data_2P7D # _entry.id 2P7D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2P7D pdb_00002p7d 10.2210/pdb2p7d/pdb NDB UR0146 ? ? RCSB RCSB042058 ? ? WWPDB D_1000042058 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2OUE ;A related minimal, all-RNA hairpin ribozyme construct solved to 2.05 angstroms resolution with waters identified in the active site. ; unspecified PDB 2P7D . unspecified PDB 2P7E . unspecified PDB 2P7F . unspecified # _pdbx_database_status.entry_id 2P7D _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.recvd_initial_deposition_date 2007-03-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_mr ? _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 'Torelli, A.T.' 1 'Krucinska, J.' 2 'Wedekind, J.E.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization ; Rna 13 1052 1070 2007 RNARFU UK 1355-8382 2122 ? 17488874 10.1261/rna.510807 1 'Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.' Biochemistry 45 686 700 2006 BICHAW US 0006-2960 0033 ? 16411744 10.1021/bi051887k 2 ;Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn. ; Biochemistry 44 14396 14408 2005 BICHAW US 0006-2960 0033 ? 16262240 10.1021/bi051550i # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Torelli, A.T.' 1 ? primary 'Krucinska, J.' 2 ? primary 'Wedekind, J.E.' 3 ? 1 'Salter, J.' 4 ? 1 'Krucinska, J.' 5 ? 1 'Alam, S.' 6 ? 1 'Grum-Tokars, V.' 7 ? 1 'Wedekind, J.E.' 8 ? 2 'Alam, S.' 9 ? 2 'Grum-Tokars, V.' 10 ? 2 'Krucinska, J.' 11 ? 2 'Kundracik, M.L.' 12 ? 2 'Wedekind, J.E.' 13 ? # _cell.entry_id 2P7D _cell.length_a 93.9 _cell.length_b 93.9 _cell.length_c 134.4 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 120.0 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2P7D _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 178 _symmetry.cell_setting ? _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 ;5' substrate strand, pentameric fragment ; 1505.960 1 ? ? ? ? 2 polymer syn 'Ribozyme strand I' 4182.585 1 ? ? ? ;domain-linking residue S9L at the 3'-end ; 3 polymer syn 'Ribozyme strand II' 5535.445 1 ? ? ? ;domain-linking residue S9L at the 5'-end ; 4 polymer syn 'Ribozyme strand III' 5991.568 1 ? ? ? 'contains the S-turn' 5 polymer syn ;3' substrate strand, octameric fragment ; 2501.553 1 ? ? ? ? 6 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 7 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 8 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 9 water nat water 18.015 37 ? ? ? ? # 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 UCCCA UCCCA A ? 2 'polydeoxyribonucleotide/polyribonucleotide hybrid' no yes 'CGGUGAGAAGGG(S9L)' CGGUGAGAAGGGX B ? 3 polyribonucleotide no no GGCAGAGAAACACACGA GGCAGAGAAACACACGA C ? 4 polyribonucleotide no no UCGUGGUACAUUACCUGCC UCGUGGUACAUUACCUGCC D ? 5 polyribonucleotide no no GUCCACCG GUCCACCG P ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 C n 1 3 C n 1 4 C n 1 5 A n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 G n 2 11 G n 2 12 G n 2 13 S9L n 3 1 G n 3 2 G n 3 3 C n 3 4 A n 3 5 G n 3 6 A n 3 7 G n 3 8 A n 3 9 A n 3 10 A n 3 11 C n 3 12 A n 3 13 C n 3 14 A n 3 15 C n 3 16 G n 3 17 A n 4 1 U n 4 2 C n 4 3 G n 4 4 U n 4 5 G n 4 6 G n 4 7 U n 4 8 A n 4 9 C n 4 10 A n 4 11 U n 4 12 U n 4 13 A n 4 14 C n 4 15 C n 4 16 U n 4 17 G n 4 18 C n 4 19 C n 5 1 G n 5 2 U n 5 3 C n 5 4 C n 5 5 A n 5 6 C n 5 7 C n 5 8 G 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 ? ? ? ? ? 