data_1ZZ5 # _entry.id 1ZZ5 # _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 1ZZ5 pdb_00001zz5 10.2210/pdb1zz5/pdb NDB DR0013 ? ? RCSB RCSB033291 ? ? WWPDB D_1000033291 ? ? # 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_seq_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.value' 6 4 'Structure model' '_struct_conn.pdbx_dist_value' 7 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ZZ5 _pdbx_database_status.recvd_initial_deposition_date 2005-06-13 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1ZX7 _pdbx_database_related.details . _pdbx_database_related.content_type 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 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer syn ;13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12-TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3-B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2,6-DIDEOXYHEXOPYRANOSIDE ; 596.628 4 ? ? ? ? 5 water nat water 18.015 25 ? ? ? ? # 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 'MAGNESIUM ION' MG 4 ;13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12-TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3-B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2,6-DIDEOXYHEXOPYRANOSIDE ; CNY 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 3' 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 CNY non-polymer . ;13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12-TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3-B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2,6-DIDEOXYHEXOPYRANOSIDE ; 'CYCLIC NEOMYCIN' 'C23 H44 N6 O12' 596.628 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 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 MG 1 100 100 MG MG A . F 4 CNY 1 42 2 CNY NCY A . G 4 CNY 1 43 3 CNY NCY A . H 4 CNY 1 41 1 CNY NCY C . I 4 CNY 1 44 4 CNY NCY C . J 3 MG 1 200 200 MG MG D . K 5 HOH 1 101 1 HOH TIP A . K 5 HOH 2 102 2 HOH TIP A . K 5 HOH 3 103 5 HOH TIP A . K 5 HOH 4 104 7 HOH TIP A . K 5 HOH 5 105 11 HOH TIP A . K 5 HOH 6 106 12 HOH TIP A . K 5 HOH 7 107 13 HOH TIP A . K 5 HOH 8 108 14 HOH TIP A . K 5 HOH 9 109 15 HOH TIP A . K 5 HOH 10 110 16 HOH TIP A . L 5 HOH 1 6 6 HOH TIP B . L 5 HOH 2 37 37 HOH TIP B . M 5 HOH 1 45 3 HOH TIP C . M 5 HOH 2 46 9 HOH TIP C . M 5 HOH 3 47 21 HOH TIP C . M 5 HOH 4 48 33 HOH TIP C . M 5 HOH 5 49 38 HOH TIP C . N 5 HOH 1 201 22 HOH TIP D . N 5 HOH 2 202 23 HOH TIP D . N 5 HOH 3 203 24 HOH TIP D . N 5 HOH 4 204 25 HOH TIP D . N 5 HOH 5 205 26 HOH TIP D . N 5 HOH 6 206 30 HOH TIP D . N 5 HOH 7 207 31 HOH TIP D . N 5 HOH 8 208 32 HOH TIP D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SCALEPACK 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement . ? 4 HKL-2000 'data reduction' . ? 5 # _cell.entry_id 1ZZ5 _cell.length_a 50.740 _cell.length_b 50.750 _cell.length_c 144.720 _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 1ZZ5 _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 1ZZ5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.4 _exptl_crystal.density_percent_sol 72.0 _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 5.6 _exptl_crystal_grow.pdbx_details 'MPD, magnesium acetate, cacodylate, pH 5.6, EVAPORATION, temperature 298K' _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 'magnesium acetate' ? ? ? 1 3 1 cacodylate ? ? ? 1 4 1 h2o ? ? ? 1 5 2 MPD ? ? ? 1 6 2 'magnesium acetate' ? ? ? 1 7 2 cacodylate ? ? ? 