data_5EAQ # _entry.id 5EAQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 5EAQ pdb_00005eaq 10.2210/pdb5eaq/pdb WWPDB D_1000214609 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details . _pdbx_database_related.db_id 5EAO _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5EAQ _pdbx_database_status.recvd_initial_deposition_date 2015-10-16 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mir, A.' 1 'Golden, B.L.' 2 # loop_ _citation.abstract _citation.abstract_id_CAS _citation.book_id_ISBN _citation.book_publisher _citation.book_publisher_city _citation.book_title _citation.coordinate_linkage _citation.country _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? US ? ? primary Biochemistry BICHAW 0033 0006-2960 ? ? 55 ? 633 636 'Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.' 2016 ? 10.1021/acs.biochem.5b01139 26551631 ? ? ? ? ? ? ? ? US ? ? 1 Biochemistry BICHAW 0033 0006-2960 ? ? 54 ? 6369 6381 'Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.' 2015 ? 10.1021/acs.biochem.5b00824 26398724 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mir, A.' 1 ? primary 'Golden, B.L.' 2 ? 1 'Mir, A.' 3 ? 1 'Chen, J.' 4 ? 1 'Robinson, K.' 5 ? 1 'Lendy, E.' 6 ? 1 'Goodman, J.' 7 ? 1 'Neau, D.' 8 ? 1 'Golden, B.L.' 9 ? # _cell.entry_id 5EAQ _cell.length_a 81.251 _cell.length_b 87.419 _cell.length_c 105.539 _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 5EAQ _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 # 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 man 'RNA (48-MER)' 15500.287 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') ; 6536.834 1 ? ? ? ? 3 non-polymer syn 'MANGANESE (II) ION' 54.938 6 ? ? ? ? # 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 GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA A ? 2 polyribonucleotide no yes 'GGGCGU(CVC)UGGGCAGUACCCA' GGGCGUXUGGGCAGUACCCA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 G n 1 4 U n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 C n 1 13 C n 1 14 C n 1 15 A n 1 16 C n 1 17 U n 1 18 G n 1 19 A n 1 20 U n 1 21 G n 1 22 A n 1 23 G n 1 24 U n 1 25 C n 1 26 G n 1 27 C n 1 28 U n 1 29 G n 1 30 G n 1 31 G n 1 32 A n 1 33 U n 1 34 G n 1 35 C n 1 36 G n 1 37 A n 1 38 C n 1 39 G n 1 40 A n 1 41 A n 1 42 A n 1 43 C n 1 44 G n 1 45 C n 1 46 C n 1 47 C n 1 48 A n 2 1 G n 2 2 G n 2 3 G n 2 4 C n 2 5 G n 2 6 U n 2 7 CVC n 2 8 U n 2 9 G n 2 10 G n 2 11 G n 2 12 C n 2 13 A n 2 14 G n 2 15 U n 2 16 A n 2 17 C n 2 18 C n 2 19 C n 2 20 A n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 48 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain DH5alpha _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pUC19 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 20 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5EAQ 5EAQ ? 1 ? 1 2 PDB 5EAQ 5EAQ ? 2 ? 1 # 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 5EAQ A 1 ? 48 ? 5EAQ 1 ? 48 ? 1 48 2 2 5EAQ B 1 ? 20 ? 5EAQ 1 ? 20 ? 1 20 # 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 CVC 'RNA linking' . ;[(1~{R},5~{R},6~{R},8~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,3-bis(oxidanyl)-2,4,7-trioxa-3$l^{4}-vanadabicyclo[3.3.0]octan-8-yl]methyl dihydrogen phosphate ; ? 