'sequence occurs naturally in tobacco ringspot virus satellite RNA' 2 1 sample ? ? ? ? ? 'sequence occurs naturally in tobacco ringspot virus satellite RNA' 3 1 sample ? ? ? ? ? 'sequence occurs naturally in tobacco ringspot virus satellite RNA' 4 1 sample ? ? ? ? ? 'sequence occurs naturally in tobacco ringspot virus satellite RNA' 5 1 sample ? ? ? ? ? 'sequence occurs naturally in tobacco ringspot virus satellite RNA' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 2P7D 2P7D ? ? ? 2 2 PDB 2P7D 2P7D ? ? ? 3 3 PDB 2P7D 2P7D ? ? ? 4 4 PDB 2P7D 2P7D ? ? ? 5 5 PDB 2P7D 2P7D ? ? ? # 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 2P7D A 1 ? 5 ? 2P7D 1 ? 5 ? 1 5 2 2 2P7D B 1 ? 13 ? 2P7D 2 ? 14 ? 2 14 3 3 2P7D C 1 ? 17 ? 2P7D 15 ? 31 ? 15 31 4 4 2P7D D 1 ? 19 ? 2P7D 31 ? 49 ? 31 49 5 5 2P7D P 1 ? 8 ? 2P7D 6 ? 13 ? 6 13 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 S9L non-polymer . '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' ? 'C6 H15 O7 P' 230.153 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 2P7D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.32 _exptl_crystal.density_percent_sol 80.78 _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.pH 6.0 _exptl_crystal_grow.pdbx_details ;250 mM Li2SO4, 2.5 mM [Co(NH3)6]Cl3, 2 mM spermidine-HCl, 20 mM NAF, 50 mM ascorbic acid, 100 mM sodium cacodylate buffer and 18.5% PEG 2000 MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.temp_details ? _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 Li2SO4 ? ? ? 1 2 1 '[Co(NH3)6]Cl3' ? ? ? 1 3 1 spermidine-HCl ? ? ? 1 4 1 NAF ? ? ? 1 5 1 'ascorbic acid' ? ? ? 1 6 1 'sodium cacodylate' ? ? ? 1 7 1 'PEG 2000 MME' ? ? ? 1 8 2 Li2SO4 ? ? ? 1 9 2 spermidine-HCl ? ? ? 1 10 2 'PEG 2000 MME' ? ? ? # _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 2006-04-21 _diffrn_detector.details 'Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97945 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97945 # _reflns.entry_id 2P7D _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 40.64 _reflns.d_resolution_high 2.25 _reflns.number_obs 16622 _reflns.number_all 16622 _reflns.percent_possible_obs 96.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.045 _reflns.pdbx_netI_over_sigmaI 23.2 _reflns.B_iso_Wilson_estimate 86.9 _reflns.pdbx_redundancy 7.24 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.25 _reflns_shell.d_res_low 2.33 _reflns_shell.percent_possible_all 95.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.434 _reflns_shell.meanI_over_sigI_obs 3.2 _reflns_shell.pdbx_redundancy 4.95 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2P7D _refine.ls_number_reflns_obs 16605 _refine.ls_number_reflns_all 16605 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 948513.14 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.10 _refine.ls_d_res_high 2.25 _refine.ls_percent_reflns_obs 96.2 _refine.ls_R_factor_obs 0.2291 _refine.ls_R_factor_all 0.2291 _refine.ls_R_factor_R_work 0.229 _refine.ls_R_factor_R_free 0.237 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 811 _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 78.7 _refine.aniso_B[1][1] -11.93 _refine.aniso_B[2][2] -11.93 _refine.aniso_B[3][3] 23.86 _refine.aniso_B[1][2] -3.49 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.337924 _refine.solvent_model_param_bsol 66.2658 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1ZFR' _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Parkinson et al. Acta Cryst.D,52,57 (1996)' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_overall_ESU_R ? _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 2P7D _refine_analyze.Luzzati_coordinate_error_obs 0.47 _refine_analyze.Luzzati_sigma_a_obs 0.54 _refine_analyze.Luzzati_d_res_low_obs 40.64 _refine_analyze.Luzzati_coordinate_error_free 0.47 _refine_analyze.Luzzati_sigma_a_free 0.62 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_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 1347 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 37 _refine_hist.number_atoms_total 1404 _refine_hist.d_res_high 2.25 _refine_hist.d_res_low 30.10 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 18.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.78 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.25 _refine_ls_shell.d_res_low 2.39 _refine_ls_shell.number_reflns_R_work 2535 _refine_ls_shell.R_factor_R_work 0.454 _refine_ls_shell.percent_reflns_obs 96.0 _refine_ls_shell.R_factor_R_free 0.442 _refine_ls_shell.R_factor_R_free_error 0.036 _refine_ls_shell.percent_reflns_R_free 5.5 _refine_ls_shell.number_reflns_R_free 148 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 dna-rnaATT dna-rnaATT 'X-RAY DIFFRACTION' 2 cobalt.par cobalt.top 'X-RAY DIFFRACTION' 3 water_rep.param water.top 'X-RAY DIFFRACTION' 4 ion.param ion.top 'X-RAY DIFFRACTION' 5 &_1_PARAMETER_INFILE_5 &_1_TOPOLOGY_INFILE_5 'X-RAY DIFFRACTION' # _struct.entry_id 2P7D _struct.title ;A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2P7D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'hairpin ribozyme; product mimic; transition-state stabilization; active site waters; induced fit, 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 4 ? E N N 5 ? F N N 6 ? G N N 7 ? H N N 8 ? I N N 8 ? J N N 9 ? K N N 9 ? L N N 9 ? M N N 9 ? N N N 9 ? # _struct_biol.id 1 _struct_biol.details 'The ribozyme-substrate complex in the asymmetric unit also represents the biological unit' _struct_biol.pdbx_parent_biol_id ? # 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 both ? B G 12 "O3'" ? ? ? 1_555 B S9L 13 P ? ? B G 13 B S9L 14 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? B S9L 13 "O3'" ? ? ? 1_555 C G 1 P ? ? B S9L 14 C G 15 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? A A 5 "O3'" ? ? ? 1_555 G NA . NA ? ? A A 5 A NA 104 1_555 ? ? ? ? ? ? ? 2.874 ? ? metalc2 metalc ? ? A A 5 "O2'" ? ? ? 1_555 G NA . NA ? ? A A 5 A NA 104 1_555 ? ? ? ? ? ? ? 2.473 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N3 ? ? ? 1_555 B A 8 N6 ? ? A A 5 B A 9 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A A 5 N3 ? ? ? 1_555 B A 9 N6 ? ? A A 5 B A 10 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog12 hydrog ? ? B C 1 N3 ? ? ? 1_555 E G 8 N1 ? ? B C 2 P G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B C 1 N4 ? ? ? 1_555 E G 8 O6 ? ? B C 2 P G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B C 1 O2 ? ? ? 1_555 E G 8 N2 ? ? B C 2 P G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B G 2 N1 ? ? ? 