data_1BGZ # _entry.id 1BGZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1BGZ pdb_00001bgz 10.2210/pdb1bgz/pdb WWPDB D_1000171745 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1BGZ _pdbx_database_status.recvd_initial_deposition_date 1998-06-03 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _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_ _audit_author.name _audit_author.pdbx_ordinal 'Kalurachchi, K.' 1 'Nikonowicz, E.P.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.' J.Mol.Biol. 280 639 654 1998 JMOBAK UK 0022-2836 0070 ? 9677294 10.1006/jmbi.1998.1915 1 'Binding Sites for Ribosomal Proteins S8 and S15 in the 16 S RNA of Escherichia Coli' Biochim.Biophys.Acta 563 422 ? 1979 BBACAQ NE 0006-3002 0113 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kalurachchi, K.' 1 ? primary 'Nikonowicz, E.P.' 2 ? 1 'Zimmermann, R.A.' 3 ? 1 'Singh-Bergmann, K.' 4 ? # _cell.entry_id 1BGZ _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BGZ _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description RNA _entity.formula_weight 7356.392 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment '16S RRNA BINDING SITE FOR S8' _entity.details 'RNA HAIRPIN' # _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 GGGAUACUGCUUCGGUAAGUCCC _entity_poly.pdbx_seq_one_letter_code_can GGGAUACUGCUUCGGUAAGUCCC _entity_poly.pdbx_strand_id A _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 G n 1 2 G n 1 3 G n 1 4 A n 1 5 U n 1 6 A n 1 7 C n 1 8 U n 1 9 G n 1 10 C n 1 11 U n 1 12 U n 1 13 C n 1 14 G n 1 15 G n 1 16 U n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 C n 1 23 C n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1BGZ _struct_ref.pdbx_db_accession 1BGZ _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1BGZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 23 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1BGZ _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 23 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 23 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 CT-HSQC 1 3 1 COSY 1 4 1 HETCOR 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure AMBIENT _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength '10mM NACL, 10mM POTASSIUM PHOSPHATE' _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents H2O/D2O # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AMX500 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1BGZ _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1BGZ _pdbx_nmr_details.text '2D AND 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS WERE USED TO OBTAIN DISTANCE AND TORSION ANGLE CONSTRAINTS.' # _pdbx_nmr_ensemble.entry_id 1BGZ _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 6 _pdbx_nmr_ensemble.conformer_selection_criteria 'FEWEST RESTRAINT VIOLATIONS' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR ? ? 2 # _exptl.entry_id 1BGZ _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1BGZ _struct.title 'S8 RRNA BINDING SITE FROM E. COLI, NMR, 6 STRUCTURES' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1BGZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RIBONUCLEIC ACID, 16S RRNA, INTERNAL LOOP, BASE TRIPLE, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 4 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 4 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 O2 ? ? ? 1_555 A C 7 N4 ? ? A U 5 A C 7 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog13 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 20 O2 ? ? A A 6 A U 20 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 7 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 7 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 7 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 8 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 8 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N1 ? ? ? 1_555 A U 16 O2 ? ? A G 9 A U 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog20 hydrog ? ? A G 9 O6 ? ? ? 1_555 A U 16 N3 ? ? A G 9 A U 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 10 A G 15 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog22 hydrog ? ? A A 17 N3 ? ? ? 1_555 A A 18 N6 ? ? A A 17 A A 18 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1BGZ _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 1BGZ _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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 H 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 A 4 4 4 A A A . n A 1 5 U 5 5 5 U U A . n A 1 6 A 6 6 6 A A A . n A 1 7 C 7 7 7 C C A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n A 1 11 U 11 11 11 U U A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 G 15 15 15 G G A . n A 1 16 U 16 16 16 U U 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 C 22 22 22 C C A . n A 1 23 C 23 23 23 C C A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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_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 1999-01-13 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other # 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' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # 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_database_status.process_site' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # 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 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.64 113.10 4.54 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.70 