'C9 H14 N3 O10 P V' 406.137 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5EAQ _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 4.25 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 71.07 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 8.2 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 273 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '50 mM Tris pH 8.2, 10 mM MgCl2, 32% MPD, 0.9 M KCl, 0.5 mM spermine 2 mM NH4VO3' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-11-17 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.501 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.501 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5EAQ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.95 _reflns.d_resolution_low 50.0 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 12773 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.4 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.3 _reflns.pdbx_Rmerge_I_obs 0.196 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 139.7 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.95 _reflns_shell.d_res_low 3.00 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 19.4 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 97.2 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.636 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 5.0 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5EAQ _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 11830 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.37 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.429 _refine.ls_d_res_high 3.201 _refine.ls_percent_reflns_obs 98.82 _refine.ls_R_factor_obs 0.2499 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2471 _refine.ls_R_factor_R_free 0.2777 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.97 _refine.ls_number_reflns_R_free 1180 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model 5DI2 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.34 _refine.pdbx_overall_phase_error 30.95 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1456 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1462 _refine_hist.d_res_high 3.201 _refine_hist.d_res_low 27.429 # 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 f_bond_d 0.007 ? ? 1628 'X-RAY DIFFRACTION' ? f_angle_d 1.251 ? ? 2533 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 12.199 ? ? 795 'X-RAY DIFFRACTION' ? f_chiral_restr 0.054 ? ? 337 'X-RAY DIFFRACTION' ? f_plane_restr 0.009 ? ? 68 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 3.2009 3.3464 1298 0.2830 96.00 0.3269 . . 147 . . . . 'X-RAY DIFFRACTION' . 3.3464 3.5224 1340 0.2475 98.00 0.2747 . . 139 . . . . 'X-RAY DIFFRACTION' . 3.5224 3.7426 1298 0.2305 99.00 0.2771 . . 148 . . . . 'X-RAY DIFFRACTION' . 3.7426 4.0308 1338 0.2228 99.00 0.3078 . . 157 . . . . 'X-RAY DIFFRACTION' . 4.0308 4.4349 1344 0.2168 100.00 0.3148 . . 142 . . . . 'X-RAY DIFFRACTION' . 4.4349 5.0731 1349 0.2309 100.00 0.2613 . . 149 . . . . 'X-RAY DIFFRACTION' . 5.0731 6.3783 1334 0.2582 100.00 0.2567 . . 149 . . . . 'X-RAY DIFFRACTION' . 6.3783 27.4300 1349 0.2632 99.00 0.2680 . . 149 . . . . # _struct.entry_id 5EAQ _struct.title 'Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5EAQ _struct_keywords.text 'ribozyme, hammerhead, RNA' _struct_keywords.pdbx_keywords 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 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? # 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 covale1 covale none ? B U 6 "C3'" ? ? ? 1_555 B CVC 7 OP2 ? ? B U 6 B CVC 7 1_555 ? ? ? ? ? ? ? 