1_555 E C 7 N3 ? ? B G 3 P C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B G 2 N2 ? ? ? 1_555 E C 7 O2 ? ? B G 3 P C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B G 2 O6 ? ? ? 1_555 E C 7 N4 ? ? B G 3 P C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B G 3 N1 ? ? ? 1_555 E C 6 N3 ? ? B G 4 P C 11 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog19 hydrog ? ? B U 4 N3 ? ? ? 1_555 E A 5 N1 ? ? B U 5 P A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B U 4 O4 ? ? ? 1_555 E A 5 N6 ? ? B U 5 P A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B G 5 N1 ? ? ? 1_555 E C 4 N3 ? ? B G 6 P C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B G 5 N2 ? ? ? 1_555 E C 4 O2 ? ? B G 6 P C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B G 5 O6 ? ? ? 1_555 E C 4 N4 ? ? B G 6 P C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B A 6 N1 ? ? ? 1_555 E C 3 N4 ? ? B A 7 P C 8 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog25 hydrog ? ? B G 7 N2 A ? ? 1_555 E U 2 O4 ? ? B G 8 P U 7 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog26 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 19 N3 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 19 O2 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 19 N4 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 18 N3 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 18 O2 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 18 N4 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 17 N1 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 17 O6 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 17 N2 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C A 4 N1 ? ? ? 1_555 D U 16 N3 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C A 4 N6 ? ? ? 1_555 D U 16 O4 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C A 6 N1 ? ? ? 1_555 D C 14 N4 ? ? C A 20 D C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog41 hydrog ? ? C G 7 N2 ? ? ? 1_555 D A 13 N7 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog42 hydrog ? ? C G 7 N3 ? ? ? 1_555 D A 13 N6 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog43 hydrog ? ? C A 8 N6 ? ? ? 1_555 D U 11 O2 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog44 hydrog ? ? C A 8 N7 ? ? ? 1_555 D U 11 N3 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog45 hydrog ? ? C A 9 N6 ? ? ? 1_555 D A 10 N1 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog46 hydrog ? ? C A 9 N7 ? ? ? 1_555 D A 10 N6 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog47 hydrog ? ? C A 10 N6 ? ? ? 1_555 D A 8 N7 ? ? C A 24 D A 38 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog48 hydrog ? ? C C 11 N3 ? ? ? 1_555 E G 1 N1 ? ? C C 25 P G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C C 11 N4 ? ? ? 1_555 E G 1 O6 ? ? C C 25 P G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C C 11 O2 ? ? ? 1_555 E G 1 N2 ? ? C C 25 P G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C A 12 N1 ? ? ? 1_555 D G 6 N1 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog52 hydrog ? ? C A 12 N6 ? ? ? 1_555 D G 6 O6 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog53 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C A 17 N1 ? ? ? 