data_1YKQ # _entry.id 1YKQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1YKQ pdb_00001ykq 10.2210/pdb1ykq/pdb NDB UR0053 ? ? RCSB RCSB031626 ? ? WWPDB D_1000031626 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1ykv . unspecified PDB 1yls . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YKQ _pdbx_database_status.recvd_initial_deposition_date 2005-01-18 _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_ _audit_author.name _audit_author.pdbx_ordinal 'Serganov, A.' 1 'Keiper, S.' 2 'Malinina, L.' 3 'Tereshko, V.' 4 'Skripkin, E.' 5 'Hobartner, C.' 6 'Polonskaia, A.' 7 'Phan, A.T.' 8 'Wombacher, R.' 9 'Micura, R.' 10 'Dauter, Z.' 11 'Jaschke, A.' 12 'Patel, D.J.' 13 # _citation.id primary _citation.title 'Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 12 _citation.page_first 218 _citation.page_last 224 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15723077 _citation.pdbx_database_id_DOI 10.1038/nsmb906 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Serganov, A.' 1 ? primary 'Keiper, S.' 2 ? primary 'Malinina, L.' 3 ? primary 'Tereshko, V.' 4 ? primary 'Skripkin, E.' 5 ? primary 'Hobartner, C.' 6 ? primary 'Polonskaia, A.' 7 ? primary 'Phan, A.T.' 8 ? primary 'Wombacher, R.' 9 ? primary 'Micura, R.' 10 ? primary 'Dauter, Z.' 11 ? primary 'Jaschke, A.' 12 ? primary 'Patel, D.J.' 13 ? # _cell.entry_id 1YKQ _cell.length_a 77.690 _cell.length_b 44.240 _cell.length_c 79.640 _cell.angle_alpha 90.00 _cell.angle_beta 107.12 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YKQ _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Diels-Alder ribozyme' 3497.146 2 ? ? ? 11-mer 2 polymer syn 'Diels-Alder ribozyme' 12262.333 2 ? ? ? 38-mer 3 non-polymer syn 'CADMIUM ION' 112.411 5 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 7 ? ? ? ? # 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 GGAGCUCGCCC GGAGCUCGCCC A,C ? 2 polyribonucleotide no no GGGCGAGGCCGUGCCAGCUCUUCGGAGCAAUACUCGGC GGGCGAGGCCGUGCCAGCUCUUCGGAGCAAUACUCGGC B,D ? # 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 A n 1 4 G n 1 5 C n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 C n 1 11 C n 2 1 G n 2 2 G n 2 3 G n 2 4 C n 2 5 G n 2 6 A n 2 7 G n 2 8 G n 2 9 C n 2 10 C n 2 11 G n 2 12 U n 2 13 G n 2 14 C n 2 15 C n 2 16 A n 2 17 G n 2 18 C n 2 19 U n 2 20 C n 2 21 U n 2 22 U n 2 23 C n 2 24 G n 2 25 G n 2 26 A n 2 27 G n 2 28 C n 2 29 A n 2 30 A n 2 31 U n 2 32 A n 2 33 C n 2 34 U n 2 35 C n 2 36 G n 2 37 G n 2 38 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 was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide ; 2 1 sample ? ? ? ? ? ;This sequence was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide ; # 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 1YKQ 1YKQ ? ? ? 2 2 PDB 1YKQ 1YKQ ? ? ? # 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 1YKQ A 1 ? 11 ? 1YKQ 101 ? 111 ? 101 111 2 2 1YKQ B 1 ? 38 ? 1YKQ 201 ? 238 ? 201 238 3 1 1YKQ C 1 ? 11 ? 1YKQ 101 ? 111 ? 101 111 4 2 1YKQ D 1 ? 38 ? 1YKQ 201 ? 238 ? 201 238 # 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 CD non-polymer . 'CADMIUM ION' ? 'Cd 2' 112.411 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 1YKQ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.04 _exptl_crystal.density_percent_sol 63 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;PEG400, sodium cacodylate, magnesium acetate, 1,6-hexandiol, sodium chloride, cadmium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 PEG400 ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 1 H2O ? ? ? 1 4 2 PEG400 ? ? ? 1 5 2 'sodium cacodylate' ? ? ? 1 6 2 'magnesium acetate' ? ? ? 1 7 2 1,6-hexandiol ? ? ? 1 8 2 'sodium chloride' ? ? ? 1 9 2 'cadmium chloride' ? ? ? 1 10 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2004-06-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111),(220)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.1 # _reflns.entry_id 1YKQ _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 3.5 _reflns.d_resolution_low 20 _reflns.number_all 6902 _reflns.number_obs 6744 _reflns.percent_possible_obs 97.7 _reflns.pdbx_Rmerge_I_obs 0.154 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 8.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.8 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 3.5 _reflns_shell.d_res_low 3.62 _reflns_shell.percent_possible_all 98.2 _reflns_shell.Rmerge_I_obs 0.729 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.8 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 673 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1YKQ _refine.ls_d_res_high 3.5 _refine.ls_d_res_low 20 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 6564 _refine.ls_number_reflns_obs 6563 _refine.ls_number_reflns_R_free 312 _refine.ls_percent_reflns_obs 97.6 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2875 _refine.ls_R_factor_R_work 0.2857 _refine.ls_R_factor_R_free 0.3238 _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 