1.513 ? ? metalc1 metalc ? ? A G 1 N7 ? ? ? 1_555 F MN . MN ? ? A G 1 A MN 104 1_555 ? ? ? ? ? ? ? 2.434 ? ? metalc2 metalc ? ? A G 1 N7 ? ? ? 1_555 F MN . MN ? ? A G 1 A MN 104 3_455 ? ? ? ? ? ? ? 2.434 ? ? metalc3 metalc ? ? A G 18 N7 ? ? ? 1_555 E MN . MN ? ? A G 18 A MN 103 1_555 ? ? ? ? ? ? ? 2.728 ? ? metalc4 metalc ? ? A A 22 OP2 ? ? ? 1_555 C MN . MN ? ? A A 22 A MN 101 1_555 ? ? ? ? ? ? ? 2.199 ? ? metalc5 metalc ? ? A G 23 N7 ? ? ? 1_555 C MN . MN ? ? A G 23 A MN 101 1_555 ? ? ? ? ? ? ? 2.723 ? ? metalc6 metalc ? ? A G 29 N7 ? ? ? 1_555 H MN . MN ? ? A G 29 A MN 106 1_555 ? ? ? ? ? ? ? 2.617 ? ? metalc7 metalc ? ? A G 39 O6 ? ? ? 1_555 D MN . MN ? ? A G 39 A MN 102 1_555 ? ? ? ? ? ? ? 2.628 ? ? metalc8 metalc ? ? A A 41 OP2 ? ? ? 1_555 G MN . MN ? ? A A 41 A MN 105 1_555 ? ? ? ? ? ? ? 2.348 ? ? metalc9 metalc ? ? B CVC 7 V ? ? ? 1_555 B U 8 "O5'" ? ? B CVC 7 B U 8 1_555 ? ? ? ? ? ? ? 1.981 ? ? hydrog1 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 13 N7 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog2 hydrog ? ? A U 7 O2 ? ? ? 1_555 B A 13 N6 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog3 hydrog ? ? A A 10 N1 ? ? ? 1_555 A G 29 N2 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog4 hydrog ? ? A A 10 N6 ? ? ? 1_555 A G 29 N3 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog5 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 15 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 15 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 18 N2 ? ? ? 1_555 A A 41 N1 ? ? A G 18 A A 41 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog23 hydrog ? ? A A 22 N6 ? ? ? 1_555 A C 38 N3 ? ? A A 22 A C 38 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog24 hydrog ? ? A A 22 N6 ? ? ? 1_555 A G 39 N3 ? ? A A 22 A G 39 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog25 hydrog ? ? A A 22 N7 ? ? ? 1_555 A G 39 N2 ? ? A A 22 A G 39 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog26 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 24 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 24 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 27 N3 ? ? ? 1_555 A G 34 N1 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 27 N4 ? ? ? 1_555 A G 34 O6 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A U 28 N3 ? ? ? 1_555 A A 32 N7 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog41 hydrog ? ? A U 28 O2 ? ? ? 1_555 A A 32 N6 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog42 hydrog ? ? A A 42 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 42 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 43 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 43 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 43 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 44 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 44 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 44 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 45 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 45 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 45 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 46 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 46 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 46 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 47 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 47 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 47 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 A MN 101 ? 