1 8 2 h2o ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103 _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 2005-03-30 _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9195 1.0 2 0.9202 1.0 3 0.9068 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-BM-C' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-BM-C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9195, 0.9202, 0.9068' # _reflns.entry_id 1ZZ5 _reflns.observed_criterion_sigma_F 3 _reflns.observed_criterion_sigma_I 3 _reflns.d_resolution_high 3.0 _reflns.d_resolution_low 30.0 _reflns.number_all 7800 _reflns.number_obs 6704 _reflns.percent_possible_obs 86.2 _reflns.pdbx_Rmerge_I_obs 0.046 _reflns.pdbx_Rsym_value 0.046 _reflns.pdbx_netI_over_sigmaI 26.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.1 _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 3.0 _reflns_shell.d_res_low 3.11 _reflns_shell.percent_possible_all 56.0 _reflns_shell.Rmerge_I_obs 0.162 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.3 _reflns_shell.pdbx_redundancy 2.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 434 _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 1ZZ5 _refine.ls_d_res_high 3.0 _refine.ls_d_res_low 8.0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_ls_sigma_I 0 _refine.ls_number_reflns_all 7462 _refine.ls_number_reflns_obs 5581 _refine.ls_number_reflns_R_free 606 _refine.ls_percent_reflns_obs 74.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.233 _refine.ls_R_factor_R_free 0.281 _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 MAD _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 ? _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 1ZZ5 _refine_analyze.Luzzati_coordinate_error_obs 0.44 _refine_analyze.Luzzati_sigma_a_obs 0.46 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.48 _refine_analyze.Luzzati_sigma_a_free 0.44 _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 166 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 1419 _refine_hist.d_res_high 3.0 _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 0.0081 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.1209 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 3.0 _refine_ls_shell.d_res_low 3.19 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.331 _refine_ls_shell.percent_reflns_obs 37.8 _refine_ls_shell.R_factor_R_free 0.362 _refine_ls_shell.R_factor_R_free_error 0.045 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 64 _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 1ZZ5 _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 1ZZ5 _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 1ZZ5 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Ribosome, RNA, A-site. double helix, restricted neomycin, cyclicneo, neocyclic' # 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 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 3 ? 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 1ZZ5 1ZZ5 ? ? ? 2 2 PDB 1ZZ5 1ZZ5 ? ? ? # 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 1ZZ5 A 1 ? 15 ? 1ZZ5 2 ? 16 ? 2 16 2 2 1ZZ5 B 1 ? 14 ? 1ZZ5 21 ? 34 ? 21 34 3 1 1ZZ5 C 1 ? 15 ? 1ZZ5 2 ? 16 ? 2 16 4 2 1ZZ5 D 1 ? 14 ? 1ZZ5 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 ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 105 1_555 ? ? ? ? ? ? ? 2.243 ? ? metalc2 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 106 1_555 ? ? ? ? ? ? ? 2.116 ? ? metalc3 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 107 1_555 ? ? ? ? ? ? ? 2.003 ? ? metalc4 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 108 1_555 ? ? ? ? ? ? ? 2.002 ? ? metalc5 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 109 1_555 ? ? ? ? ? ? ? 2.015 ? ? metalc6 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 100 A HOH 110 1_555 ? ? ? ? ? ? ? 2.170 ? ? metalc7 metalc ? ? M HOH . O ? ? ? 1_555 J MG . MG ? ? C HOH 47 D MG 200 1_555 ? ? ? ? ? ? ? 2.244 ? ? metalc8 metalc ? ? J MG . MG ? ? ? 