4.8 _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 'Diels-Alder ribozyme from the ribozyme-product complex, pdb entry 1YLS' _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 'MAXIMUM LIKELIHOOD' _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model overall _refine.B_iso_mean 40.00 _refine.aniso_B[1][1] 2.45 _refine.aniso_B[1][2] 0 _refine.aniso_B[1][3] 1.26 _refine.aniso_B[2][2] -8.91 _refine.aniso_B[2][3] 0 _refine.aniso_B[3][3] 7.20 _refine.details ? _refine.correlation_coeff_Fo_to_Fc 0.896 _refine.correlation_coeff_Fo_to_Fc_free 0.852 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B 109.285 _refine.overall_SU_ML 0.730 _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.671 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 1YKQ _refine_analyze.Luzzati_coordinate_error_obs 0.755 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _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 2078 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 2090 _refine_hist.d_res_high 3.5 _refine_hist.d_res_low 20 # 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 r_bond_refined_d 0.015 0.021 ? 2320 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.612 3.000 ? 3610 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.085 0.200 ? 480 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 1018 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.262 0.200 ? 1209 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.218 0.200 ? 71 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.098 0.200 ? 1 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.184 0.200 ? 42 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.262 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 0.000 3.000 ? 3325 'X-RAY DIFFRACTION' ? r_scangle_it 0.000 4.500 ? 3610 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight 1 'loose positional' A 230 0.48 5.00 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? 1 'loose positional' B 809 0.38 5.00 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? 1 'loose thermal' A 230 0.00 10.00 1 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? 1 'loose thermal' B 809 0.00 10.00 2 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.5 _refine_ls_shell.d_res_low 3.588 _refine_ls_shell.number_reflns_R_work 447 _refine_ls_shell.R_factor_R_work 0.364 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.326 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 24 _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 ? # loop_ _struct_ncs_dom.pdbx_ens_id _struct_ncs_dom.id _struct_ncs_dom.details 1 1 A 1 2 C 2 1 B 2 2 D # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details 1 1 1 A G 1 . A C 11 . A G 101 A C 111 6 ? 1 2 1 C G 1 . C C 11 . C G 101 C C 111 6 ? 2 1 1 B G 1 . B C 38 . B G 201 B C 238 6 ? 2 2 1 D G 1 . D C 38 . D G 201 D C 238 6 ? # loop_ _struct_ncs_ens.id _struct_ncs_ens.details _struct_ncs_ens.point_group 1 ? ? 2 ? ? # _struct.entry_id 1YKQ _struct.title 'Crystal structure of Diels-Alder ribozyme' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YKQ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'carbon-carbon bond, catalytic mechanism, RNA crystal structure, Diels-Alder reaction, ribozyme, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 1 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 3 ? I N N 3 ? J N N 4 ? K N N 4 ? L N N 4 ? M N N 4 ? N N N 3 ? O N N 3 ? P N N 4 ? # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 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 E CD . CD ? ? A G 101 A CD 249 1_555 ? ? ? ? ? ? ? 2.319 ? ? metalc2 metalc ? ? A G 1 O6 ? ? ? 1_555 E CD . CD ? ? A G 101 A CD 249 1_555 ? ? ? ? ? ? ? 2.602 ? ? metalc3 metalc ? ? B G 1 N7 ? ? ? 1_555 I CD . CD ? ? B G 201 B CD 243 1_555 ? ? ? ? ? ? ? 2.698 ? ? metalc4 metalc ? ? B G 13 OP1 ? ? ? 1_555 J MG . MG ? ? B G 213 B MG 246 1_555 ? ? ? ? ? ? ? 2.146 ? ? metalc5 metalc ? ? B A 16 OP2 ? ? ? 1_555 H CD . CD ? ? B A 216 B CD 242 1_555 ? ? ? ? ? ? ? 2.542 ? ? metalc6 metalc ? ? B C 33 OP2 ? ? ? 1_555 G MG . MG ? ? B C 233 B MG 241 1_555 ? ? ? ? ? ? ? 2.352 ? ? metalc7 metalc ? ? B U 34 OP1 ? ? ? 1_555 F MG . MG ? ? B U 234 B MG 240 1_555 ? ? ? ? ? ? ? 1.892 ? ? metalc8 metalc ? ? J MG . MG ? ? ? 1_555 D G 13 OP1 ? ? B MG 246 D G 213 1_555 ? ? ? ? ? ? ? 2.304 ? ? metalc9 metalc ? ? C G 1 N7 ? ? ? 1_555 K MG . MG ? ? C G 101 C MG 349 1_555 ? ? ? ? ? ? ? 2.195 ? ? metalc10 metalc ? ? C G 1 O6 ? ? ? 1_555 K MG . MG ? ? C G 101 C MG 349 1_555 ? ? ? ? ? ? ? 2.582 ? ? metalc11 metalc ? ? D G 1 N7 ? ? ? 1_555 O CD . CD ? ? D G 201 D CD 343 1_555 ? ? ? ? ? ? ? 2.668 ? ? metalc12 metalc ? ? D A 16 OP2 ? ? ? 1_555 N CD . CD ? ? D A 216 D CD 342 1_555 ? ? ? ? ? ? ? 2.254 ? ? metalc13 metalc ? ? D G 25 N7 ? ? ? 1_555 P MG . MG ? ? D G 225 D MG 348 1_555 ? ? ? ? ? ? ? 2.359 ? ? metalc14 metalc ? ? D C 33 OP2 ? ? ? 1_555 M MG . MG ? ? D C 233 D MG 341 1_555 ? ? ? ? ? ? ? 