2 'binding site for residue MN A 101' AC2 Software A MN 102 ? 1 'binding site for residue MN A 102' AC3 Software A MN 103 ? 1 'binding site for residue MN A 103' AC4 Software A MN 104 ? 2 'binding site for residue MN A 104' AC5 Software A MN 105 ? 1 'binding site for residue MN A 105' AC6 Software A MN 106 ? 1 'binding site for residue MN A 106' # 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 A A 22 ? A A 22 . ? 1_555 ? 2 AC1 2 G A 23 ? G A 23 . ? 1_555 ? 3 AC2 1 G A 39 ? G A 39 . ? 1_555 ? 4 AC3 1 G A 18 ? G A 18 . ? 1_555 ? 5 AC4 2 G A 1 ? G A 1 . ? 1_555 ? 6 AC4 2 G A 1 ? G A 1 . ? 3_455 ? 7 AC5 1 A A 41 ? A A 41 . ? 1_555 ? 8 AC6 1 G A 29 ? G A 29 . ? 1_555 ? # _atom_sites.entry_id 5EAQ _atom_sites.fract_transf_matrix[1][1] 0.012308 _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] 0.011439 _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] 0.009475 _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 MN N O P V # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 C 16 16 16 C C A . n A 1 17 U 17 17 17 U U A . n A 1 18 G 18 18 18 G G A . n A 1 19 A 19 19 19 A A A . n A 1 20 U 20 20 20 U U A . n A 1 21 G 21 21 21 G G A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 U 28 28 28 U U A . n A 1 29 G 29 29 29 G G A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 A 32 32 32 A A A . n A 1 33 U 33 33 33 U U A . n A 1 34 G 34 34 34 G G A . n A 1 35 C 35 35 35 C C A . n A 1 36 G 36 36 36 G G A . n A 1 37 A 37 37 37 A A A . n A 1 38 C 38 38 38 C C A . n A 1 39 G 39 39 39 G G A . n A 1 40 A 40 40 40 A A A . n A 1 41 A 41 41 41 A A A . n A 1 42 A 42 42 42 A A A . n A 1 43 C 43 43 43 C C A . n A 1 44 G 44 44 44 G G A . n A 1 45 C 45 45 45 C C A . n A 1 46 C 46 46 46 C C A . n A 1 47 C 47 47 47 C C A . n A 1 48 A 48 48 48 A A A . n B 2 1 G 1 1 1 G G B . n B 2 2 G 2 2 2 G G B . n B 2 3 G 3 3 3 G G B . n B 2 4 C 4 4 4 C C B . n B 2 5 G 5 5 5 G G B . n B 2 6 U 6 6 6 U U B . n B 2 7 CVC 7 7 7 CVC CVC B . n B 2 8 U 8 8 8 U U B . n B 2 9 G 9 9 9 G G B . n B 2 10 G 10 10 10 G G B . n B 2 11 G 11 11 11 G G B . n B 2 12 C 12 12 12 C C B . n B 2 13 A 13 13 13 A A B . n B 2 14 G 14 14 14 G G B . n B 2 15 U 15 15 15 U U B . n B 2 16 A 16 16 16 A A B . n B 2 17 C 17 17 17 C C B . n B 2 18 C 18 18 18 C C B . n B 2 19 C 19 19 19 C C B . n B 2 20 A 20 20 20 A A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 MN 1 101 3 MN MN A . D 3 MN 1 102 4 MN MN A . E 3 MN 1 103 5 MN MN A . F 3 MN 1 104 7 MN MN A . G 3 MN 1 105 8 MN MN A . H 3 MN 1 106 9 MN MN A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2620 ? 1 MORE -34 ? 1 'SSA (A^2)' 12190 ? # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id MN _pdbx_struct_special_symmetry.auth_seq_id 104 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id MN _pdbx_struct_special_symmetry.label_seq_id . # 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 1 ? 1_555 MN ? F MN . ? A MN 104 ? 1_555 N7 ? A G 1 ? A G 1 ? 1_555 0.0 ? 2 OP2 ? A A 22 ? A A 22 ? 1_555 MN ? C MN . ? A MN 101 ? 1_555 N7 ? A G 23 ? A G 23 ? 1_555 99.1 ? 3 "O5'" ? B U 8 ? B U 8 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 "O2'" ? B CVC 7 ? B CVC 7 ? 1_555 174.1 ? 4 "O5'" ? B U 8 ? B U 8 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O1V ? B CVC 7 ? B CVC 7 ? 1_555 82.5 ? 