1_555 N HOH . O ? ? D MG 200 D HOH 201 1_555 ? ? ? ? ? ? ? 2.117 ? ? metalc9 metalc ? ? J MG . MG ? ? ? 1_555 N HOH . O ? ? D MG 200 D HOH 202 1_555 ? ? ? ? ? ? ? 2.004 ? ? metalc10 metalc ? ? J MG . MG ? ? ? 1_555 N HOH . O ? ? D MG 200 D HOH 203 1_555 ? ? ? ? ? ? ? 2.001 ? ? metalc11 metalc ? ? J MG . MG ? ? ? 1_555 N HOH . O ? ? D MG 200 D HOH 204 1_555 ? ? ? ? ? ? ? 2.014 ? ? metalc12 metalc ? ? J MG . MG ? ? ? 1_555 N HOH . O ? ? D MG 200 D HOH 205 1_555 ? ? ? ? ? ? ? 2.169 ? ? 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 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 6 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 6 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 7 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 10 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 12 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 13 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 14 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 14 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 14 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 15 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 14 N3 ? ? ? 1_555 C G 15 N1 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 14 N4 ? ? ? 1_555 C G 15 O6 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 14 O2 ? ? ? 1_555 C G 15 N2 ? ? B C 34 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 13 N3 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 13 O2 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 13 N4 ? ? C G 2 D C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C U 2 N3 ? ? ? 1_555 D A 12 N1 ? ? C U 3 D A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C U 2 O4 ? ? ? 1_555 D A 12 N6 ? ? C U 3 D A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 11 N3 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 11 O2 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 11 N4 ? ? C G 4 D C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 10 N3 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 10 O2 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 10 N4 ? ? C G 5 D C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C U 5 N3 ? ? ? 1_555 D A 9 N1 ? ? C U 6 D A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C U 5 O4 ? ? ? 1_555 D A 9 N6 ? ? C U 6 D A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 6 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 7 D C 28 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog47 hydrog ? ? C G 9 N1 ? ? ? 1_555 D C 6 N3 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 9 N2 ? ? ? 1_555 D C 6 O2 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 9 O6 ? ? ? 1_555 D C 6 N4 ? ? C G 10 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C U 10 O4 ? ? ? 1_555 D U 5 N3 ? ? C U 11 D U 25 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog51 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 4 N1 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 4 O6 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 4 N2 ? ? C C 12 D G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 12 N1 ? ? ? 1_555 D C 3 N3 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C G 12 N2 ? ? ? 1_555 D C 3 O2 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C G 12 O6 ? ? ? 1_555 D C 3 N4 ? ? C G 13 D C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 14 D G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C G 14 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 15 D C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C G 14 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 15 D C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 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 ? ? # 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 O ? K HOH . ? A HOH 105 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 106 ? 