2.419 ? ? metalc15 metalc ? ? D U 34 OP1 ? ? ? 1_555 L MG . MG ? ? D U 234 D MG 340 1_555 ? ? ? ? ? ? ? 2.716 ? ? hydrog1 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 101 B C 215 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 34 O4 ? ? A A 103 B U 234 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 33 N3 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 33 O2 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 33 N4 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 106 B A 206 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 4 N3 ? ? A G 108 B C 204 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog17 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 2 N1 ? ? A C 110 B G 202 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog21 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 111 B G 201 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog22 hydrog ? ? B G 8 N1 ? ? ? 1_555 B C 38 N3 ? ? B G 208 B C 238 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog23 hydrog ? ? B C 9 N3 ? ? ? 1_555 B G 37 N1 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 37 O6 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B C 9 O2 ? ? ? 1_555 B G 37 N2 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B C 10 N3 ? ? ? 1_555 B G 36 N1 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B C 10 N4 ? ? ? 1_555 B G 36 O6 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B C 10 O2 ? ? ? 1_555 B G 36 N2 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B G 11 N1 ? ? ? 1_555 B C 35 N3 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B G 11 N2 ? ? ? 1_555 B C 35 O2 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 11 O6 ? ? ? 1_555 B C 35 N4 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B U 12 N3 ? ? ? 1_555 B A 32 N7 ? ? B U 212 B A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog33 hydrog ? ? B U 12 O2 ? ? ? 1_555 B A 32 N6 ? ? B U 212 B A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog34 hydrog ? ? B A 16 N6 ? ? ? 1_555 B A 29 N1 ? ? B A 216 B A 229 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog35 hydrog ? ? B G 17 N1 ? ? ? 1_555 B C 28 N3 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 17 N2 ? ? ? 1_555 B C 28 O2 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B G 17 O6 ? ? ? 1_555 B C 28 N4 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 18 N3 ? ? ? 1_555 B G 27 N1 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B C 18 N4 ? ? ? 1_555 B G 27 O6 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B C 18 O2 ? ? ? 1_555 B G 27 N2 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B U 19 N3 ? ? ? 1_555 B A 26 N1 ? ? B U 219 B A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B U 19 O4 ? ? ? 1_555 B A 26 N6 ? ? B U 219 B A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B C 20 O2 ? ? ? 1_555 B G 25 N2 ? ? B C 220 B G 225 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog44 hydrog ? ? B U 21 O2 ? ? ? 1_555 B G 24 N1 ? ? B U 221 B G 224 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog45 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 101 D C 215 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog46 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 14 N3 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 14 O2 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 14 N4 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C A 3 N6 ? ? ? 1_555 D U 34 O4 ? ? C A 103 D U 234 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog50 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 33 N3 ? ? C G 104 D C 233 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog51 hydrog ? ? C G 4 N2 ? ? ? 1_555 D U 34 O2 ? ? C G 104 D U 234 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog52 hydrog ? ? C C 5 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 105 D G 207 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog53 hydrog ? ? C C 5 N4 ? ? ? 1_555 D C 33 N3 ? ? C C 105 D C 233 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog54 hydrog ? ? C U 6 N3 ? ? ? 1_555 D A 6 N1 ? ? C U 106 D A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C U 6 O4 ? ? ? 1_555 D A 6 N6 ? ? C U 106 D A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C C 7 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C C 7 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C C 7 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C G 8 N1 ? ? ? 1_555 D C 4 N3 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C G 8 N2 ? ? ? 1_555 D C 4 O2 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C G 8 O6 ? ? ? 1_555 D C 4 N4 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C C 9 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C C 9 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C C 9 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C C 10 O2 ? ? ? 1_555 D G 2 N1 ? ? C C 110 D G 202 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog66 hydrog ? ? D G 8 N2 ? ? ? 