5 "O2'" ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O1V ? B CVC 7 ? B CVC 7 ? 1_555 95.5 ? 6 "O5'" ? B U 8 ? B U 8 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 "O3'" ? B CVC 7 ? B CVC 7 ? 1_555 89.1 ? 7 "O2'" ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 "O3'" ? B CVC 7 ? B CVC 7 ? 1_555 87.2 ? 8 O1V ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 "O3'" ? B CVC 7 ? B CVC 7 ? 1_555 121.6 ? 9 "O5'" ? B U 8 ? B U 8 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O2V ? B CVC 7 ? B CVC 7 ? 1_555 75.1 ? 10 "O2'" ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O2V ? B CVC 7 ? B CVC 7 ? 1_555 110.6 ? 11 O1V ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O2V ? B CVC 7 ? B CVC 7 ? 1_555 120.9 ? 12 "O3'" ? B CVC 7 ? B CVC 7 ? 1_555 V ? B CVC 7 ? B CVC 7 ? 1_555 O2V ? B CVC 7 ? B CVC 7 ? 1_555 112.1 ? # 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 2016-02-24 2 'Structure model' 1 1 2023-09-27 # _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' Advisory 2 2 'Structure model' 'Data collection' 3 2 'Structure model' 'Database references' 4 2 'Structure model' 'Derived calculations' 5 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_initial_refinement_model 5 2 'Structure model' pdbx_struct_oper_list 6 2 'Structure model' pdbx_unobs_or_zero_occ_atoms 7 2 'Structure model' struct_conn 8 2 'Structure model' struct_conn_type # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 2 'Structure model' '_struct_conn.conn_type_id' 5 2 'Structure model' '_struct_conn.id' 6 2 'Structure model' '_struct_conn.pdbx_dist_value' 7 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 2 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 9 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 10 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 11 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 12 2 'Structure model' '_struct_conn.ptnr1_label_atom_id' 13 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 14 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 15 2 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 16 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 17 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 18 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 19 2 'Structure model' '_struct_conn.ptnr2_label_atom_id' 20 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 21 2 'Structure model' '_struct_conn.ptnr2_label_seq_id' 22 2 'Structure model' '_struct_conn.ptnr2_symmetry' 23 2 'Structure model' '_struct_conn_type.id' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.10_2155)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.10_2155)' 4 # 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 "O5'" B U 6 ? ? "C5'" B U 6 ? ? "C4'" B U 6 ? ? 104.22 109.40 -5.18 0.80 N 2 1 "C5'" B U 6 ? ? "C4'" B U 6 ? ? "O4'" B U 6 ? ? 117.46 109.80 7.66 0.90 N 3 1 "O4'" B U 6 ? ? "C1'" B U 6 ? ? N1 B U 6 ? ? 