1_555 85.8 ? 2 O ? K HOH . ? A HOH 105 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 107 ? 1_555 89.2 ? 3 O ? K HOH . ? A HOH 106 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 107 ? 1_555 82.7 ? 4 O ? K HOH . ? A HOH 105 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 108 ? 1_555 176.8 ? 5 O ? K HOH . ? A HOH 106 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 108 ? 1_555 91.2 ? 6 O ? K HOH . ? A HOH 107 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 108 ? 1_555 89.3 ? 7 O ? K HOH . ? A HOH 105 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 109 ? 1_555 89.6 ? 8 O ? K HOH . ? A HOH 106 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 109 ? 1_555 171.5 ? 9 O ? K HOH . ? A HOH 107 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 109 ? 1_555 90.2 ? 10 O ? K HOH . ? A HOH 108 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 109 ? 1_555 93.3 ? 11 O ? K HOH . ? A HOH 105 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 110 ? 1_555 94.0 ? 12 O ? K HOH . ? A HOH 106 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 110 ? 1_555 98.0 ? 13 O ? K HOH . ? A HOH 107 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 110 ? 1_555 176.8 ? 14 O ? K HOH . ? A HOH 108 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 110 ? 1_555 87.5 ? 15 O ? K HOH . ? A HOH 109 ? 1_555 MG ? E MG . ? A MG 100 ? 1_555 O ? K HOH . ? A HOH 110 ? 1_555 89.4 ? 16 O ? M HOH . ? C HOH 47 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 201 ? 1_555 85.7 ? 17 O ? M HOH . ? C HOH 47 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 202 ? 1_555 89.2 ? 18 O ? N HOH . ? D HOH 201 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 202 ? 1_555 82.6 ? 19 O ? M HOH . ? C HOH 47 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 203 ? 1_555 176.7 ? 20 O ? N HOH . ? D HOH 201 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 203 ? 1_555 91.2 ? 21 O ? N HOH . ? D HOH 202 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 203 ? 1_555 89.4 ? 22 O ? M HOH . ? C HOH 47 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 204 ? 1_555 89.6 ? 23 O ? N HOH . ? D HOH 201 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 204 ? 1_555 171.4 ? 24 O ? N HOH . ? D HOH 202 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 204 ? 1_555 90.1 ? 25 O ? N HOH . ? D HOH 203 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 204 ? 1_555 93.3 ? 26 O ? M HOH . ? C HOH 47 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 205 ? 1_555 94.0 ? 27 O ? N HOH . ? D HOH 201 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 205 ? 1_555 98.0 ? 28 O ? N HOH . ? D HOH 202 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 205 ? 1_555 176.8 ? 29 O ? N HOH . ? D HOH 203 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 205 ? 1_555 87.5 ? 30 O ? N HOH . ? D HOH 204 ? 1_555 MG ? J MG . ? D MG 200 ? 1_555 O ? N HOH . ? D HOH 205 ? 1_555 89.5 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MG 100 ? 6 'BINDING SITE FOR RESIDUE MG A 100' AC2 Software D MG 200 ? 6 'BINDING SITE FOR RESIDUE MG D 200' AC3 Software C CNY 41 ? 9 'BINDING SITE FOR RESIDUE CNY C 41' AC4 Software A CNY 42 ? 10 'BINDING SITE FOR RESIDUE CNY A 42' AC5 Software A CNY 43 ? 10 'BINDING SITE FOR RESIDUE CNY A 43' AC6 Software C CNY 44 ? 9 'BINDING SITE FOR RESIDUE CNY C 44' 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 6 HOH K . ? HOH A 105 . ? 1_555 ? 2 AC1 6 HOH K . ? HOH A 106 . ? 1_555 ? 3 AC1 6 HOH K . ? HOH A 107 . ? 1_555 ? 4 AC1 6 HOH K . ? HOH A 108 . ? 