1_555 D C 38 O2 ? ? D G 208 D C 238 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog67 hydrog ? ? D C 9 N3 ? ? ? 1_555 D G 37 N1 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? D C 9 N4 ? ? ? 1_555 D G 37 O6 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? D C 9 O2 ? ? ? 1_555 D G 37 N2 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? D C 10 N3 ? ? ? 1_555 D G 36 N1 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? D C 10 N4 ? ? ? 1_555 D G 36 O6 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? D C 10 O2 ? ? ? 1_555 D G 36 N2 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? D G 11 N1 ? ? ? 1_555 D C 35 N3 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? D G 11 N2 ? ? ? 1_555 D C 35 O2 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? D G 11 O6 ? ? ? 1_555 D C 35 N4 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? D U 12 N3 ? ? ? 1_555 D A 32 N7 ? ? D U 212 D A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog77 hydrog ? ? D U 12 O2 ? ? ? 1_555 D A 32 N6 ? ? D U 212 D A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog78 hydrog ? ? D C 14 N4 ? ? ? 1_555 D U 31 O2 ? ? D C 214 D U 231 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog79 hydrog ? ? D A 16 N6 ? ? ? 1_555 D A 29 N1 ? ? D A 216 D A 229 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog80 hydrog ? ? D G 17 N1 ? ? ? 1_555 D C 28 N3 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? D G 17 N2 ? ? ? 1_555 D C 28 O2 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? D G 17 O6 ? ? ? 1_555 D C 28 N4 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? D C 18 N3 ? ? ? 1_555 D G 27 N1 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? D C 18 N4 ? ? ? 1_555 D G 27 O6 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? D C 18 O2 ? ? ? 1_555 D G 27 N2 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? D U 19 N3 ? ? ? 1_555 D A 26 N1 ? ? D U 219 D A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? D U 19 O4 ? ? ? 1_555 D A 26 N6 ? ? D U 219 D A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? D C 20 O2 ? ? ? 1_555 D G 25 N2 ? ? D C 220 D G 225 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog89 hydrog ? ? D U 21 O2 ? ? ? 1_555 D G 24 N1 ? ? D U 221 D G 224 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog90 hydrog ? ? D G 24 N2 ? ? ? 1_555 D G 25 N3 ? ? D G 224 D G 225 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B MG 240 ? 2 'BINDING SITE FOR RESIDUE MG B 240' AC2 Software B MG 241 ? 1 'BINDING SITE FOR RESIDUE MG B 241' AC3 Software B CD 242 ? 2 'BINDING SITE FOR RESIDUE CD B 242' AC4 Software B CD 243 ? 1 'BINDING SITE FOR RESIDUE CD B 243' AC5 Software B MG 246 ? 2 'BINDING SITE FOR RESIDUE MG B 246' AC6 Software A CD 249 ? 1 'BINDING SITE FOR RESIDUE CD A 249' AC7 Software D MG 340 ? 1 'BINDING SITE FOR RESIDUE MG D 340' AC8 Software D MG 341 ? 1 'BINDING SITE FOR RESIDUE MG D 341' AC9 Software D CD 342 ? 1 'BINDING SITE FOR RESIDUE CD D 342' BC1 Software D CD 343 ? 1 'BINDING SITE FOR RESIDUE CD D 343' BC2 Software D MG 348 ? 1 'BINDING SITE FOR RESIDUE MG D 348' BC3 Software C MG 349 ? 1 'BINDING SITE FOR RESIDUE MG C 349' # 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 2 U B 34 ? U B 234 . ? 1_555 ? 2 AC1 2 G B 36 ? G B 236 . ? 1_555 ? 3 AC2 1 C B 33 ? C B 233 . ? 1_555 ? 4 AC3 2 A B 16 ? A B 216 . ? 1_555 ? 5 AC3 2 G B 17 ? G B 217 . ? 1_555 ? 6 AC4 1 G B 1 ? G B 201 . ? 1_555 ? 7 AC5 2 G B 13 ? G B 213 . ? 1_555 ? 8 AC5 2 G D 13 ? G D 213 . ? 1_555 ? 9 AC6 1 G A 1 ? G A 101 . ? 1_555 ? 10 AC7 1 U D 34 ? U D 234 . ? 1_555 ? 11 AC8 1 C D 33 ? C D 233 . ? 1_555 ? 12 AC9 1 A D 16 ? A D 216 . ? 1_555 ? 13 BC1 1 G D 1 ? G D 201 . ? 1_555 ? 14 BC2 1 G D 25 ? G D 225 . ? 1_555 ? 15 BC3 1 G C 1 ? G C 101 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YKQ _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 1YKQ _atom_sites.fract_transf_matrix[1][1] 0.012872 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003965 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022604 _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] 0.013139 _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 CD MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 101 101 G G A . n A 1 2 G 2 102 102 G G A . n A 1 3 A 3 103 103 A A A . n A 1 4 G 4 104 104 G G A . n A 1 5 C 5 105 105 C C A . n A 1 6 U 6 106 106 U U A . n A 1 7 C 7 107 107 C C A . n A 1 8 G 8 108 108 G G A . n A 1 9 C 9 109 109 C C A . n A 1 10 C 10 110 110 C C A . n A 1 11 C 11 111 111 C C A . n B 2 1 G 1 201 201 G G B . n B 2 2 G 2 202 202 G G B . n B 2 3 G 3 203 203 G G B . n B 2 4 C 4 204 204 C C B . n B 2 5 G 5 205 205 G G B . n B 2 6 A 6 206 206 A A B . n B 2 7 G 7 207 207 G G B . n B 2 8 G 8 208 208 G G B . n B 2 9 C 9 209 209 C C B . n B 2 10 C 10 210 210 C C B . n B 2 11 G 11 211 211 G G B . n B 2 12 U 12 212 212 U U B . n B 2 13 G 13 213 213 G G B . n B 2 