1_555 D U 1 N3 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C A 17 N6 ? ? ? 1_555 D U 1 O4 ? ? C A 31 D U 31 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 SO4 103 ? 3 'BINDING SITE FOR RESIDUE SO4 A 103' AC2 Software A NA 104 ? 2 'BINDING SITE FOR RESIDUE NA A 104' AC3 Software D NCO 101 ? 4 'BINDING SITE FOR RESIDUE NCO D 101' AC4 Software B NCO 102 ? 6 'BINDING SITE FOR RESIDUE NCO B 102' # 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 3 U A 1 ? U A 1 . ? 1_555 ? 2 AC1 3 C A 2 ? C A 2 . ? 1_555 ? 3 AC1 3 NCO H . ? NCO B 102 . ? 1_555 ? 4 AC2 2 A A 5 ? A A 5 . ? 1_555 ? 5 AC2 2 G B 7 ? G B 8 . ? 1_555 ? 6 AC3 4 A C 6 ? A C 20 . ? 1_555 ? 7 AC3 4 G C 7 ? G C 21 . ? 1_555 ? 8 AC3 4 A D 10 ? A D 40 . ? 1_555 ? 9 AC3 4 U D 11 ? U D 41 . ? 1_555 ? 10 AC4 6 C A 2 ? C A 2 . ? 1_555 ? 11 AC4 6 C A 3 ? C A 3 . ? 1_555 ? 12 AC4 6 SO4 F . ? SO4 A 103 . ? 1_555 ? 13 AC4 6 G B 10 ? G B 11 . ? 1_555 ? 14 AC4 6 G B 11 ? G B 12 . ? 1_555 ? 15 AC4 6 G B 12 ? G B 13 . ? 1_555 ? # _atom_sites.entry_id 2P7D _atom_sites.fract_transf_matrix[1][1] 0.010650 _atom_sites.fract_transf_matrix[1][2] 0.006149 _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] 0.012297 _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] 0.007440 _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 CO N NA O P S # 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 U 1 1 1 U U A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n B 2 1 C 1 2 2 C C B . n B 2 2 G 2 3 3 G G B . n B 2 3 G 3 4 4 G G B . n B 2 4 U 4 5 5 U U B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 G 7 8 8 G G B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 G 11 12 12 G G B . n B 2 12 G 12 13 13 G G B . n B 2 13 S9L 13 14 14 S9L S9L B . n C 3 1 G 1 15 15 G G C . n C 3 2 G 2 16 16 G G C . n C 3 3 C 3 17 17 C C C . n C 3 4 A 4 18 18 A A C . n C 3 5 G 5 19 19 G G C . n C 3 6 A 6 20 20 A A C . n C 3 7 G 7 21 21 G G C . n C 3 8 A 8 22 22 A A C . n C 3 9 A 9 23 23 A A C . n C 3 10 A 10 24 24 A A C . n C 3 11 C 11 25 25 C C C . n C 3 12 A 12 26 26 A A C . n C 3 13 C 13 27 27 C C C . n C 3 14 A 14 28 28 A A C . n C 3 15 C 15 29 29 C C C . n C 3 16 G 16 30 30 G G C . n C 3 17 A 17 31 31 A A C . n D 4 1 U 1 31 31 U U D . n D 4 2 C 2 32 32 C C D . n D 4 3 G 3 33 33 G G D . n D 4 4 U 4 34 34 U U D . n D 4 5 G 5 35 35 G G D . n D 4 6 G 6 36 36 G G D . n D 4 7 U 7 37 37 U U D . n D 4 8 A 8 38 38 A A D . n D 4 9 C 9 39 39 C C D . n D 4 10 A 10 40 40 A A D . n D 4 11 U 11 41 41 U U D . n D 4 12 U 12 42 42 U U D . n D 4 13 A 13 43 43 A A D . n D 4 14 C 14 44 44 C C D . n D 4 15 C 15 45 45 C C D . n D 4 16 U 16 46 46 U U D . n D 4 17 G 17 47 47 G G D . n D 4 18 C 18 48 48 C C D . n D 4 19 C 19 49 49 C C D . n E 5 1 G 1 6 6 G G P . n E 5 2 U 2 7 7 U U P . n E 5 3 C 3 8 8 C C P . n E 5 4 C 4 9 9 C C P . n E 5 5 A 5 10 10 A A P . n E 5 6 C 6 11 11 C C P . n E 5 7 C 7 12 12 C C P . n E 5 8 G 8 13 13 G G P . 