114.18 108.50 5.68 0.70 N # 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 CVC O01 O N N 73 CVC C02 C N N 74 CVC P P N N 75 CVC "C5'" C N N 76 CVC "O5'" O N N 77 CVC "C4'" C N R 78 CVC "O4'" O N N 79 CVC "C3'" C N R 80 CVC "O3'" O N N 81 CVC "C2'" C N R 82 CVC "O2'" O N N 83 CVC "C1'" C N R 84 CVC C01 C N N 85 CVC N01 N N N 86 CVC O1V O N N 87 CVC N02 N N N 88 CVC O02 O N N 89 CVC O2V O N N 90 CVC N9 N N N 91 CVC OP1 O N N 92 CVC OP2 O N N 93 CVC V V N N 94 CVC C4 C N N 95 CVC C8 C N N 96 CVC H1 H N N 97 CVC H2 H N N 98 CVC H3 H N N 99 CVC H4 H N N 100 CVC H5 H N N 101 CVC H6 H N N 102 CVC H7 H N N 103 CVC H8 H N N 104 CVC H9 H N N 105 CVC H10 H N N 106 CVC H11 H N N 107 CVC H12 H N N 108 CVC H13 H N N 109 CVC H14 H N N 110 G OP3 O N N 111 G P P N N 112 G OP1 O N N 113 G OP2 O N N 114 G "O5'" O N N 115 G "C5'" C N N 116 G "C4'" C N R 117 G "O4'" O N N 118 G "C3'" C N S 119 G "O3'" O N N 120 G "C2'" C N R 121 G "O2'" O N N 122 G "C1'" C N R 123 G N9 N Y N 124 G C8 C Y N 125 G N7 N Y N 126 G C5 C Y N 127 G C6 C N N 128 G O6 O N N 129 G N1 N N N 130 G C2 C N N 131 G N2 N N N 132 G N3 N N N 133 G C4 C Y N 134 G HOP3 H N N 135 G HOP2 H N N 136 G "H5'" H N N 137 G "H5''" H N N 138 G "H4'" H N N 139 G "H3'" H N N 140 G "HO3'" H N N 141 G "H2'" H N N 142 G "HO2'" H N N 143 G "H1'" H N N 144 G H8 H N N 145 G H1 H N N 146 G H21 H N N 147 G H22 H N N 148 MN MN MN N N 149 U OP3 O N N 150 U P P N N 151 U OP1 O N N 152 U OP2 O N N 153 U "O5'" O N N 154 U "C5'" C N N 155 U "C4'" C N R 156 U "O4'" O N N 157 U "C3'" C N S 158 U "O3'" O N N 159 U "C2'" C N R 160 U "O2'" O N N 161 U "C1'" C N R 162 U N1 N N N 163 U C2 C N N 164 U O2 O N N 165 U N3 N N N 166 U C4 C N N 167 U O4 O N N 168 U C5 C N N 169 U C6 C N N 170 U HOP3 H N N 171 U HOP2 H N N 172 U "H5'" H N N 173 U "H5''" H N N 174 U "H4'" H N N 175 U "H3'" H N N 176 U "HO3'" H N N 177 U "H2'" H N N 178 U "HO2'" H N N 179 U "H1'" H N N 180 U H3 H N N 181 U H5 H N N 182 U H6 H N N 183 # 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 CVC N02 C02 sing N N 76 CVC C02 N01 doub N N 77 CVC C02 C01 sing N N 78 CVC N01 C4 sing N N 79 CVC OP2 P doub N N 80 CVC C01 C8 doub N N 81 CVC C4 O01 doub N N 82 CVC C4 N9 sing N N 83 CVC N9 C8 sing N N 84 CVC N9 "C1'" sing N N 85 CVC "O5'" P sing N N 86 CVC "O5'" "C5'" sing N N 87 CVC "O4'" "C1'" sing N N 88 CVC "O4'" "C4'" sing N N 89 CVC P OP1 sing N N 90 CVC P O02 sing N N 91 CVC "C1'" "C2'" sing N N 92 CVC "C5'" "C4'" sing N N 93 CVC "C4'" "C3'" sing N N 94 CVC "C2'" "O2'" sing N N 95 CVC "C2'" "C3'" sing N N 96 CVC "O2'" V sing N N 97 CVC "C3'" "O3'" sing N N 98 CVC O1V V sing N N 99 CVC "O3'" V sing N N 100 CVC V O2V sing N N 101 CVC "C5'" H1 sing N N 102 CVC "C5'" H2 sing N N 103 CVC "C4'" H3 sing N N 104 CVC "C3'" H4 sing N N 105 CVC "C2'" H5 sing N N 106 CVC "C1'" H6 sing N N 107 CVC C01 H7 sing N N 108 CVC O1V H8 sing N N 109 CVC N02 H9 sing N N 110 CVC N02 H10 sing N N 111 CVC O02 H11 sing N N 112 CVC O2V H12 sing N N 113 CVC OP1 H13 sing N N 114 CVC C8 H14 sing N N 115 G OP3 P sing N N 116 G OP3 HOP3 sing N N 117 G P OP1 doub N N 118 G P OP2 sing N N 119 G P "O5'" sing N N 120 G OP2 HOP2 sing N N 121 G "O5'" "C5'" sing N N 122 G "C5'" "C4'" sing N N 123 G "C5'" "H5'" sing N N 124 G "C5'" "H5''" sing N N 125 G "C4'" "O4'" sing N N 126 G "C4'" "C3'" sing N N 127 G "C4'" "H4'" sing N N 128 G "O4'" "C1'" sing N N 129 G "C3'" "O3'" sing N N 130 G "C3'" "C2'" sing N N 131 G "C3'" "H3'" sing N N 132 G "O3'" "HO3'" sing N N 133 G "C2'" "O2'" sing N N 134 G "C2'" "C1'" sing N N 135 G "C2'" "H2'" sing N N 136 G "O2'" "HO2'" sing N N 137 G "C1'" N9 sing N N 138 G "C1'" "H1'" sing N N 139 G N9 C8 sing Y N 140 G N9 C4 sing Y N 141 G C8 N7 doub Y N 142 G C8 H8 sing N N 143 G N7 C5 sing Y N 144 G C5 C6 sing N N 145 G C5 C4 doub Y N 146 G C6 O6 doub N N 147 G C6 N1 sing N N 148 G N1 C2 sing N N 149 G N1 H1 sing N N 150 G C2 N2 sing N N 151 G C2 N3 