14 C 14 214 214 C C B . n B 2 15 C 15 215 215 C C B . n B 2 16 A 16 216 216 A A B . n B 2 17 G 17 217 217 G G B . n B 2 18 C 18 218 218 C C B . n B 2 19 U 19 219 219 U U B . n B 2 20 C 20 220 220 C C B . n B 2 21 U 21 221 221 U U B . n B 2 22 U 22 222 222 U U B . n B 2 23 C 23 223 223 C C B . n B 2 24 G 24 224 224 G G B . n B 2 25 G 25 225 225 G G B . n B 2 26 A 26 226 226 A A B . n B 2 27 G 27 227 227 G G B . n B 2 28 C 28 228 228 C C B . n B 2 29 A 29 229 229 A A B . n B 2 30 A 30 230 230 A A B . n B 2 31 U 31 231 231 U U B . n B 2 32 A 32 232 232 A A B . n B 2 33 C 33 233 233 C C B . n B 2 34 U 34 234 234 U U B . n B 2 35 C 35 235 235 C C B . n B 2 36 G 36 236 236 G G B . n B 2 37 G 37 237 237 G G B . n B 2 38 C 38 238 238 C C B . n C 1 1 G 1 101 101 G G C . n C 1 2 G 2 102 102 G G C . n C 1 3 A 3 103 103 A A C . n C 1 4 G 4 104 104 G G C . n C 1 5 C 5 105 105 C C C . n C 1 6 U 6 106 106 U U C . n C 1 7 C 7 107 107 C C C . n C 1 8 G 8 108 108 G G C . n C 1 9 C 9 109 109 C C C . n C 1 10 C 10 110 110 C C C . n C 1 11 C 11 111 111 C C C . n D 2 1 G 1 201 201 G G D . n D 2 2 G 2 202 202 G G D . n D 2 3 G 3 203 203 G G D . n D 2 4 C 4 204 204 C C D . n D 2 5 G 5 205 205 G G D . n D 2 6 A 6 206 206 A A D . n D 2 7 G 7 207 207 G G D . n D 2 8 G 8 208 208 G G D . n D 2 9 C 9 209 209 C C D . n D 2 10 C 10 210 210 C C D . n D 2 11 G 11 211 211 G G D . n D 2 12 U 12 212 212 U U D . n D 2 13 G 13 213 213 G G D . n D 2 14 C 14 214 214 C C D . n D 2 15 C 15 215 215 C C D . n D 2 16 A 16 216 216 A A D . n D 2 17 G 17 217 217 G G D . n D 2 18 C 18 218 218 C C D . n D 2 19 U 19 219 219 U U D . n D 2 20 C 20 220 220 C C D . n D 2 21 U 21 221 221 U U D . n D 2 22 U 22 222 222 U U D . n D 2 23 C 23 223 223 C C D . n D 2 24 G 24 224 224 G G D . n D 2 25 G 25 225 225 G G D . n D 2 26 A 26 226 226 A A D . n D 2 27 G 27 227 227 G G D . n D 2 28 C 28 228 228 C C D . n D 2 29 A 29 229 229 A A D . n D 2 30 A 30 230 230 A A D . n D 2 31 U 31 231 231 U U D . n D 2 32 A 32 232 232 A A D . n D 2 33 C 33 233 233 C C D . n D 2 34 U 34 234 234 U U D . n D 2 35 C 35 235 235 C C D . n D 2 36 G 36 236 236 G G D . n D 2 37 G 37 237 237 G G D . n D 2 38 C 38 238 238 C C 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 CD 1 249 249 CD CD A . F 4 MG 1 240 240 MG MG B . G 4 MG 1 241 241 MG MG B . H 3 CD 1 242 242 CD CD B . I 3 CD 1 243 243 CD CD B . J 4 MG 1 246 246 MG MG B . K 4 MG 1 349 349 MG MG C . L 4 MG 1 340 340 MG MG D . M 4 MG 1 341 341 MG MG D . N 3 CD 1 342 342 CD CD D . O 3 CD 1 343 343 CD CD D . P 4 MG 1 348 348 MG MG D . # 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,H,I,J 2 1 C,D,K,L,M,N,O,P # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? A G 1 ? A G 101 ? 1_555 CD ? E CD . ? A CD 249 ? 1_555 O6 ? A G 1 ? A G 101 ? 1_555 77.2 ? 2 OP1 ? B G 13 ? B G 213 ? 1_555 MG ? J MG . ? B MG 246 ? 1_555 OP1 ? D G 13 ? D G 213 ? 1_555 78.8 ? 3 N7 ? C G 1 ? C G 101 ? 1_555 MG ? K MG . ? C MG 349 ? 1_555 O6 ? C G 1 ? C G 101 ? 1_555 76.1 ? # 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 2005-02-22 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Refinement description' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' 'Refinement description' # 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_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_ncs_dom_lim 7 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' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 4 'Structure model' '_struct_ncs_dom_lim.beg_auth_comp_id' 17 4 'Structure model' '_struct_ncs_dom_lim.end_auth_comp_id' 18 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 19 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 20 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 34.8903 26.3165 23.0536 -0.1432 -0.0335 -0.2140 -0.1055 0.0076 0.0686 1.9947 3.8868 4.1616 -0.0839 -1.1069 -0.1312 -0.2032 0.5006 -0.2973 0.3208 -0.0009 0.5116 -0.1677 0.4317 -0.0485 'X-RAY DIFFRACTION' 2 ? refined 58.1887 33.3438 22.9837 -0.0431 0.0349 -0.1638 -0.0849 0.0227 -0.1458 2.3200 2.5376 4.4194 -0.6245 2.5601 -0.8796 -0.2539 0.3263 -0.0724 0.2170 0.3499 -0.4412 -0.4012 -0.5310 0.2039 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 101 A 111 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 B 201 B 238 ? . . . . ? 'X-RAY DIFFRACTION' 3 1 A 249 A 249 ? . . . . ? 'X-RAY DIFFRACTION' 4 1 B 240 B 246 ? . . . . ? 'X-RAY DIFFRACTION' 5 2 C 101 C 111 ? . . . . ? 'X-RAY DIFFRACTION' 6 2 D 201 D 238 ? . . . . ? 'X-RAY DIFFRACTION' 7 2 D 340 D 348 ? . . . . ? 'X-RAY DIFFRACTION' 8 2 C 349 C 349 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.9999 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 SHARP phasing . ? 4 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A U 106 ? ? "C1'" A U 106 ? ? 1.475 1.526 -0.051 0.008 N 2 1 "O5'" B A 232 ? ? "C5'" B A 232 ? ? 1.362 1.420 -0.058 0.009 N # 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 "O4'" A G 101 ? ? "C4'" A G 101 ? ? "C3'" A G 101 ? ? 