1 O N N 116 NMY C2 C N R 117 NMY N2 N N N 118 NMY C3 C N R 119 NMY O3 O N N 120 NMY C4 C N S 121 NMY O4 O N N 122 NMY C5 C N R 123 NMY O5 O N N 124 NMY C6 C N N 125 NMY C7 C N R 126 NMY N7 N N N 127 NMY C12 C N S 128 NMY C11 C N R 129 NMY O11 O N N 130 NMY C10 C N R 131 NMY C9 C N S 132 NMY N9 N N N 133 NMY C8 C N N 134 NMY C13 C N S 135 NMY C14 C N R 136 NMY C15 C N S 137 NMY C16 C N R 138 NMY O16 O N N 139 NMY C17 C N N 140 NMY C21 C N S 141 NMY C20 C N R 142 NMY C19 C N R 143 NMY C18 C N R 144 NMY O18 O N N 145 NMY C22 C N S 146 NMY O22 O N N 147 NMY C23 C N N 148 NMY N6 N N N 149 NMY O14 O N N 150 NMY O20 O N N 151 NMY O21 O N N 152 NMY O17 O N N 153 NMY O12 O N N 154 NMY N19 N N N 155 NMY N23 N N N 156 NMY H1 H N N 157 NMY H2 H N N 158 NMY HN21 H N N 159 NMY HN22 H N N 160 NMY H3 H N N 161 NMY HO3 H N N 162 NMY H4 H N N 163 NMY HO4 H N N 164 NMY H5 H N N 165 NMY H61 H N N 166 NMY H62 H N N 167 NMY H7 H N N 168 NMY H71 H N N 169 NMY H72 H N N 170 NMY H12 H N N 171 NMY H11 H N N 172 NMY H10 H N N 173 NMY H9 H N N 174 NMY H91 H N N 175 NMY H92 H N N 176 NMY H81 H N N 177 NMY H82 H N N 178 NMY H13 H N N 179 NMY H14 H N N 180 NMY H15 H N N 181 NMY H16 H N N 182 NMY H171 H N N 183 NMY H172 H N N 184 NMY H21 H N N 185 NMY H20 H N N 186 NMY H19 H N N 187 NMY H18 H N N 188 NMY H22 H N N 189 NMY H231 H N N 190 NMY H232 H N N 191 NMY HN61 H N N 192 NMY HN62 H N N 193 NMY HO41 H N N 194 NMY HO22 H N N 195 NMY HO21 H N N 196 NMY H17 H N N 197 NMY HO12 H N N 198 NMY H191 H N N 199 NMY H192 H N N 200 NMY HN31 H N N 201 NMY HN32 H N N 202 U OP3 O N N 203 U P P N N 204 U OP1 O N N 205 U OP2 O N N 206 U "O5'" O N N 207 U "C5'" C N N 208 U "C4'" C N R 209 U "O4'" O N N 210 U "C3'" C N S 211 U "O3'" O N N 212 U "C2'" C N R 213 U "O2'" O N N 214 U "C1'" C N R 215 U N1 N N N 216 U C2 C N N 217 U O2 O N N 218 U N3 N N N 219 U C4 C N N 220 U O4 O N N 221 U C5 C N N 222 U C6 C N N 223 U HOP3 H N N 224 U HOP2 H N N 225 U "H5'" H N N 226 U "H5''" H N N 227 U "H4'" H N N 228 U "H3'" H N N 229 U "HO3'" H N N 230 U "H2'" H N N 231 U "HO2'" H N N 232 U "H1'" H N N 233 U H3 H N N 234 U H5 H N N 235 U H6 H N N 236 # 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 NMY C1 O5 sing N N 118 NMY C1 O1 sing N N 119 NMY C1 C2 sing N N 120 NMY C1 H1 sing N N 121 NMY O1 C10 sing N N 122 NMY C2 N2 sing N N 123 NMY C2 C3 sing N N 124 NMY C2 