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 F 6 SO4 1 103 103 SO4 SO4 A . G 7 NA 1 104 104 NA NA A . H 8 NCO 1 102 102 NCO NCO B . I 8 NCO 1 101 101 NCO NCO D . J 9 HOH 1 105 2 HOH HOH A . J 9 HOH 2 106 6 HOH HOH A . J 9 HOH 3 107 19 HOH HOH A . K 9 HOH 1 103 1 HOH HOH B . K 9 HOH 2 104 5 HOH HOH B . K 9 HOH 3 105 10 HOH HOH B . L 9 HOH 1 32 7 HOH HOH C . L 9 HOH 2 33 8 HOH HOH C . L 9 HOH 3 34 9 HOH HOH C . L 9 HOH 4 35 12 HOH HOH C . L 9 HOH 5 36 13 HOH HOH C . L 9 HOH 6 37 14 HOH HOH C . L 9 HOH 7 38 16 HOH HOH C . L 9 HOH 8 39 21 HOH HOH C . L 9 HOH 9 40 22 HOH HOH C . L 9 HOH 10 41 24 HOH HOH C . L 9 HOH 11 42 26 HOH HOH C . L 9 HOH 12 43 29 HOH HOH C . L 9 HOH 13 44 31 HOH HOH C . L 9 HOH 14 45 32 HOH HOH C . M 9 HOH 1 102 3 HOH HOH D . M 9 HOH 2 103 4 HOH HOH D . M 9 HOH 3 104 11 HOH HOH D . M 9 HOH 4 105 15 HOH HOH D . M 9 HOH 5 106 17 HOH HOH D . M 9 HOH 6 107 18 HOH HOH D . M 9 HOH 7 108 20 HOH HOH D . M 9 HOH 8 109 23 HOH HOH D . M 9 HOH 9 110 25 HOH HOH D . M 9 HOH 10 111 27 HOH HOH D . M 9 HOH 11 112 28 HOH HOH D . M 9 HOH 12 113 33 HOH HOH D . M 9 HOH 13 114 34 HOH HOH D . M 9 HOH 14 115 35 HOH HOH D . M 9 HOH 15 116 36 HOH HOH D . M 9 HOH 16 117 37 HOH HOH D . N 9 HOH 1 30 30 HOH HOH P . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 # _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,I,J,K,L,M,N # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id "O3'" _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id A _pdbx_struct_conn_angle.ptnr1_label_seq_id 5 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id A _pdbx_struct_conn_angle.ptnr1_auth_seq_id 5 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id G _pdbx_struct_conn_angle.ptnr2_label_comp_id NA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id NA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 104 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id "O2'" _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id A _pdbx_struct_conn_angle.ptnr3_label_seq_id 5 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id A _pdbx_struct_conn_angle.ptnr3_auth_seq_id 5 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 54.3 _pdbx_struct_conn_angle.value_esd ? # 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 2007-05-22 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 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_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_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Blu-Ice 'data collection' . ? 1 CNS refinement . ? 2 CrystalClear 'data reduction' . ? 3 CrystalClear 'data scaling' . ? 4 CNS phasing . ? 5 # 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 U 1 ? B "C1'" A U 1 ? B N1 A U 1 ? B 98.32 108.20 -9.88 0.80 N 2 1 N9 A A 5 ? ? "C1'" A A 5 ? ? "C2'" A A 5 ? ? 97.93 112.00 -14.07 1.10 N 3 1 "O4'" A A 5 ? ? "C1'" A A 5 ? ? N9 A A 5 ? ? 117.50 108.50 9.00 0.70 N 4 1 N9 B G 8 ? B "C1'" B G 8 ? B "C2'" B G 8 ? B 122.40 114.00 8.40 1.30 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id D _pdbx_validate_planes.auth_seq_id 37 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.092 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 NA NA NA N N 114 NCO CO CO N N 115 NCO N1 N N N 116 NCO N2 N N N 117 NCO N3 N N N 118 NCO N4 N N N 119 NCO N5 N N N 120 NCO N6 N N N 121 NCO HN11 H N N 122 NCO HN12 H N N 123 NCO HN13 H N N 124 NCO HN21 H N N 125 NCO HN22 H N N 126 NCO HN23 H N N 127 NCO HN31 H N N 128 NCO HN32 H N N 129 NCO HN33 H N N 130 NCO HN41 H N N 131 NCO HN42 H N N 132 NCO HN43 H N N 133 NCO HN51 H N N 134 NCO HN52 H N N 135 NCO HN53 H N N 136 NCO HN61 H N N 137 NCO HN62 H N N 138 NCO HN63 H N N 139 S9L O3P O N N 140 S9L P P N N 141 S9L O1P O N N 142 S9L O2P