96.02 104.00 -7.98 1.00 N 2 1 "C4'" A G 101 ? ? "C3'" A G 101 ? ? "C2'" A G 101 ? ? 95.68 102.60 -6.92 1.00 N 3 1 "O4'" A G 101 ? ? "C1'" A G 101 ? ? N9 A G 101 ? ? 113.04 108.50 4.54 0.70 N 4 1 "C1'" A A 103 ? ? "O4'" A A 103 ? ? "C4'" A A 103 ? ? 104.68 109.70 -5.02 0.70 N 5 1 "O4'" A A 103 ? ? "C1'" A A 103 ? ? N9 A A 103 ? ? 114.51 108.50 6.01 0.70 N 6 1 "C3'" A U 106 ? ? "C2'" A U 106 ? ? "C1'" A U 106 ? ? 96.57 101.30 -4.73 0.70 N 7 1 "C3'" A U 106 ? ? "O3'" A U 106 ? ? P A C 107 ? ? 110.37 119.70 -9.33 1.20 Y 8 1 "C3'" B C 204 ? ? "C2'" B C 204 ? ? "C1'" B C 204 ? ? 92.97 101.30 -8.33 0.70 N 9 1 "C3'" B C 223 ? ? "C2'" B C 223 ? ? "C1'" B C 223 ? ? 96.64 101.30 -4.66 0.70 N 10 1 "C3'" B A 230 ? ? "C2'" B A 230 ? ? "C1'" B A 230 ? ? 95.28 101.30 -6.02 0.70 N 11 1 "O4'" C A 103 ? ? "C1'" C A 103 ? ? N9 C A 103 ? ? 114.36 108.50 5.86 0.70 N 12 1 "C1'" C G 108 ? ? "O4'" C G 108 ? ? "C4'" C G 108 ? ? 105.12 109.70 -4.58 0.70 N 13 1 "C4'" C G 108 ? ? "C3'" C G 108 ? ? "C2'" C G 108 ? ? 96.49 102.60 -6.11 1.00 N 14 1 "C5'" D G 201 ? ? "C4'" D G 201 ? ? "O4'" D G 201 ? ? 116.66 109.80 6.86 0.90 N 15 1 "C1'" D G 201 ? ? "O4'" D G 201 ? ? "C4'" D G 201 ? ? 101.86 109.70 -7.84 0.70 N 16 1 "C4'" D G 201 ? ? "C3'" D G 201 ? ? "C2'" D G 201 ? ? 96.29 102.60 -6.31 1.00 N 17 1 "O4'" D G 201 ? ? "C1'" D G 201 ? ? N9 D G 201 ? ? 114.51 108.50 6.01 0.70 N 18 1 "C3'" D C 204 ? ? "C2'" D C 204 ? ? "C1'" D C 204 ? ? 96.53 101.30 -4.77 0.70 N 19 1 "C3'" D G 227 ? ? "C2'" D G 227 ? ? "C1'" D G 227 ? ? 95.72 101.30 -5.58 0.70 N 20 1 "C3'" D C 238 ? ? "C2'" D C 238 ? ? "C1'" D C 238 ? ? 96.79 101.30 -4.51 0.70 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 110 ? "O2'" ? A C 10 "O2'" 2 1 Y 1 B C 204 ? "O2'" ? B C 4 "O2'" 3 1 Y 1 B C 209 ? "O2'" ? B C 9 "O2'" 4 1 Y 1 C C 110 ? "O2'" ? C C 10 "O2'" 5 1 Y 1 D C 204 ? "O2'" ? D C 4 "O2'" 6 1 Y 1 D C 209 ? "O2'" ? D C 9 "O2'" # 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 CD CD CD N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 MG MG MG N N 112 U OP3 O N N 113 U P P N N 114 U OP1 O N N 115 U OP2 O N N 116 U "O5'" O N N 117 U "C5'" C N N 118 U "C4'" C N R 119 U "O4'" O N N 120 U "C3'" C N S 121 U "O3'" O N N 122 U "C2'" C N R 123 U "O2'" O N N 124 U "C1'" C N R 125 U N1 N N N 126 U C2 C N N 127 U O2 O N N 128 U N3 N N N 129 U C4 C N N 130 U O4 O N N 131 U C5 C N N 132 U C6 C N N 133 U HOP3 H N N 134 U HOP2 H N N 135 U "H5'" H N N 136 U "H5''" H N N 137 U "H4'" H N N 138 U "H3'" H N N 139 U "HO3'" H N N 140 U "H2'" H N N 141 U "HO2'" H N N 142 U "H1'" H N N 143 U H3 H N N 144 U H5 H N N 145 U H6 H N N 146 # 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 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1YKQ 'double helix' 1YKQ 'a-form double helix' 1YKQ tetraloop 1YKQ 'bulge loop' 1YKQ 'mismatched base pair' 1YKQ 'triple helix' 1YKQ '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 B C 14 1_555 A G 2 1_555 0.341 -0.318 -0.593 12.319 -0.692 -0.670 1 B_C214:G102_A B 214 ? A 102 ? 19 1 1 B C 15 1_555 A G 1 1_555 -1.916 0.359 0.388 5.930 -13.427 6.409 2 B_C215:G101_A B 215 ? A 101 ? ? 1 1 B A 16 1_555 B A 29 1_555 -1.753 2.259 0.101 14.846 -10.703 -32.240 3 B_A216:A229_B B 216 ? B 229 ? ? ? 1 B G 17 1_555 B C 28 1_555 0.887 -0.113 1.031 19.532 -15.151 4.554 4 B_G217:C228_B B 217 ? B 228 ? 19 1 1 B C 18 1_555 B G 27 1_555 -0.388 -0.342 0.347 9.109 -25.443 -1.479 5 B_C218:G227_B B 218 ? B 227 ? 19 1 1 B U 19 1_555 B A 26 1_555 -0.343 -0.273 0.508 5.692 -1.035 2.082 6 B_U219:A226_B B 219 ? B 226 ? 20 1 1 B C 20 1_555 B G 25 1_555 -0.917 0.562 -0.833 2.470 -15.373 18.530 7 B_C220:G225_B B 220 ? B 225 ? ? 1 1 B U 21 1_555 B G 24 1_555 0.467 -5.416 1.306 -14.230 -12.530 -121.214 8 B_U221:G224_B B 221 ? B 224 ? ? 2 1 A A 3 1_555 B U 34 1_555 -1.987 -0.345 -0.706 -0.149 -22.243 -12.731 9 A_A103:U234_B A 103 ? B 234 ? ? ? 1 A G 4 1_555 B C 33 1_555 -1.868 -0.609 -0.174 -6.040 -13.363 2.945 10 A_G104:C233_B A 104 ? B 233 ? 19 1 1 A C 5 1_555 B G 7 1_555 -1.805 -0.266 1.006 -28.508 -4.544 -11.587 11 A_C105:G207_B A 105 ? B 207 ? 19 1 1 A U 6 1_555 B A 6 1_555 -0.891 -0.049 0.919 0.921 -7.273 11.702 12 A_U106:A206_B A 106 ? B 206 ? ? ? 1 A C 7 1_555 B G 5 1_555 0.668 -0.281 -0.769 17.892 -17.749 13.016 13 A_C107:G205_B A 107 ? B 205 ? 19 1 1 A G 8 1_555 B C 4 1_555 2.432 -0.048 0.970 5.169 -13.972 -24.885 14 A_G108:C204_B A 108 ? B 204 ? ? ? 1 A C 9 1_555 B G 3 1_555 -0.112 -0.015 0.376 8.723 -12.605 9.088 15 A_C109:G203_B A 109 ? B 203 ? 19 1 1 A C 10 1_555 B G 2 1_555 1.728 0.277 0.995 -10.147 -16.702 22.004 16 A_C110:G202_B A 110 ? B 202 ? ? 1 1 A C 11 1_555 B G 1 1_555 -0.701 1.108 1.596 -14.568 17.076 -39.012 17 A_C111:G201_B A 111 ? B 201 ? ? ? 1 B G 8 1_555 B C 38 1_555 -1.051 0.382 -0.313 0.937 -9.918 14.011 18 B_G208:C238_B B 208 ? B 238 ? ? 1 1 B C 9 1_555 B G 37 1_555 0.575 -0.318 0.153 2.293 -14.381 -2.121 19 B_C209:G237_B B 209 ? B 237 ? 