H2 sing N N 125 NMY N2 HN21 sing N N 126 NMY N2 HN22 sing N N 127 NMY C3 C4 sing N N 128 NMY C3 O3 sing N N 129 NMY C3 H3 sing N N 130 NMY O3 HO3 sing N N 131 NMY C4 C5 sing N N 132 NMY C4 O4 sing N N 133 NMY C4 H4 sing N N 134 NMY O4 HO4 sing N N 135 NMY C5 O5 sing N N 136 NMY C5 C6 sing N N 137 NMY C5 H5 sing N N 138 NMY C6 N6 sing N N 139 NMY C6 H61 sing N N 140 NMY C6 H62 sing N N 141 NMY C7 N7 sing N N 142 NMY C7 C12 sing N N 143 NMY C7 C8 sing N N 144 NMY C7 H7 sing N N 145 NMY N7 H71 sing N N 146 NMY N7 H72 sing N N 147 NMY C12 O12 sing N N 148 NMY C12 C11 sing N N 149 NMY C12 H12 sing N N 150 NMY C11 O11 sing N N 151 NMY C11 C10 sing N N 152 NMY C11 H11 sing N N 153 NMY O11 C13 sing N N 154 NMY C10 C9 sing N N 155 NMY C10 H10 sing N N 156 NMY C9 C8 sing N N 157 NMY C9 N9 sing N N 158 NMY C9 H9 sing N N 159 NMY N9 H91 sing N N 160 NMY N9 H92 sing N N 161 NMY C8 H81 sing N N 162 NMY C8 H82 sing N N 163 NMY C13 C14 sing N N 164 NMY C13 O16 sing N N 165 NMY C13 H13 sing N N 166 NMY C14 O14 sing N N 167 NMY C14 C15 sing N N 168 NMY C14 H14 sing N N 169 NMY C15 O18 sing N N 170 NMY C15 C16 sing N N 171 NMY C15 H15 sing N N 172 NMY C16 O16 sing N N 173 NMY C16 C17 sing N N 174 NMY C16 H16 sing N N 175 NMY C17 O17 sing N N 176 NMY C17 H171 sing N N 177 NMY C17 H172 sing N N 178 NMY C21 C20 sing N N 179 NMY C21 C22 sing N N 180 NMY C21 O21 sing N N 181 NMY C21 H21 sing N N 182 NMY C20 C19 sing N N 183 NMY C20 O20 sing N N 184 NMY C20 H20 sing N N 185 NMY C19 N23 sing N N 186 NMY C19 C18 sing N N 187 NMY C19 H19 sing N N 188 NMY C18 O22 sing N N 189 NMY C18 O18 sing N N 190 NMY C18 H18 sing N N 191 NMY C22 O22 sing N N 192 NMY C22 C23 sing N N 193 NMY C22 H22 sing N N 194 NMY C23 N19 sing N N 195 NMY C23 H231 sing N N 196 NMY C23 H232 sing N N 197 NMY N6 HN61 sing N N 198 NMY N6 HN62 sing N N 199 NMY O14 HO41 sing N N 200 NMY O20 HO22 sing N N 201 NMY O21 HO21 sing N N 202 NMY O17 H17 sing N N 203 NMY O12 HO12 sing N N 204 NMY N19 H191 sing N N 205 NMY N19 H192 sing N N 206 NMY N23 HN31 sing N N 207 NMY N23 HN32 sing N N 208 U OP3 P sing N N 209 U OP3 HOP3 sing N N 210 U P OP1 doub N N 211 U P OP2 sing N N 212 U P "O5'" sing N N 213 U OP2 HOP2 sing N N 214 U "O5'" "C5'" sing N N 215 U "C5'" "C4'" sing N N 216 U "C5'" "H5'" sing N N 217 U "C5'" "H5''" sing N N 218 U "C4'" "O4'" sing N N 219 U "C4'" "C3'" sing