106.40 -2.70 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.65 113.10 4.55 0.50 N 4 1 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.64 106.40 -2.76 0.40 N 5 1 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.57 113.10 4.47 0.50 N 6 1 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.75 106.40 -2.65 0.40 N 7 1 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.48 113.80 3.68 0.50 N 8 1 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.54 113.80 3.74 0.50 N 9 1 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.65 113.10 4.55 0.50 N 10 1 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.71 106.40 -2.69 0.40 N 11 1 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.62 113.10 4.52 0.50 N 12 1 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.68 106.40 -2.72 0.40 N 13 1 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.63 113.10 4.53 0.50 N 14 1 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.67 106.40 -2.73 0.40 N 15 1 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.63 113.80 3.83 0.50 N 16 1 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.53 113.80 3.73 0.50 N 17 1 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.63 113.10 4.53 0.50 N 18 1 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.67 106.40 -2.73 0.40 N 19 2 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.65 113.10 4.55 0.50 N 20 2 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.71 106.40 -2.69 0.40 N 21 2 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.70 113.10 4.60 0.50 N 22 2 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.63 106.40 -2.77 0.40 N 23 2 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.71 113.10 4.61 0.50 N 24 2 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.62 106.40 -2.78 0.40 N 25 2 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.59 113.80 3.79 0.50 N 26 2 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.47 113.80 3.67 0.50 N 27 2 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.58 113.10 4.48 0.50 N 28 2 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.77 106.40 -2.63 0.40 N 29 2 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.71 113.10 4.61 0.50 N 30 2 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.70 106.40 -2.70 0.40 N 31 2 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.64 113.10 4.54 0.50 N 32 2 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.74 106.40 -2.66 0.40 N 33 2 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.35 113.80 3.55 0.50 N 34 2 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.54 113.80 3.74 0.50 N 35 2 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.67 113.10 4.57 0.50 N 36 2 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.63 106.40 -2.77 0.40 N 37 3 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.64 113.10 4.54 0.50 N 38 3 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.70 106.40 -2.70 0.40 N 39 3 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.69 113.10 4.59 0.50 N 40 3 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.66 106.40 -2.74 0.40 N 41 3 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.63 113.10 4.53 0.50 N 42 3 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.64 106.40 -2.76 0.40 N 43 3 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.46 113.80 3.66 0.50 N 44 3 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.57 113.80 3.77 0.50 N 45 3 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.65 113.10 4.55 0.50 N 46 3 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.62 106.40 -2.78 0.40 N 47 3 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.65 113.10 4.55 0.50 N 48 3 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.60 106.40 -2.80 0.40 N 49 3 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.65 113.10 4.55 0.50 N 50 3 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.66 106.40 -2.74 0.40 N 51 3 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.63 113.80 3.83 0.50 N 52 3 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.57 113.80 3.77 0.50 N 53 3 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.64 113.10 4.54 0.50 N 54 3 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.61 106.40 -2.79 0.40 N 55 4 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.72 113.10 4.62 0.50 N 56 4 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.66 106.40 -2.74 0.40 N 57 4 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.67 113.10 4.57 0.50 N 58 4 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.70 106.40 -2.70 0.40 N 59 4 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.63 113.10 4.53 0.50 N 60 4 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.68 106.40 -2.72 0.40 N 61 4 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.56 113.80 3.76 0.50 N 62 4 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.55 113.80 3.75 0.50 N 63 4 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.57 113.10 4.47 0.50 N 64 4 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.77 106.40 -2.63 0.40 N 65 4 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.75 113.10 4.65 0.50 N 66 4 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.64 106.40 -2.76 0.40 N 67 4 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.76 113.10 4.66 0.50 N 68 4 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.67 106.40 -2.73 0.40 N 69 4 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.64 113.80 3.84 0.50 N 70 4 C8 A A 17 ? ? N9 A A 17 ? ? C4 A A 17 ? ? 