19 1 1 B C 10 1_555 B G 36 1_555 0.165 -0.459 0.290 1.788 -27.169 2.809 20 B_C210:G236_B B 210 ? B 236 ? 19 1 1 B G 11 1_555 B C 35 1_555 -1.041 -0.317 0.537 8.635 -6.598 -5.259 21 B_G211:C235_B B 211 ? B 235 ? 19 1 1 B U 12 1_555 B A 32 1_555 3.819 -1.905 0.089 4.751 -2.528 -96.036 22 B_U212:A232_B B 212 ? B 232 ? 24 4 1 D C 14 1_555 C G 2 1_555 -0.372 -0.067 0.522 4.816 5.291 4.397 23 D_C214:G102_C D 214 ? C 102 ? 19 1 1 D C 15 1_555 C G 1 1_555 -2.392 0.275 0.425 18.255 -18.087 8.855 24 D_C215:G101_C D 215 ? C 101 ? ? 1 1 D A 16 1_555 D A 29 1_555 -3.268 1.663 0.039 20.637 -1.750 -28.435 25 D_A216:A229_D D 216 ? D 229 ? ? ? 1 D G 17 1_555 D C 28 1_555 -0.589 -0.384 0.500 10.623 -9.096 3.073 26 D_G217:C228_D D 217 ? D 228 ? 19 1 1 D C 18 1_555 D G 27 1_555 -1.630 0.009 0.164 6.675 -11.613 -6.194 27 D_C218:G227_D D 218 ? D 227 ? 19 1 1 D U 19 1_555 D A 26 1_555 0.203 -0.212 0.330 1.159 -0.255 4.467 28 D_U219:A226_D D 219 ? D 226 ? 20 1 1 D C 20 1_555 D G 25 1_555 -1.361 0.234 -0.543 2.491 0.785 6.762 29 D_C220:G225_D D 220 ? D 225 ? ? 1 1 D U 21 1_555 D G 24 1_555 1.014 -5.073 1.406 -22.722 -5.471 -121.100 30 D_U221:G224_D D 221 ? D 224 ? ? ? 1 C A 3 1_555 D U 34 1_555 -0.559 0.460 -1.742 -35.699 -21.463 -19.095 31 C_A103:U234_D C 103 ? D 234 ? ? ? 1 C G 4 1_555 D C 33 1_555 1.499 0.268 0.123 2.325 -21.072 13.736 32 C_G104:C233_D C 104 ? D 233 ? ? 1 1 C C 5 1_555 D G 7 1_555 -0.436 -0.246 -1.961 22.957 -24.593 3.326 33 C_C105:G207_D C 105 ? D 207 ? ? ? 1 C U 6 1_555 D A 6 1_555 -0.354 -0.050 0.633 -0.976 -1.191 1.873 34 C_U106:A206_D C 106 ? D 206 ? 20 1 1 C C 7 1_555 D G 5 1_555 0.449 -0.445 0.064 11.311 -17.381 6.238 35 C_C107:G205_D C 107 ? D 205 ? 19 1 1 C G 8 1_555 D C 4 1_555 0.824 -0.298 1.228 7.602 -8.226 -17.297 36 C_G108:C204_D C 108 ? D 204 ? 19 1 1 C C 9 1_555 D G 3 1_555 -1.034 -0.354 0.351 6.044 -15.069 0.706 37 C_C109:G203_D C 109 ? D 203 ? 19 1 1 C C 10 1_555 D G 2 1_555 1.475 -0.151 1.267 -10.934 -4.479 8.514 38 C_C110:G202_D C 110 ? D 202 ? ? 1 1 D G 8 1_555 D C 38 1_555 -1.123 0.504 -0.369 14.815 -2.578 14.357 39 D_G208:C238_D D 208 ? D 238 ? ? ? 1 D C 9 1_555 D G 37 1_555 -0.123 -0.431 -0.967 13.247 -4.799 -2.695 40 D_C209:G237_D D 209 ? D 237 ? 19 1 1 D C 10 1_555 D G 36 1_555 0.623 -0.496 -0.101 -4.986 -7.421 -1.979 41 D_C210:G236_D D 210 ? D 236 ? 19 1 1 D G 11 1_555 D C 35 1_555 -1.108 -0.384 -0.163 -16.860 -18.782 -2.879 42 D_G211:C235_D D 211 ? D 235 ? 19 1 1 D U 12 1_555 D A 32 1_555 4.238 -2.093 1.310 -0.120 17.174 -97.354 43 D_U212:A232_D D 212 ? D 232 ? 24 4 # 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 14 1_555 A G 2 1_555 B C 15 1_555 A G 1 1_555 0.695 -2.349 3.363 -8.554 9.834 29.311 -5.837 -2.633 2.198 18.334 15.947 32.020 1 BB_C214C215:G101G102_AA B 214 ? A 102 ? B 215 ? A 101 ? 1 B C 15 1_555 A G 1 1_555 B A 16 1_555 B A 29 1_555 3.759 -1.045 3.684 -7.429 -13.003 73.183 -0.417 -3.360 3.463 -10.796 6.168 74.490 2 BB_C215A216:A229G101_BA B 215 ? A 101 ? B 216 ? B 229 ? 1 B A 16 1_555 B A 29 1_555 B G 17 1_555 B C 28 1_555 1.442 -1.296 2.867 -8.636 6.745 43.051 -2.222 -2.557 2.332 9.018 11.546 44.360 3 BB_A216G217:C228A229_BB B 216 ? B 229 ? B 217 ? B 228 ? 1 B G 17 1_555 B C 28 1_555 B C 18 1_555 B G 27 1_555 -0.175 -2.267 3.226 0.303 1.700 28.111 -5.043 0.428 3.085 3.495 -0.623 28.163 4 BB_G217C218:G227C228_BB B 217 ? B 228 ? B 218 ? B 227 ? 1 B C 18 1_555 B G 27 1_555 B U 19 1_555 B A 26 1_555 -0.084 -2.347 3.144 -7.362 5.160 30.334 -5.175 -1.082 2.665 9.599 13.695 31.608 5 BB_C218U219:A226G227_BB B 218 ? B 227 ? B 219 ? B 226 ? 1 B U 19 1_555 B A 26 1_555 B C 20 1_555 B G 25 1_555 1.040 -1.917 2.941 11.138 9.174 26.061 -5.412 0.008 2.387 18.636 -22.626 29.729 6 BB_U219C220:G225A226_BB B 219 ? B 226 ? B 220 ? B 225 ? 1 B C 20 1_555 B G 25 1_555 B U 21 1_555 B G 24 1_555 -2.282 -0.750 3.374 -6.196 16.736 106.054 -0.695 1.334 3.362 10.427 3.860 107.095 7 BB_C220U221:G224G225_BB B 220 ? B 225 ? B 221 ? B 224 ? 1 A A 3 1_555 B U 34 1_555 A G 4 1_555 B C 33 1_555 2.284 -1.034 3.230 -2.807 14.057 28.072 -4.238 -4.679 2.237 26.875 5.367 31.455 8 AA_A103G104:C233U234_BB A 103 ? B 234 ? A 104 ? B 233 ? 1 A G 4 1_555 B C 33 1_555 A C 5 1_555 B G 7 1_555 -1.186 -2.704 3.651 -11.447 11.356 23.067 -8.303 -0.308 2.406 24.872 25.072 28.081 9 AA_G104C105:G207C233_BB A 104 ? B 233 ? A 105 ? B 207 ? 1 A C 5 1_555 B G 7 1_555 A U 6 1_555 B A 6 1_555 0.441 -1.720 2.447 -5.358 -1.789 44.372 -2.139 -0.947 2.444 -2.357 7.061 44.713 10 AA_C105U106:A206G207_BB A 105 ? B 207 ? A 106 ? B 206 ? 1 A U 6 1_555 B A 6 1_555 A C 7 1_555 B G 5 1_555 0.212 -1.631 2.707 13.576 2.606 31.522 -3.098 1.394 2.451 4.534 -23.620 34.349 11 AA_U106C107:G205A206_BB A 106 ? B 206 ? A 107 ? B 205 ? 1 A C 7 1_555 B G 5 1_555 A G 8 1_555 B C 4 1_555 -0.905 -2.369 3.322 -7.663 15.493 42.430 -4.304 0.548 2.477 20.422 10.101 45.664 12 AA_C107G108:C204G205_BB A 107 ? B 205 ? A 108 ? B 204 ? 1 A G 8 1_555 B C 4 1_555 A C 9 1_555 B G 3 1_555 1.615 -1.525 2.905 10.007 4.842 23.347 -4.687 -0.978 2.966 11.188 -23.121 25.825 13 AA_G108C109:G203C204_BB A 108 ? B 204 ? A 109 ? B 203 ? 