O N N 143 S9L "O5'" O N N 144 S9L C12 C N N 145 S9L C22 C N N 146 S9L OH3 O N N 147 S9L C13 C N N 148 S9L C23 C N N 149 S9L OH4 O N N 150 S9L C14 C N N 151 S9L C24 C N N 152 S9L "O3'" O N N 153 S9L HO3P H N N 154 S9L HO1P H N N 155 S9L H121 H N N 156 S9L H122 H N N 157 S9L H221 H N N 158 S9L H222 H N N 159 S9L H131 H N N 160 S9L H132 H N N 161 S9L H231 H N N 162 S9L H232 H N N 163 S9L H141 H N N 164 S9L H142 H N N 165 S9L H241 H N N 166 S9L H242 H N N 167 S9L "HO3'" H N N 168 SO4 S S N N 169 SO4 O1 O N N 170 SO4 O2 O N N 171 SO4 O3 O N N 172 SO4 O4 O N N 173 U OP3 O N N 174 U P P N N 175 U OP1 O N N 176 U OP2 O N N 177 U "O5'" O N N 178 U "C5'" C N N 179 U "C4'" C N R 180 U "O4'" O N N 181 U "C3'" C N S 182 U "O3'" O N N 183 U "C2'" C N R 184 U "O2'" O N N 185 U "C1'" C N R 186 U N1 N N N 187 U C2 C N N 188 U O2 O N N 189 U N3 N N N 190 U C4 C N N 191 U O4 O N N 192 U C5 C N N 193 U C6 C N N 194 U HOP3 H N N 195 U HOP2 H N N 196 U "H5'" H N N 197 U "H5''" H N N 198 U "H4'" H N N 199 U "H3'" H N N 200 U "HO3'" H N N 201 U "H2'" H N N 202 U "HO2'" H N N 203 U "H1'" H N N 204 U H3 H N N 205 U H5 H N N 206 U H6 H N N 207 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 NCO CO N1 sing N N 118 NCO CO N2 sing N N 119 NCO CO N3 sing N N 120 NCO CO N4 sing N N 121 NCO CO N5 sing N N 122 NCO CO N6 sing N N 123 NCO N1 HN11 sing N N 124 NCO N1 HN12 sing N N 125 NCO N1 HN13 sing N N 126 NCO N2 HN21 sing N N 127 NCO N2 HN22 sing N N 128 NCO N2 HN23 sing N N 129 NCO N3 HN31 sing N N 130 NCO N3 HN32 sing N N 131 NCO N3 HN33 sing N N 132 NCO N4 HN41 sing N N 133 NCO N4 HN42 sing N N 134 NCO N4 HN43 sing N N 135 NCO N5 HN51 sing N N 136 NCO N5 HN52 sing N N 137 NCO N5 HN53 sing N N 138 NCO N6 HN61 sing N N 139 NCO N6 HN62 sing N N 140 NCO N6 HN63 sing N N 141 S9L O3P P sing N N 142 S9L O3P HO3P sing N N 143 S9L P O2P doub N N 144 S9L P O1P sing N N 145 S9L P "O5'" sing N N 146 S9L O1P HO1P sing N N 147 S9L "O5'" C12 sing N N 148 S9L C12 C22 sing N N 149 S9L C12 H121 sing N N 150 S9L C12 H122 sing N N 151 S9L C22 OH3 sing N N 152 S9L C22 H221 sing N N 153 S9L C22 H222 sing N N 154 S9L OH3 C23 sing N N 155 S9L C13 C23 sing N N 156 S9L C13 OH4 sing N N 157 S9L C13 H131 sing N N 158 S9L C13 H132 sing N N 159 S9L C23 H231 sing N N 160 S9L C23 H232 sing N N 161 S9L OH4 C24 sing N N 162 S9L C14 C24 sing N N 163 S9L C14 "O3'" sing N N 164 S9L C14 H141 sing N N 165 S9L C14 H142 sing N N 166 S9L C24 H241 sing N N 167 S9L C24 H242 sing N N 168 S9L "O3'" "HO3'" sing N N 169 SO4 S O1 doub N N 170 SO4 S O2 doub N N 171 SO4 S O3 sing N N 172 SO4 S O4 sing N N 173 U OP3 P sing N N 174 U OP3 HOP3 sing N N 175 U P OP1 doub N N 176 U P OP2 sing N N 177 U P "O5'" sing N N 178 U OP2 HOP2 sing N N 179 U "O5'" "C5'" sing N N 180 U "C5'" "C4'" sing N N 181 U "C5'" "H5'" sing N N 182 U "C5'" "H5''" sing N N 183 U "C4'" "O4'" sing N N 184 U "C4'" "C3'" sing N N 185 U "C4'" "H4'" sing N N 186 U "O4'" "C1'" sing N N 187 U "C3'" "O3'" sing N N 188 U "C3'" "C2'" sing N N 189 U "C3'" "H3'" sing N N 190 U "O3'" "HO3'" sing N N 191 U "C2'" "O2'" sing N N 192 U "C2'" "C1'" sing N N 193 U "C2'" "H2'" sing N N 194 U "O2'" "HO2'" sing N N 195 U "C1'" N1 sing N N 196 U "C1'" "H1'" sing N N 197 U N1 C2 sing N N 198 U N1 C6 sing N N 199 U C2 O2 doub N N 200 U C2 N3 sing N N 201 U N3 C4 sing N