103.39 105.80 -2.41 0.40 N 71 4 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.54 113.80 3.74 0.50 N 72 4 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.64 113.10 4.54 0.50 N 73 4 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.69 106.40 -2.71 0.40 N 74 5 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.78 113.10 4.68 0.50 N 75 5 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.61 106.40 -2.79 0.40 N 76 5 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.73 113.10 4.63 0.50 N 77 5 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.62 106.40 -2.78 0.40 N 78 5 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.62 113.10 4.52 0.50 N 79 5 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.70 106.40 -2.70 0.40 N 80 5 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.54 113.80 3.74 0.50 N 81 5 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.56 113.80 3.76 0.50 N 82 5 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.64 113.10 4.54 0.50 N 83 5 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.70 106.40 -2.70 0.40 N 84 5 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.77 113.10 4.67 0.50 N 85 5 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.60 106.40 -2.80 0.40 N 86 5 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.57 113.10 4.47 0.50 N 87 5 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.81 106.40 -2.59 0.40 N 88 5 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.48 113.80 3.68 0.50 N 89 5 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.50 113.80 3.70 0.50 N 90 5 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.61 113.10 4.51 0.50 N 91 5 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.73 106.40 -2.67 0.40 N 92 6 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.63 113.10 4.53 0.50 N 93 6 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.66 106.40 -2.74 0.40 N 94 6 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.62 113.10 4.52 0.50 N 95 6 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.68 106.40 -2.72 0.40 N 96 6 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.61 113.10 4.51 0.50 N 97 6 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.75 106.40 -2.65 0.40 N 98 6 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.50 113.80 3.70 0.50 N 99 6 N7 A A 6 ? ? C8 A A 6 ? ? N9 A A 6 ? ? 117.55 113.80 3.75 0.50 N 100 6 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.61 113.10 4.51 0.50 N 101 6 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.71 106.40 -2.69 0.40 N 102 6 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.77 113.10 4.67 0.50 N 103 6 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.55 106.40 -2.85 0.40 N 104 6 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.72 113.10 4.62 0.50 N 105 6 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.68 106.40 -2.72 0.40 N 106 6 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.60 113.80 3.80 0.50 N 107 6 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.63 113.80 3.83 0.50 N 108 6 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 117.67 113.10 4.57 0.50 N 109 6 C8 A G 19 ? ? N9 A G 19 ? ? C4 A G 19 ? ? 103.66 106.40 -2.74 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1BGZ 'double helix' 1BGZ 'a-form double helix' 1BGZ 'hairpin loop' 1BGZ 'bulge loop' 1BGZ 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 23 1_555 0.076 -0.282 1.437 -9.777 15.326 16.116 1 A_G1:C23_A A 1 ? A 23 ? 19 1 1 A G 2 1_555 A C 22 1_555 0.348 -0.145 1.326 -2.693 9.656 12.572 2 A_G2:C22_A A 2 ? A 22 ? 19 1 1 A G 3 1_555 A C 21 1_555 0.482 0.304 -0.762 -22.683 -7.298 7.070 3 A_G3:C21_A A 3 ? A 21 ? 19 1 1 A A 4 1_555 A U 20 1_555 0.156 0.118 0.253 -9.044 2.336 -7.177 4 A_A4:U20_A A 4 ? A 20 ? 20 1 1 A C 7 1_555 A G 19 1_555 -0.337 0.283 0.036 17.296 -8.867 6.132 5 A_C7:G19_A A 7 ? A 19 ? 19 1 1 A U 8 1_555 A A 18 1_555 0.283 0.089 -0.731 -6.144 -12.504 -9.933 6 A_U8:A18_A A 8 ? A 18 ? 20 1 1 A G 9 1_555 A U 16 1_555 -1.720 -0.453 0.797 -5.092 -23.451 -12.354 7 A_G9:U16_A A 9 ? A 16 ? 28 ? 1 A C 10 1_555 A G 15 1_555 1.687 -0.328 0.570 5.337 7.829 -7.928 8 A_C10:G15_A A 10 ? A 15 ? ? ? # 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 1 1_555 A C 23 1_555 A G 2 1_555 A C 22 1_555 -0.051 -1.702 3.146 2.283 14.400 32.620 -4.575 0.367 2.214 24.188 -3.834 35.649 1 AA_G1G2:C22C23_AA A 1 ? A 23 ? A 2 ? A 22 ? 1 A G 2 1_555 A C 22 1_555 A G 3 1_555 A C 21 1_555 -0.047 -2.060 4.528 12.371 4.457 29.458 -4.781 3.047 3.855 8.265 -22.942 32.200 2 AA_G2G3:C21C22_AA A 2 ? A 22 ? A 3 ? A 21 ? 1 A G 3 1_555 A C 21 1_555 A A 4 1_555 A U 20 1_555 -1.055 -1.822 3.305 -6.356 -12.379 29.288 -0.738 0.593 3.883 -22.922 11.770 32.360 3 AA_G3A4:U20C21_AA A 3 ? A 21 ? A 4 ? A 20 ? 1 A A 4 1_555 A U 20 1_555 A C 7 1_555 A G 19 1_555 -4.651 -1.209 4.577 21.821 -17.327 68.800 -0.306 4.769 3.358 -14.741 -18.564 73.579 4 AA_A4C7:G19U20_AA A 4 ? A 20 ? A 7 ? A 19 ? 1 A C 7 1_555 A G 19 1_555 A U 8 1_555 A A 18 1_555 -1.254 -1.746 4.769 6.790 -7.519 29.357 -1.117 4.284 4.664 -14.310 -12.923 31.019 5 AA_C7U8:A18G19_AA A 7 ? A 19 ? A 8 ? A 18 ? 1 A U 8 1_555 A A 18 1_555 A G 9 1_555 A U 16 1_555 3.327 -0.754 2.999 -7.891 23.537 55.112 -1.709 -3.645 2.098 24.123 8.087 60.043 6 AA_U8G9:U16A18_AA A 8 ? A 18 ? A 9 ? A 16 ? 1 A G 9 1_555 A U 16 1_555 A C 10 1_555 A G 15 1_555 -0.372 -0.632 3.665 -1.251 7.407 38.378 -1.930 0.389 3.498 11.138 1.880 39.079 7 AA_G9C10:G15U16_AA A 9 ? A 16 ? A 10 ? A 15 ? #