1 A C 9 1_555 B G 3 1_555 A C 10 1_555 B G 2 1_555 0.956 -0.390 3.456 -0.311 10.582 41.138 -1.662 -1.355 3.256 14.767 0.434 42.421 14 AA_C109C110:G202G203_BB A 109 ? B 203 ? A 110 ? B 202 ? 1 A C 10 1_555 B G 2 1_555 A C 11 1_555 B G 1 1_555 -2.151 -1.892 3.139 -2.152 12.178 29.381 -5.393 3.580 2.338 22.780 4.025 31.824 15 AA_C110C111:G201G202_BB A 110 ? B 202 ? A 111 ? B 201 ? 1 B G 8 1_555 B C 38 1_555 B C 9 1_555 B G 37 1_555 -1.243 -1.518 3.171 -10.644 4.701 45.485 -2.294 0.688 3.205 5.966 13.507 46.873 16 BB_G208C209:G237C238_BB B 208 ? B 238 ? B 209 ? B 237 ? 1 B C 9 1_555 B G 37 1_555 B C 10 1_555 B G 36 1_555 -0.078 -2.166 2.939 2.261 11.463 27.724 -5.994 0.509 1.901 22.687 -4.475 30.041 17 BB_C209C210:G236G237_BB B 209 ? B 237 ? B 210 ? B 236 ? 1 B C 10 1_555 B G 36 1_555 B G 11 1_555 B C 35 1_555 -0.250 -1.910 2.796 -8.372 9.007 25.014 -5.636 -1.028 1.983 19.372 18.006 27.831 18 BB_C210G211:C235G236_BB B 210 ? B 236 ? B 211 ? B 235 ? 1 B G 11 1_555 B C 35 1_555 B U 12 1_555 B A 32 1_555 -2.548 -1.918 3.565 3.387 -0.055 84.125 -1.429 1.987 3.481 -0.041 -2.527 84.181 19 BB_G211U212:A232C235_BB B 211 ? B 235 ? B 212 ? B 232 ? 1 D C 14 1_555 C G 2 1_555 D C 15 1_555 C G 1 1_555 0.735 -2.252 2.564 1.241 0.828 30.706 -4.375 -1.196 2.531 1.562 -2.343 30.741 20 DD_C214C215:G101G102_CC D 214 ? C 102 ? D 215 ? C 101 ? 1 D C 15 1_555 C G 1 1_555 D A 16 1_555 D A 29 1_555 4.014 -0.613 3.771 -5.295 -14.594 68.375 0.055 -3.718 3.544 -12.819 4.651 69.906 21 DD_C215A216:A229G101_DC D 215 ? C 101 ? D 216 ? D 229 ? 1 D A 16 1_555 D A 29 1_555 D G 17 1_555 D C 28 1_555 1.588 -1.271 3.260 -9.196 10.383 44.737 -2.392 -2.701 2.563 13.268 11.751 46.732 22 DD_A216G217:C228A229_DD D 216 ? D 229 ? D 217 ? D 228 ? 1 D G 17 1_555 D C 28 1_555 D C 18 1_555 D G 27 1_555 -0.478 -2.399 3.226 -3.351 1.184 25.744 -5.655 0.160 3.150 2.642 7.475 25.984 23 DD_G217C218:G227C228_DD D 217 ? D 228 ? D 218 ? D 227 ? 1 D C 18 1_555 D G 27 1_555 D U 19 1_555 D A 26 1_555 0.185 -2.020 3.271 -4.126 4.486 46.205 -2.919 -0.569 3.046 5.687 5.230 46.583 24 DD_C218U219:A226G227_DD D 218 ? D 227 ? D 219 ? D 226 ? 1 D U 19 1_555 D A 26 1_555 D C 20 1_555 D G 25 1_555 -0.001 -2.010 2.868 5.467 11.684 22.412 -6.886 1.119 1.597 27.342 -12.794 25.818 25 DD_U219C220:G225A226_DD D 219 ? D 226 ? D 220 ? D 225 ? 1 D C 20 1_555 D G 25 1_555 D U 21 1_555 D G 24 1_555 -2.347 -0.513 3.352 -2.205 17.486 101.258 -0.594 1.473 3.299 11.250 1.419 102.364 26 DD_C220U221:G224G225_DD D 220 ? D 225 ? D 221 ? D 224 ? 1 C A 3 1_555 D U 34 1_555 C G 4 1_555 D C 33 1_555 1.500 -0.166 2.678 -8.620 -13.158 45.713 0.609 -2.369 2.336 -16.377 10.729 48.206 27 CC_A103G104:C233U234_DD C 103 ? D 234 ? C 104 ? D 233 ? 1 C G 4 1_555 D C 33 1_555 C C 5 1_555 D G 7 1_555 -1.720 -2.286 2.515 11.978 9.023 7.857 -9.318 7.900 -1.261 37.605 -49.922 16.919 28 CC_G104C105:G207C233_DD C 104 ? D 233 ? C 105 ? D 207 ? 1 C C 5 1_555 D G 7 1_555 C U 6 1_555 D A 6 1_555 -0.345 -1.699 4.020 -27.510 27.214 38.345 -3.819 -1.587 2.255 32.994 33.353 53.954 29 CC_C105U106:A206G207_DD C 105 ? D 207 ? C 106 ? D 206 ? 1 C U 6 1_555 D A 6 1_555 C C 7 1_555 D G 5 1_555 -0.483 -1.325 2.737 0.219 1.885 37.137 -2.285 0.781 2.666 2.957 -0.344 37.183 30 CC_U106C107:G205A206_DD C 106 ? D 206 ? C 107 ? D 205 ? 1 C C 7 1_555 D G 5 1_555 C G 8 1_555 D C 4 1_555 -1.582 -1.989 2.962 -12.076 7.154 28.710 -4.836 0.828 2.823 13.459 22.718 31.892 31 CC_C107G108:C204G205_DD C 107 ? D 205 ? C 108 ? D 204 ? 1 C G 8 1_555 D C 4 1_555 C C 9 1_555 D G 3 1_555 0.551 -2.375 3.081 8.649 1.852 26.792 -5.285 0.779 2.944 3.866 -18.050 28.189 32 CC_G108C109:G203C204_DD C 108 ? D 204 ? C 109 ? D 203 ? 1 C C 9 1_555 D G 3 1_555 C C 10 1_555 D G 2 1_555 0.543 -0.899 3.514 -6.308 5.228 47.425 -1.535 -1.187 3.309 6.444 7.775 48.087 33 CC_C109C110:G202G203_DD C 109 ? D 203 ? C 110 ? D 202 ? 1 D G 8 1_555 D C 38 1_555 D C 9 1_555 D G 37 1_555 -1.092 -1.945 3.324 -4.551 -0.262 40.555 -2.760 1.046 3.434 -0.376 6.540 40.799 34 DD_G208C209:G237C238_DD D 208 ? D 238 ? D 209 ? D 237 ? 1 D C 9 1_555 D G 37 1_555 D C 10 1_555 D G 36 1_555 -0.102 -1.875 3.784 -6.529 9.628 33.487 -4.622 -0.876 3.109 16.117 10.929 35.396 35 DD_C209C210:G236G237_DD D 209 ? D 237 ? D 210 ? D 236 ? 1 D C 10 1_555 D G 36 1_555 D G 11 1_555 D C 35 1_555 0.329 -2.050 3.208 2.475 17.465 26.614 -6.309 -0.235 1.613 33.648 -4.768 31.841 36 DD_C210G211:C235G236_DD D 210 ? D 236 ? D 211 ? D 235 ? 1 D G 11 1_555 D C 35 1_555 D U 12 1_555 D A 32 1_555 -3.129 -1.587 3.128 -8.781 4.112 84.929 -1.263 2.109 3.313 3.037 6.485 85.376 37 DD_G211U212:A232C235_DD D 211 ? D 235 ? D 212 ? D 232 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'CADMIUM ION' CD 4 'MAGNESIUM ION' MG # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1YLS _pdbx_initial_refinement_model.details 'Diels-Alder ribozyme from the ribozyme-product complex, pdb entry 1YLS' #