1_555 ? 5 AC1 6 HOH K . ? HOH A 109 . ? 1_555 ? 6 AC1 6 HOH K . ? HOH A 110 . ? 1_555 ? 7 AC2 6 HOH M . ? HOH C 47 . ? 1_555 ? 8 AC2 6 HOH N . ? HOH D 201 . ? 1_555 ? 9 AC2 6 HOH N . ? HOH D 202 . ? 1_555 ? 10 AC2 6 HOH N . ? HOH D 203 . ? 1_555 ? 11 AC2 6 HOH N . ? HOH D 204 . ? 1_555 ? 12 AC2 6 HOH N . ? HOH D 205 . ? 1_555 ? 13 AC3 9 U C 5 ? U C 6 . ? 1_555 ? 14 AC3 9 G C 6 ? G C 7 . ? 1_555 ? 15 AC3 9 A C 7 ? A C 8 . ? 1_555 ? 16 AC3 9 A C 8 ? A C 9 . ? 1_555 ? 17 AC3 9 G C 9 ? G C 10 . ? 1_555 ? 18 AC3 9 U C 10 ? U C 11 . ? 1_555 ? 19 AC3 9 HOH M . ? HOH C 45 . ? 1_555 ? 20 AC3 9 U D 5 ? U D 25 . ? 1_555 ? 21 AC3 9 A D 7 ? A D 27 . ? 1_555 ? 22 AC4 10 G A 6 ? G A 7 . ? 1_555 ? 23 AC4 10 A A 7 ? A A 8 . ? 1_555 ? 24 AC4 10 A A 8 ? A A 9 . ? 1_555 ? 25 AC4 10 G A 9 ? G A 10 . ? 1_555 ? 26 AC4 10 U A 10 ? U A 11 . ? 1_555 ? 27 AC4 10 HOH K . ? HOH A 101 . ? 1_555 ? 28 AC4 10 G B 4 ? G B 24 . ? 1_555 ? 29 AC4 10 U B 5 ? U B 25 . ? 1_555 ? 30 AC4 10 C B 6 ? C B 26 . ? 1_555 ? 31 AC4 10 A B 7 ? A B 27 . ? 1_555 ? 32 AC5 10 U A 10 ? U A 11 . ? 1_555 ? 33 AC5 10 C A 11 ? C A 12 . ? 1_555 ? 34 AC5 10 C A 13 ? C A 14 . ? 1_555 ? 35 AC5 10 G A 14 ? G A 15 . ? 1_555 ? 36 AC5 10 G A 15 ? G A 16 . ? 1_555 ? 37 AC5 10 A B 12 ? A B 32 . ? 3_645 ? 38 AC5 10 C B 13 ? C B 33 . ? 3_645 ? 39 AC5 10 C B 14 ? C B 34 . ? 3_645 ? 40 AC5 10 G C 1 ? G C 2 . ? 2_665 ? 41 AC5 10 C D 14 ? C D 34 . ? 2_665 ? 42 AC6 9 G A 1 ? G A 2 . ? 1_555 ? 43 AC6 9 C B 14 ? C B 34 . ? 1_555 ? 44 AC6 9 U C 10 ? U C 11 . ? 1_555 ? 45 AC6 9 C C 11 ? C C 12 . ? 1_555 ? 46 AC6 9 C C 13 ? C C 14 . ? 1_555 ? 47 AC6 9 G C 14 ? G C 15 . ? 1_555 ? 48 AC6 9 G C 15 ? G C 16 . ? 1_555 ? 49 AC6 9 C D 13 ? C D 33 . ? 4_465 ? 50 AC6 9 C D 14 ? C D 34 . ? 4_465 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 24 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.056 _pdbx_validate_planes.type 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text bis-intercalation # 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 CNY C11 C N R 73 CNY O11 O N N 74 CNY C21 C N R 75 CNY N21 N N N 76 CNY C31 C N R 77 CNY O31 O N N 78 CNY C41 C N S 79 CNY O41 O N N 80 CNY C51 C N R 81 CNY O51 O N N 82 CNY C61 C N N 83 CNY N61 N N N 84 CNY C12 C N R 85 CNY N12 N N N 86 CNY C22 C N N 87 CNY C32 C N S 88 CNY N32 N N N 89 CNY C42 C N R 90 CNY C52 C N R 91 CNY O52 O N N 92 CNY C62 C N S 93 CNY O62 O N N 94 CNY C13 C N S 95 CNY C23 C N R 96 CNY O23 O N N 97 CNY C33 C N S 98 CNY O33 O N N 99 CNY C43 C N R 100 CNY O43 O N N 101 CNY C53 C N N 102 CNY C14 C N R 103 CNY C24 C N R 104 CNY N24 N N N 105 CNY C34 C N R 106 CNY O34 O N N 107 CNY C44 C N S 108 CNY O44 O N N 109 CNY C54 C N S 110 CNY O54 O N N 111 CNY C64 C N N 112 CNY N64 N N N 113 CNY H11 H N N 114 CNY H21 H N N 115 CNY H1 H N N 116 CNY H31 H N N 117 CNY H2 H N N 118 CNY H41 H N N 119 CNY H3 H N N 120 CNY H51 H N N 121 CNY H611 H N N 122 CNY H612 H N N 123 CNY H11A H N N 124 CNY H12A H N N 125 CNY H12 H N N 126 CNY H121 H N N 127 CNY H122 H N N 128 CNY H221 H N N 129 CNY H222 H N N 130 CNY H32 H N N 131 CNY H321 H N N 132 CNY H322 H N N 133 CNY H42 H N N 134 CNY H52 H N N 135 CNY H62 H N N 136 CNY H4 H N N 137 CNY H13 H N N 138 CNY H23 H N N 139 CNY H5 H N N 140 CNY H33 H N N 141 CNY H43 H N N 142 CNY H531 H N N 143 CNY H532 H N N 144 CNY H14 H N N 145 CNY H24 H N N 146 CNY H241 H N N 147 CNY H242 H N N 148 CNY H34 H N N 149 CNY H6 H N N 150 CNY H44 H N N 151 CNY H7 H N N 152 CNY H54 H N N 153 CNY H641 H N N 154 CNY H642 H N N 155 CNY H21A H N N 156 CNY H22 H N N 157 G OP3 O N N 158 G P P N N 159 G OP1 O N N 160 G OP2 O N N 161 G "O5'" O N N 162 G "C5'" C N N 163 G "C4'" C N R 164 G "O4'" O N N 165 G "C3'" C N S 166 G "O3'" O N N 