doub N N 152 G N2 H21 sing N N 153 G N2 H22 sing N N 154 G N3 C4 sing N N 155 U OP3 P sing N N 156 U OP3 HOP3 sing N N 157 U P OP1 doub N N 158 U P OP2 sing N N 159 U P "O5'" sing N N 160 U OP2 HOP2 sing N N 161 U "O5'" "C5'" sing N N 162 U "C5'" "C4'" sing N N 163 U "C5'" "H5'" sing N N 164 U "C5'" "H5''" sing N N 165 U "C4'" "O4'" sing N N 166 U "C4'" "C3'" sing N N 167 U "C4'" "H4'" sing N N 168 U "O4'" "C1'" sing N N 169 U "C3'" "O3'" sing N N 170 U "C3'" "C2'" sing N N 171 U "C3'" "H3'" sing N N 172 U "O3'" "HO3'" sing N N 173 U "C2'" "O2'" sing N N 174 U "C2'" "C1'" sing N N 175 U "C2'" "H2'" sing N N 176 U "O2'" "HO2'" sing N N 177 U "C1'" N1 sing N N 178 U "C1'" "H1'" sing N N 179 U N1 C2 sing N N 180 U N1 C6 sing N N 181 U C2 O2 doub N N 182 U C2 N3 sing N N 183 U N3 C4 sing N N 184 U N3 H3 sing N N 185 U C4 O4 doub N N 186 U C4 C5 sing N N 187 U C5 C6 doub N N 188 U C5 H5 sing N N 189 U C6 H6 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5EAQ 'double helix' 5EAQ 'a-form double helix' 5EAQ 'hairpin loop' 5EAQ 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A U 7 1_555 B A 13 1_555 4.412 -2.263 -0.449 -5.820 -10.369 -91.241 1 A_U7:A13_B A 7 ? B 13 ? 24 4 1 A A 10 1_555 A G 29 1_555 -3.300 4.001 0.224 -14.536 -4.775 67.389 2 A_A10:G29_A A 10 ? A 29 ? 10 6 1 A A 32 1_555 A U 28 1_555 -4.286 -1.984 0.580 1.942 9.055 -93.734 3 A_A32:U28_A A 32 ? A 28 ? 24 4 1 A G 34 1_555 A C 27 1_555 -0.075 -0.109 0.455 9.513 -3.628 -0.829 4 A_G34:C27_A A 34 ? A 27 ? 19 1 1 A C 35 1_555 A G 26 1_555 0.146 -0.178 0.013 5.248 -9.338 1.772 5 A_C35:G26_A A 35 ? A 26 ? 19 1 1 A G 36 1_555 A C 25 1_555 -0.100 -0.077 0.133 -4.896 -11.651 -2.753 6 A_G36:C25_A A 36 ? A 25 ? 19 1 1 A A 37 1_555 A U 24 1_555 0.060 -0.173 0.660 -4.574 -8.942 -6.413 7 A_A37:U24_A A 37 ? A 24 ? 20 1 1 A C 38 1_555 A G 23 1_555 0.153 -0.164 0.802 -6.078 5.701 2.970 8 A_C38:G23_A A 38 ? A 23 ? 19 1 1 A G 39 1_555 A A 22 1_555 6.302 -4.069 1.367 20.478 9.290 9.173 9 A_G39:A22_A A 39 ? A 22 ? 11 9 1 A G 11 1_555 B C 12 1_555 -0.239 -0.117 -0.332 -5.250 -8.135 -1.566 10 A_G11:C12_B A 11 ? B 12 ? 19 1 1 A C 12 1_555 B G 11 1_555 0.156 -0.140 -0.404 -2.540 -5.434 0.808 11 A_C12:G11_B A 12 ? B 11 ? 19 1 1 A C 13 1_555 B G 10 1_555 0.186 -0.087 -0.223 0.122 -6.039 1.390 12 A_C13:G10_B A 13 ? B 10 ? 19 1 1 A C 14 1_555 B G 9 1_555 0.187 -0.166 -0.301 -0.471 -7.129 -2.143 13 A_C14:G9_B A 14 ? B 9 ? 19 1 1 A A 15 1_555 B U 8 1_555 0.065 -0.084 -0.025 -2.905 -1.701 -3.753 14 A_A15:U8_B A 15 ? B 8 ? 20 1 1 A C 16 1_555 A G 21 1_555 0.238 -0.110 0.170 7.186 -3.225 1.597 15 A_C16:G21_A A 16 ? A 21 ? 19 1 1 A A 41 1_555 A G 18 1_555 -4.953 2.441 0.039 38.309 -32.540 71.996 16 A_A41:G18_A A 41 ? A 18 ? ? ? 1 A A 42 1_555 B U 6 1_555 -0.092 -0.283 0.537 7.323 7.227 -2.682 17 A_A42:U6_B A 42 ? B 6 ? 20 1 1 A C 43 1_555 B G 5 1_555 0.081 -0.198 0.555 4.972 -3.369 -0.818 18 A_C43:G5_B A 43 ? B 5 ? 19 1 1 A G 44 1_555 B C 4 1_555 -0.201 -0.045 0.168 5.085 -6.466 0.857 19 A_G44:C4_B A 44 ? B 4 ? 19 1 1 A C 45 1_555 B G 3 1_555 0.285 -0.114 0.047 3.093 -6.066 -0.056 20 A_C45:G3_B A 45 ? B 3 ? 19 1 1 A C 46 1_555 B G 2 1_555 0.178 -0.156 0.027 -0.041 -1.907 0.644 21 A_C46:G2_B A 46 ? B 2 ? 19 1 1 A C 47 1_555 B G 1 1_555 0.175 -0.180 0.337 -2.768 -4.818 -1.567 22 A_C47:G1_B A 47 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A A 10 1_555 A G 29 1_555 A A 32 1_555 A U 28 1_555 -3.279 -2.258 -2.223 163.775 -50.456 -22.834 1.103 -1.740 1.978 26.246 85.193 -171.542 1 AA_A10A32:U28G29_AA A 10 ? A 29 ? A 32 ? A 28 ? 