N N 220 U "C4'" "H4'" sing N N 221 U "O4'" "C1'" sing N N 222 U "C3'" "O3'" sing N N 223 U "C3'" "C2'" sing N N 224 U "C3'" "H3'" sing N N 225 U "O3'" "HO3'" sing N N 226 U "C2'" "O2'" sing N N 227 U "C2'" "C1'" sing N N 228 U "C2'" "H2'" sing N N 229 U "O2'" "HO2'" sing N N 230 U "C1'" N1 sing N N 231 U "C1'" "H1'" sing N N 232 U N1 C2 sing N N 233 U N1 C6 sing N N 234 U C2 O2 doub N N 235 U C2 N3 sing N N 236 U N3 C4 sing N N 237 U N3 H3 sing N N 238 U C4 O4 doub N N 239 U C4 C5 sing N N 240 U C5 C6 doub N N 241 U C5 H5 sing N N 242 U C6 H6 sing N N 243 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2A04 'double helix' 2A04 'a-form double helix' 2A04 'mismatched base pair' 2A04 '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 B C 8 1_555 A G 6 1_555 0.077 -0.483 0.124 4.495 -15.722 1.386 1 B_C28:G7_A B 28 ? A 7 ? 19 1 1 B A 9 1_555 A U 5 1_555 -0.671 -0.257 0.090 2.541 -16.454 5.038 2 B_A29:U6_A B 29 ? A 6 ? 20 1 1 B C 10 1_555 A G 4 1_555 -0.503 -0.328 0.103 6.594 -16.728 -5.648 3 B_C30:G5_A B 30 ? A 5 ? 19 1 1 B C 11 1_555 A G 3 1_555 0.176 -0.099 -0.041 9.573 -16.381 -1.228 4 B_C31:G4_A B 31 ? A 4 ? 19 1 1 B A 12 1_555 A U 2 1_555 0.438 -0.372 0.283 -4.846 -14.155 -0.830 5 B_A32:U3_A B 32 ? A 3 ? 20 1 1 B C 13 1_555 A G 1 1_555 0.544 -0.621 0.649 -8.915 -12.320 -8.094 6 B_C33:G2_A B 33 ? A 2 ? 19 1 1 B C 14 1_555 C G 15 1_555 0.507 -0.413 -0.135 7.293 -10.306 -1.329 7 B_C34:G16_C B 34 ? C 16 ? 19 1 1 D C 1 1_555 C G 14 1_555 0.723 -0.320 -0.272 8.580 -13.705 2.714 8 D_C21:G15_C D 21 ? C 15 ? 19 1 1 D G 2 1_555 C C 13 1_555 0.048 0.009 -0.325 -7.577 -14.663 11.598 9 D_G22:C14_C D 22 ? C 14 ? 19 1 1 D C 3 1_555 C G 12 1_555 0.308 0.047 0.015 1.789 -6.758 4.752 10 D_C23:G13_C D 23 ? C 13 ? 19 1 1 D G 4 1_555 C C 11 1_555 0.489 -0.117 0.243 -0.655 -7.058 0.390 11 D_G24:C12_C D 24 ? C 12 ? 19 1 1 A G 9 1_555 B C 6 1_555 -0.279 -0.216 -0.084 -8.104 -0.135 -3.253 12 A_G10:C26_B A 10 ? B 26 ? 19 1 1 A U 10 1_555 B U 5 1_555 1.715 -0.977 -0.499 -5.230 -13.708 -19.105 13 A_U11:U25_B A 11 ? B 25 ? ? ? 1 A C 11 1_555 B G 4 1_555 -0.239 -0.107 0.160 -2.575 -3.950 4.579 14 A_C12:G24_B A 12 ? B 24 ? 19 1 1 A G 12 1_555 B C 3 1_555 0.083 -0.084 0.004 -3.643 -10.306 1.611 15 A_G13:C23_B A 13 ? B 23 ? 19 1 1 A C 13 1_555 B G 2 1_555 1.527 0.178 0.396 -5.474 -10.442 17.137 16 A_C14:G22_B A 14 ? B 22 ? ? 