167 G "C2'" C N R 168 G "O2'" O N N 169 G "C1'" C N R 170 G N9 N Y N 171 G C8 C Y N 172 G N7 N Y N 173 G C5 C Y N 174 G C6 C N N 175 G O6 O N N 176 G N1 N N N 177 G C2 C N N 178 G N2 N N N 179 G N3 N N N 180 G C4 C Y N 181 G HOP3 H N N 182 G HOP2 H N N 183 G "H5'" H N N 184 G "H5''" H N N 185 G "H4'" H N N 186 G "H3'" H N N 187 G "HO3'" H N N 188 G "H2'" H N N 189 G "HO2'" H N N 190 G "H1'" H N N 191 G H8 H N N 192 G H1 H N N 193 G H21 H N N 194 G H22 H N N 195 HOH O O N N 196 HOH H1 H N N 197 HOH H2 H N N 198 MG MG MG N N 199 U OP3 O N N 200 U P P N N 201 U OP1 O N N 202 U OP2 O N N 203 U "O5'" O N N 204 U "C5'" C N N 205 U "C4'" C N R 206 U "O4'" O N N 207 U "C3'" C N S 208 U "O3'" O N N 209 U "C2'" C N R 210 U "O2'" O N N 211 U "C1'" C N R 212 U N1 N N N 213 U C2 C N N 214 U O2 O N N 215 U N3 N N N 216 U C4 C N N 217 U O4 O N N 218 U C5 C N N 219 U C6 C N N 220 U HOP3 H N N 221 U HOP2 H N N 222 U "H5'" H N N 223 U "H5''" H N N 224 U "H4'" H N N 225 U "H3'" H N N 226 U "HO3'" H N N 227 U "H2'" H N N 228 U "HO2'" H N N 229 U "H1'" H N N 230 U H3 H N N 231 U H5 H N N 232 U H6 H N N 233 # 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 CNY C11 O11 sing N N 76 CNY C11 C21 sing N N 77 CNY C11 O51 sing N N 78 CNY C11 H11 sing N N 79 CNY O11 C42 sing N N 80 CNY C21 N21 sing N N 81 CNY C21 C31 sing N N 82 CNY C21 H21 sing N N 83 CNY N21 C53 sing N N 84 CNY N21 H1 sing N N 85 CNY C31 O31 sing N N 86 CNY C31 C41 sing N N 87 CNY C31 H31 sing N N 88 CNY O31 H2 sing N N 89 CNY C41 O41 sing N N 90 CNY C41 C51 sing N N 91 CNY C41 H41 sing N N 92 CNY O41 H3 sing N N 93 CNY C51 O51 sing N N 94 CNY C51 C61 sing N N 95 CNY C51 H51 sing N N 96 CNY C61 N61 sing N N 97 CNY C61 H611 sing N N 98 CNY C61 H612 sing N N 99 CNY N61 H11A sing N N 100 CNY N61 H12A sing N N 101 CNY C12 N12 sing N N 102 CNY C12 C22 sing N N 103 CNY C12 C62 sing N N 104 CNY C12 H12 sing N N 105 CNY N12 H121 sing N N 106 CNY N12 H122 sing N N 107 CNY C22 C32 sing N N 108 CNY C22 H221 sing N N 109 CNY C22 H222 sing N N 110 CNY C32 N32 sing N N 111 CNY C32 C42 sing N N 112 CNY C32 H32 sing N N 113 CNY N32 H321 sing N N 114 CNY N32 H322 sing N N 115 CNY C42 C52 sing N N 116 CNY C42 H42 sing N N 117 CNY C52 O52 sing N N 118 CNY C52 C62 sing N N 119 CNY C52 H52 sing N N 120 CNY O52 C13 sing N N 121 CNY C62 O62 sing N N 122 CNY C62 H62 sing N N 123 CNY O62 H4 sing N N 124 CNY C13 C23 sing N N 125 CNY C13 O43 sing N N 126 CNY C13 H13 sing N N 127 CNY C23 O23 sing N N 128 CNY C23 C33 sing N N 129 CNY C23 H23 sing N N 130 CNY O23 H5 sing N N 131 CNY C33 O33 sing N N 132 CNY C33 C43 sing N N 133 CNY C33 H33 sing N N 134 CNY O33 C14 sing N N 135 CNY C43 O43 sing N N 136 CNY C43 C53 sing N N 137 CNY C43 H43 sing N N 138 CNY C53 H531 sing N N 139 CNY C53 H532 sing N N 140 CNY C14 C24 sing N N 141 CNY C14 O54 sing N N 142 CNY C14 H14 sing N N 143 CNY C24 N24 sing N N 144 CNY C24 C34 sing N N 145 CNY C24 H24 sing N N 146 CNY N24 H241 sing N N 147 CNY N24 H242 sing N N 148 CNY C34 O34 sing N N 149 CNY C34 C44 sing N N 150 CNY C34 H34 sing N N 151 CNY O34 H6 sing N N 152 CNY C44 O44 sing N N 153 CNY C44 C54 sing N N 154 CNY C44 H44 sing N N 155 CNY O44 H7 sing N N 156 CNY C54 O54 sing N N 157 CNY C54 C64 sing N N 158 CNY C54 H54 sing N N 159 CNY C64 N64 sing N N 160 CNY C64 H641 sing N N 161 CNY C64 H642 sing N N 162 CNY N64 H21A sing N N 163 CNY N64 H22 sing N N 164 G OP3 P sing N N 165 G OP3 HOP3 sing N N 166 G P OP1 doub N N 167 G P OP2 sing N N 168 G P "O5'" sing N N 169 G OP2 HOP2 sing N N 170 G "O5'" "C5'" sing N N 171 G "C5'" "C4'" sing N N 172 G "C5'" "H5'" sing N N 173 G "C5'" "H5''" sing N N 174 G "C4'" "O4'" sing N N 175 G "C4'" "C3'" sing N N 176 G "C4'" "H4'" sing N N 177 