1 A A 32 1_555 A U 28 1_555 A G 34 1_555 A C 27 1_555 2.800 -1.781 3.055 -6.227 3.162 75.305 -1.538 -2.452 2.786 2.583 5.087 75.581 2 AA_A32G34:C27U28_AA A 32 ? A 28 ? A 34 ? A 27 ? 1 A G 34 1_555 A C 27 1_555 A C 35 1_555 A G 26 1_555 0.294 -1.417 3.321 2.641 4.464 38.509 -2.672 -0.123 3.156 6.731 -3.982 38.844 3 AA_G34C35:G26C27_AA A 34 ? A 27 ? A 35 ? A 26 ? 1 A C 35 1_555 A G 26 1_555 A G 36 1_555 A C 25 1_555 -0.026 -1.863 3.426 2.719 9.754 29.857 -5.182 0.535 2.686 18.282 -5.097 31.490 4 AA_C35G36:C25G26_AA A 35 ? A 26 ? A 36 ? A 25 ? 1 A G 36 1_555 A C 25 1_555 A A 37 1_555 A U 24 1_555 -0.011 -1.834 3.005 -0.368 5.103 34.344 -3.761 -0.032 2.713 8.583 0.619 34.712 5 AA_G36A37:U24C25_AA A 36 ? A 25 ? A 37 ? A 24 ? 1 A A 37 1_555 A U 24 1_555 A C 38 1_555 A G 23 1_555 1.000 -1.575 3.350 0.755 2.605 32.691 -3.241 -1.641 3.240 4.618 -1.339 32.800 6 AA_A37C38:G23U24_AA A 37 ? A 24 ? A 38 ? A 23 ? 1 A C 38 1_555 A G 23 1_555 A G 39 1_555 A A 22 1_555 0.504 0.693 2.830 3.255 11.891 51.298 0.089 -0.379 2.937 13.513 -3.699 52.661 7 AA_C38G39:A22G23_AA A 38 ? A 23 ? A 39 ? A 22 ? 1 A G 11 1_555 B C 12 1_555 A C 12 1_555 B G 11 1_555 -0.449 -1.446 3.251 -2.594 4.994 33.397 -3.262 0.366 3.035 8.615 4.474 33.854 8 AA_G11C12:G11C12_BB A 11 ? B 12 ? A 12 ? B 11 ? 1 A C 12 1_555 B G 11 1_555 A C 13 1_555 B G 10 1_555 -0.024 -1.704 3.379 -1.370 5.260 31.976 -3.969 -0.196 3.066 9.462 2.464 32.423 9 AA_C12C13:G10G11_BB A 12 ? B 11 ? A 13 ? B 10 ? 1 A C 13 1_555 B G 10 1_555 A C 14 1_555 B G 9 1_555 -0.353 -2.004 3.433 0.653 3.534 28.954 -4.759 0.846 3.162 7.033 -1.299 29.172 10 AA_C13C14:G9G10_BB A 13 ? B 10 ? A 14 ? B 9 ? 1 A C 14 1_555 B G 9 1_555 A A 15 1_555 B U 8 1_555 -0.102 -1.685 3.257 -0.380 12.979 31.983 -4.664 0.119 2.413 22.435 0.657 34.454 11 AA_C14A15:U8G9_BB A 14 ? B 9 ? A 15 ? B 8 ? 1 A A 15 1_555 B U 8 1_555 A C 16 1_555 A G 21 1_555 -1.207 -1.005 3.232 2.182 15.696 18.452 -6.665 3.463 1.713 40.571 -5.641 24.278 12 AA_A15C16:G21U8_AB A 15 ? B 8 ? A 16 ? A 21 ? 1 A A 41 1_555 A G 18 1_555 A A 42 1_555 B U 6 1_555 1.085 2.456 3.535 1.750 -24.448 93.014 2.098 -0.702 2.997 -16.626 -1.190 95.467 13 AA_A41A42:U6G18_BA A 41 ? A 18 ? A 42 ? B 6 ? 1 A A 42 1_555 B U 6 1_555 A C 43 1_555 B G 5 1_555 0.069 -1.481 3.472 0.784 8.307 30.979 -4.184 0.016 2.986 15.209 -1.435 32.056 14 AA_A42C43:G5U6_BB A 42 ? B 6 ? A 43 ? B 5 ? 1 A C 43 1_555 B G 5 1_555 A G 44 1_555 B C 4 1_555 -0.530 -2.052 2.842 -1.193 12.891 29.638 -5.400 0.795 1.833 23.820 2.205 32.284 15 AA_C43G44:C4G5_BB A 43 ? B 5 ? A 44 ? B 4 ? 1 A G 44 1_555 B C 4 1_555 A C 45 1_555 B G 3 1_555 -0.258 -1.712 3.316 -2.922 5.054 34.410 -3.607 -0.004 3.052 8.468 4.895 34.887 16 AA_G44C45:G3C4_BB A 44 ? B 4 ? A 45 ? B 3 ? 1 A C 45 1_555 B G 3 1_555 A C 46 1_555 B G 2 1_555 0.014 -1.971 3.184 -0.476 8.009 31.173 -4.846 -0.102 2.609 14.603 0.867 32.164 17 AA_C45C46:G2G3_BB A 45 ? B 3 ? A 46 ? B 2 ? 1 A C 46 1_555 B G 2 1_555 A C 47 1_555 B G 1 1_555 -0.434 -1.830 3.273 -0.679 4.330 33.199 -3.867 0.646 3.025 7.537 1.182 33.479 18 AA_C46C47:G1G2_BB A 46 ? B 2 ? A 47 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'MANGANESE (II) ION' _pdbx_entity_nonpoly.comp_id MN # _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 5DI2 _pdbx_initial_refinement_model.details ? #