1 1 A G 14 1_555 B C 1 1_555 -0.207 -0.233 -0.136 -2.171 -9.637 2.651 17 A_G15:C21_B A 15 ? B 21 ? 19 1 1 C G 1 1_555 D C 13 1_555 -0.148 -0.352 0.711 7.891 -13.035 -6.281 18 C_G2:C33_D C 2 ? D 33 ? 19 1 1 C U 2 1_555 D A 12 1_555 -0.346 -0.380 0.243 4.714 -15.366 -0.779 19 C_U3:A32_D C 3 ? D 32 ? 20 1 1 C G 3 1_555 D C 11 1_555 -0.096 -0.030 0.066 -2.537 -10.564 -4.792 20 C_G4:C31_D C 4 ? D 31 ? 19 1 1 C G 4 1_555 D C 10 1_555 0.576 0.000 0.100 -2.338 -11.540 1.319 21 C_G5:C30_D C 5 ? D 30 ? 19 1 1 C U 5 1_555 D A 9 1_555 0.184 -0.134 0.184 -0.870 -15.714 7.659 22 C_U6:A29_D C 6 ? D 29 ? 20 1 1 C G 6 1_555 D C 8 1_555 -0.081 -0.429 0.189 -1.150 -15.336 0.131 23 C_G7:C28_D C 7 ? D 28 ? 19 1 1 C G 9 1_555 D C 6 1_555 -0.356 -0.220 -0.028 5.249 4.059 2.339 24 C_G10:C26_D C 10 ? D 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 B C 8 1_555 A G 6 1_555 B A 9 1_555 A U 5 1_555 0.259 -1.629 3.158 -0.211 13.310 29.861 -4.899 -0.493 2.246 24.364 0.386 32.632 1 BB_C28A29:U6G7_AA B 28 ? A 7 ? B 29 ? A 6 ? 1 B A 9 1_555 A U 5 1_555 B C 10 1_555 A G 4 1_555 -0.771 -1.201 3.200 -1.756 1.353 31.922 -2.417 1.090 3.185 2.456 3.188 31.997 2 BB_A29C30:G5U6_AA B 29 ? A 6 ? B 30 ? A 5 ? 1 B C 10 1_555 A G 4 1_555 B C 11 1_555 A G 3 1_555 0.703 -1.754 3.245 5.391 4.858 35.411 -3.497 -0.392 3.056 7.885 -8.750 36.123 3 BB_C30C31:G4G5_AA B 30 ? A 5 ? B 31 ? A 4 ? 1 B C 11 1_555 A G 3 1_555 B A 12 1_555 A U 2 1_555 0.508 -1.928 3.398 1.136 14.642 32.800 -5.072 -0.675 2.367 24.460 -1.898 35.855 4 BB_C31A32:U3G4_AA B 31 ? A 4 ? B 32 ? A 3 ? 1 B A 12 1_555 A U 2 1_555 B C 13 1_555 A G 1 1_555 -0.339 -1.815 3.285 1.621 2.281 35.623 -3.282 0.783 3.148 3.721 -2.645 35.729 5 BB_A32C33:G2U3_AA B 32 ? A 3 ? B 33 ? A 2 ? 1 B C 13 1_555 A G 1 1_555 B C 14 1_555 C G 15 1_555 -2.523 -1.303 2.837 5.069 6.222 8.316 -11.248 16.421 0.238 34.155 -27.823 11.552 6 BB_C33C34:G16G2_CA B 33 ? A 2 ? B 34 ? C 16 ? 1 B C 14 1_555 C G 15 1_555 D C 1 1_555 C G 14 1_555 -0.949 -1.838 3.435 0.096 -0.834 39.992 -2.586 1.399 3.469 -1.220 -0.141 40.001 7 BD_C34C21:G15G16_CC B 34 ? C 16 ? D 21 ? C 15 ? 1 D C 1 1_555 C G 14 1_555 D G 2 1_555 C C 13 1_555 -0.091 -1.600 3.698 3.113 13.838 22.784 -7.032 1.001 2.327 31.420 -7.068 26.788 8 DD_C21G22:C14G15_CC D 21 ? C 15 ? D 22 ? C 14 ? 