G "O4'" "C1'" sing N N 178 G "C3'" "O3'" sing N N 179 G "C3'" "C2'" sing N N 180 G "C3'" "H3'" sing N N 181 G "O3'" "HO3'" sing N N 182 G "C2'" "O2'" sing N N 183 G "C2'" "C1'" sing N N 184 G "C2'" "H2'" sing N N 185 G "O2'" "HO2'" sing N N 186 G "C1'" N9 sing N N 187 G "C1'" "H1'" sing N N 188 G N9 C8 sing Y N 189 G N9 C4 sing Y N 190 G C8 N7 doub Y N 191 G C8 H8 sing N N 192 G N7 C5 sing Y N 193 G C5 C6 sing N N 194 G C5 C4 doub Y N 195 G C6 O6 doub N N 196 G C6 N1 sing N N 197 G N1 C2 sing N N 198 G N1 H1 sing N N 199 G C2 N2 sing N N 200 G C2 N3 doub N N 201 G N2 H21 sing N N 202 G N2 H22 sing N N 203 G N3 C4 sing N N 204 HOH O H1 sing N N 205 HOH O H2 sing N N 206 U OP3 P sing N N 207 U OP3 HOP3 sing N N 208 U P OP1 doub N N 209 U P OP2 sing N N 210 U P "O5'" sing N N 211 U OP2 HOP2 sing N N 212 U "O5'" "C5'" sing N N 213 U "C5'" "C4'" sing N N 214 U "C5'" "H5'" sing N N 215 U "C5'" "H5''" sing N N 216 U "C4'" "O4'" sing N N 217 U "C4'" "C3'" sing N N 218 U "C4'" "H4'" sing N N 219 U "O4'" "C1'" sing N N 220 U "C3'" "O3'" sing N N 221 U "C3'" "C2'" sing N N 222 U "C3'" "H3'" sing N N 223 U "O3'" "HO3'" sing N N 224 U "C2'" "O2'" sing N N 225 U "C2'" "C1'" sing N N 226 U "C2'" "H2'" sing N N 227 U "O2'" "HO2'" sing N N 228 U "C1'" N1 sing N N 229 U "C1'" "H1'" sing N N 230 U N1 C2 sing N N 231 U N1 C6 sing N N 232 U C2 O2 doub N N 233 U C2 N3 sing N N 234 U N3 C4 sing N N 235 U N3 H3 sing N N 236 U C4 O4 doub N N 237 U C4 C5 sing N N 238 U C5 C6 doub N N 239 U C5 H5 sing N N 240 U C6 H6 sing N N 241 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1ZZ5 'double helix' 1ZZ5 'a-form double helix' 1ZZ5 'mismatched base pair' 1ZZ5 '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 -0.253 0.095 0.172 -2.798 -16.458 -0.175 1 B_C28:G7_A B 28 ? A 7 ? 19 1 1 B A 9 1_555 A U 5 1_555 -0.371 -0.289 0.102 -0.949 -12.504 2.904 2 B_A29:U6_A B 29 ? A 6 ? 20 1 1 B C 10 1_555 A G 4 1_555 1.405 -0.234 0.350 0.376 -18.377 -15.890 3 B_C30:G5_A B 30 ? A 5 ? ? ? 1 B C 11 1_555 A G 3 1_555 0.295 -0.327 -0.082 1.042 -14.811 -6.826 4 B_C31:G4_A B 31 ? A 4 ? 19 1 1 B A 12 1_555 A U 2 1_555 1.271 -0.114 0.019 -8.665 -13.072 -6.125 5 B_A32:U3_A B 32 ? A 3 ? 20 1 1 B C 13 1_555 A G 1 1_555 0.321 -0.291 0.699 -11.513 -13.219 -11.406 6 B_C33:G2_A B 33 ? A 2 ? 19 1 1 B C 14 1_555 C G 15 1_555 0.243 0.152 -0.185 5.565 -2.904 -1.521 7 B_C34:G16_C B 34 ? C 16 ? 19 1 1 D C 1 1_555 C G 14 1_555 0.403 -0.270 -0.274 5.476 -2.218 -6.075 8 D_C21:G15_C D 21 ? C 15 ? 19 1 1 D G 2 1_555 C C 13 1_555 0.367 -0.234 -0.227 -1.839 -6.485 -0.580 9 D_G22:C14_C D 22 ? C 14 ? 19 1 1 D C 3 1_555 C G 12 1_555 0.090 -0.068 -0.094 8.276 -12.470 6.422 10 D_C23:G13_C D 23 ? C 13 ? 19 1 1 D G 4 1_555 C C 11 1_555 1.057 -0.167 -0.199 -8.923 -3.312 -1.452 11 D_G24:C12_C D 24 ? C 12 ? 19 1 1 D U 5 1_555 C U 10 1_555 0.394 -1.314 0.266 5.792 4.049 -12.464 12 D_U25:U11_C D 25 ? C 11 ? ? ? 1 D C 6 1_555 C G 9 1_555 0.551 0.155 -0.513 8.179 -0.023 -2.322 13 D_C26:G10_C D 26 ? C 10 ? 19 1 1 A G 9 1_555 B C 6 1_555 -0.773 -0.141 -0.663 -8.528 -8.048 2.650 14 A_G10:C26_B A 10 ? B 26 ? 19 1 1 A C 11 1_555 B G 4 1_555 -1.309 0.063 -0.474 14.873 -8.515 1.528 15 A_C12:G24_B A 12 ? B 24 ? 19 1 1 A G 12 1_555 B C 3 1_555 -1.379 -0.378 0.156 -3.677 -9.820 2.905 16 A_G13:C23_B A 13 ? B 23 ? 19 1 1 A C 13 1_555 B G 2 1_555 0.441 -0.237 -0.047 5.266 -12.586 0.236 17 A_C14:G22_B A 14 ? B 22 ? 19 1 1 A G 14 1_555 B C 1 1_555 -0.383 -0.267 -0.404 -10.436 -3.689 -4.190 18 A_G15:C21_B A 15 ? B 21 ? 19 1 1 C G 1 1_555 D C 13 1_555 -0.703 -0.312 0.663 7.701 -13.029 -8.186 19 C_G2:C33_D C 2 ? D 33 ? 19 1 1 C U 2 1_555 D A 12 1_555 0.112 0.173 -0.078 7.236 -16.279 6.622 20 C_U3:A32_D C 3 ? D 32 ? 20 1 1 C G 3 1_555 D C 11 1_555 -0.467 -0.370 -0.003 1.027 -14.757 -6.994 21 C_G4:C31_D C 4 ? D 31 ? 19 1 1 C G 4 1_555 D C 10 1_555 -0.349 -0.029 0.144 -5.029 -16.743 -8.601 22 C_G5:C30_D C 5 ? D 30 ? 19 1 1 C U 5 1_555 D A 9 1_555 0.306 -0.145 0.284 -3.518 -16.300 14.143 23 C_U6:A29_D C 6 ? D 29 ? 20 1 1 C G 6 1_555 D C 8 1_555 0.387 0.229 0.311 -0.953 -15.197 5.328 24 C_G7:C28_D C 7 ? D 28 ? ? 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 -0.067 -1.869 3.170 -1.766 8.695 31.886 -4.602 -0.150 2.585 15.456 3.139 33.066 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 -1.107 -1.431 3.275 -5.607 7.171 40.788 -2.753 0.971 3.109 10.137 7.926 41.749 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 0.209 -2.002 3.189 2.550 0.154 27.214 -4.274 0.176 3.184 0.327 -5.404 27.331 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 -0.084 -1.988 3.437 3.230 7.436 36.863 -4.029 0.544 2.977 11.588 -5.033 37.714 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 0.217 -2.653 3.125 2.533 7.007 28.231 -6.582 0.045 2.420 14.057 -5.082 29.178 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 -2.806 -1.759 2.780 5.454 7.358 11.610 -10.146 13.359 0.282 30.831 -22.852 14.777 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 -1.083 -2.302 3.341 -1.618 -1.646 36.415 -3.439 1.496 3.482 -2.631 2.586 36.486 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 -0.468 -1.774 3.519 2.693 7.117 27.491 -5.232 1.567 2.918 14.624 -5.534 28.505 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 0.798 -1.476 3.006 1.469 4.652 30.974 -3.513 -1.230 2.794 8.643 -2.729 31.346 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 0.263 -1.668 3.499 0.531 12.458 38.265 -3.839 -0.323 2.845 18.418 -0.785 40.173 10 DD_C23G24:C12G13_CC D 23 ? C 13 ? D 24 ? C 12 ? 1 D G 4 1_555 C C 11 1_555 D U 5 1_555 C U 10 1_555 -0.846 -2.092 2.767 -1.707 2.573 26.416 -5.105 1.470 2.604 5.606 3.718 26.592 11 DD_G24U25:U11C12_CC D 24 ? C 12 ? D 25 ? C 11 ? 1 D U 5 1_555 C U 10 1_555 D C 6 1_555 C G 9 1_555 0.897 -2.450 3.247 5.182 0.060 29.102 -4.817 -0.641 3.348 0.118 -10.211 29.550 12 DD_U25C26:G10U11_CC D 25 ? C 11 ? D 26 ? C 10 ? 1 A G 9 1_555 B C 6 1_555 A C 11 1_555 B G 4 1_555 -0.884 -3.674 5.941 -4.814 5.399 54.415 -4.561 0.449 5.634 5.875 5.238 54.857 13 AA_G10C12:G24C26_BB A 10 ? B 26 ? 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 -0.125 -1.941 3.536 -7.939 11.823 28.653 -5.625 -1.180 2.508 22.239 14.933 31.931 14 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 -0.575 -1.274 3.083 -1.107 2.529 43.433 -1.946 0.676 3.021 3.413 1.494 43.517 15 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 0.390 -1.814 3.732 -1.627 7.749 23.977 -6.534 -1.393 2.975 18.034 3.786 25.232 16 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 -0.117 -2.115 3.125 0.708 4.673 38.148 -3.747 0.259 2.853 7.116 -1.079 38.429 17 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 -0.732 -2.013 3.367 -3.698 8.723 27.570 -5.821 0.685 2.691 17.656 7.486 29.123 18 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 0.126 -2.215 3.435 -1.321 4.613 30.475 -5.062 -0.494 3.066 8.709 2.493 30.842 19 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 1.219 -1.010 3.214 2.962 8.814 34.869 -2.835 -1.566 2.970 14.395 -4.838 36.050 20 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 -0.256 -1.420 3.118 -1.315 8.456 34.160 -3.489 0.246 2.708 14.122 2.196 35.184 21 CC_U6G7:C28A29_DD C 6 ? D 29 ? C 7 ? D 28 ? # _atom_sites.entry_id 1ZZ5 _atom_sites.fract_transf_matrix[1][1] 0.019708 _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] 0.019704 _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] 0.006910 _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_