1 D G 2 1_555 C C 13 1_555 D C 3 1_555 C G 12 1_555 -0.253 -1.004 3.040 -2.549 7.617 34.021 -2.710 0.075 2.769 12.798 4.283 34.929 9 DD_G22C23:G13C14_CC D 22 ? C 14 ? D 23 ? C 13 ? 1 D C 3 1_555 C G 12 1_555 D G 4 1_555 C C 11 1_555 -0.230 -1.709 3.136 -0.517 4.732 31.367 -3.928 0.333 2.858 8.689 0.948 31.718 10 DD_C23G24:C12G13_CC D 23 ? C 13 ? D 24 ? C 12 ? 1 A G 9 1_555 B C 6 1_555 A U 10 1_555 B U 5 1_555 -1.981 -2.406 3.168 1.918 2.700 39.626 -3.829 3.120 2.909 3.974 -2.824 39.758 11 AA_G10U11:U25C26_BB A 10 ? B 26 ? A 11 ? B 25 ? 1 A U 10 1_555 B U 5 1_555 A C 11 1_555 B G 4 1_555 0.731 -2.321 3.281 -6.228 2.239 20.919 -6.913 -4.178 2.692 5.976 16.626 21.930 12 AA_U11C12:G24U25_BB A 11 ? B 25 ? A 12 ? B 24 ? 1 A C 11 1_555 B G 4 1_555 A G 12 1_555 B C 3 1_555 -0.117 -1.723 3.163 -0.406 4.623 32.410 -3.800 0.142 2.898 8.230 0.723 32.732 13 AA_C12G13:C23G24_BB A 12 ? B 24 ? A 13 ? B 23 ? 1 A G 12 1_555 B C 3 1_555 A C 13 1_555 B G 2 1_555 0.484 -0.939 3.346 -0.737 4.726 37.135 -2.087 -0.852 3.197 7.384 1.152 37.431 14 AA_G13C14:G22C23_BB A 13 ? B 23 ? A 14 ? B 22 ? 1 A C 13 1_555 B G 2 1_555 A G 14 1_555 B C 1 1_555 -0.392 -1.995 2.993 1.610 9.778 20.130 -7.937 1.471 1.802 26.033 -4.287 22.415 15 AA_C14G15:C21G22_BB A 14 ? B 22 ? A 15 ? B 21 ? 1 C G 1 1_555 D C 13 1_555 C U 2 1_555 D A 12 1_555 0.153 -1.824 3.216 -0.616 2.350 35.754 -3.289 -0.334 3.091 3.821 1.002 35.834 16 CC_G2U3:A32C33_DD C 2 ? D 33 ? C 3 ? D 32 ? 1 C U 2 1_555 D A 12 1_555 C G 3 1_555 D C 11 1_555 -0.467 -2.200 3.208 -2.429 12.544 30.011 -5.801 0.470 2.169 22.958 4.446 32.560 17 CC_U3G4:C31A32_DD C 3 ? D 32 ? C 4 ? D 31 ? 1 C G 3 1_555 D C 11 1_555 C G 4 1_555 D C 10 1_555 -0.163 -1.521 3.367 -2.315 3.776 38.638 -2.749 -0.039 3.214 5.684 3.485 38.881 18 CC_G4G5:C30C31_DD C 4 ? D 31 ? C 5 ? D 30 ? 1 C G 4 1_555 D C 10 1_555 C U 5 1_555 D A 9 1_555 0.696 -1.171 3.172 2.074 4.447 27.981 -3.359 -0.965 2.996 9.107 -4.248 28.400 19 CC_G5U6:A29C30_DD C 5 ? D 30 ? C 6 ? D 29 ? 1 C U 5 1_555 D A 9 1_555 C G 6 1_555 D C 8 1_555 -0.315 -1.796 3.098 -0.274 12.550 30.940 -4.898 0.510 2.224 22.403 0.490 33.332 20 CC_U6G7:C28A29_DD C 6 ? D 29 ? C 7 ? D 28 ? # _atom_sites.entry_id 2A04 _atom_sites.fract_transf_matrix[1][1] 0.020080 _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] 0.020040 _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] 0.006916 _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 MG N O P # loop_