N 202 U N3 H3 sing N N 203 U C4 O4 doub N N 204 U C4 C5 sing N N 205 U C5 C6 doub N N 206 U C5 H5 sing N N 207 U C6 H6 sing N N 208 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2P7D 'double helix' 2P7D 'a-form double helix' 2P7D 'bulge loop' 2P7D 'mismatched base pair' 2P7D 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 2 1_555 B G 12 1_555 0.114 -0.278 -0.323 7.581 -17.882 1.948 1 A_C2:G13_B A 2 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 0.289 -0.232 -0.151 -1.773 -8.315 1.593 2 A_C3:G12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 0.361 -0.227 0.059 3.213 1.936 1.186 3 A_C4:G11_B A 4 ? B 11 ? 19 1 1 A A 5 1_555 B A 8 1_555 6.590 -3.884 -0.469 11.311 4.016 -31.225 4 A_A5:A9_B A 5 ? B 9 ? ? 10 1 E U 2 1_555 B G 7 1_555 -7.863 -2.307 0.181 9.026 6.851 0.688 5 P_U7:G8_B P 7 ? B 8 ? ? ? 1 E C 3 1_555 B A 6 1_555 -1.733 0.520 -0.842 21.017 -19.173 4.714 6 P_C8:A7_B P 8 ? B 7 ? ? ? 1 E C 4 1_555 B G 5 1_555 0.056 0.196 -0.228 14.743 -19.689 2.117 7 P_C9:G6_B P 9 ? B 6 ? 19 1 1 E A 5 1_555 B U 4 1_555 0.284 -0.026 0.458 7.168 -15.008 -0.372 8 P_A10:U5_B P 10 ? B 5 ? 20 1 1 E C 6 1_555 B G 3 1_555 0.364 0.255 0.346 -0.501 -11.166 5.177 9 P_C11:G4_B P 11 ? B 4 ? ? 1 1 E C 7 1_555 B G 2 1_555 0.469 -0.047 0.294 0.277 -10.179 2.319 10 P_C12:G3_B P 12 ? B 3 ? 19 1 1 E G 8 1_555 B C 1 1_555 0.368 0.182 -0.010 -2.612 -8.927 7.931 11 P_G13:C2_B P 13 ? B 2 ? 19 1 1 C G 1 1_555 D C 19 1_555 -0.306 -0.057 0.091 -2.650 -14.240 1.388 12 C_G15:C49_D C 15 ? D 49 ? 19 1 1 C G 2 1_555 D C 18 1_555 -0.584 -0.229 0.459 11.727 -10.978 -3.244 13 C_G16:C48_D C 16 ? D 48 ? 19 1 1 C C 3 1_555 D G 17 1_555 -0.106 0.026 0.070 6.219 -13.689 -0.152 14 C_C17:G47_D C 17 ? D 47 ? 19 1 1 C A 4 1_555 D U 16 1_555 -0.227 -0.007 -0.209 -1.825 -11.313 2.906 15 C_A18:U46_D C 18 ? D 46 ? 20 1 1 C G 5 1_555 D C 15 1_555 -0.490 -0.202 -0.487 -9.029 -4.971 4.510 16 C_G19:C45_D C 19 ? D 45 ? 19 1 1 C A 6 1_555 D C 14 1_555 2.202 0.176 -0.518 -15.844 -5.489 14.626 17 C_A20:C44_D C 20 ? D 44 ? ? 1 1 C G 7 1_555 D A 13 1_555 6.965 -4.564 -0.016 -7.827 0.637 -8.068 18 C_G21:A43_D C 21 ? D 43 ? 11 10 1 C A 8 1_555 D U 11 1_555 -4.166 -1.650 -0.205 -3.019 -11.125 -102.979 19 C_A22:U41_D C 22 ? D 41 ? 24 4 1 C A 9 1_555 D A 10 1_555 -4.162 1.321 -0.428 -0.422 -21.759 -102.627 20 C_A23:A40_D C 23 ? D 40 ? 5 4 1 C A 10 1_555 D A 8 1_555 5.121 3.609 -0.540 -3.770 -18.410 -158.751 21 C_A24:A38_D C 24 ? D 38 ? ? ? 1 C C 11 1_555 E G 1 1_555 0.217 -0.157 0.026 17.854 -11.644 -3.338 22 C_C25:G6_P C 25 ? P 6 ? 19 1 1 C A 12 1_555 D G 6 1_555 0.232 1.293 -0.571 -10.242 -16.544 -18.766 23 C_A26:G36_D C 26 ? D 36 ? 8 ? 1 C C 13 1_555 D G 5 1_555 -0.087 -0.191 0.049 6.334 -23.668 0.968 24 C_C27:G35_D C 27 ? D 35 ? 19 1 1 C A 14 1_555 D U 4 1_555 0.241 -0.280 0.166 2.602 -21.718 -0.388 25 C_A28:U34_D C 28 ? D 34 ? 20 1 1 C C 15 1_555 D G 3 1_555 0.189 -0.202 -0.101 5.198 -13.592 2.413 26 C_C29:G33_D C 29 ? D 33 ? 19 1 1 C G 16 1_555 D C 2 1_555 -0.350 -0.049 -0.018 -10.296 -15.406 -1.909 27 C_G30:C32_D C 30 ? D 32 ? 19 1 1 C A 17 1_555 D U 1 1_555 0.502 -0.101 0.278 0.165 -9.230 0.769 28 C_A31:U31_D C 31 ? D 31 ? 20 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 C 2 1_555 B G 12 1_555 A C 3 1_555 B G 11 1_555 -0.618 -1.735 3.555 -0.874 10.313 33.278 -4.492 0.898 2.919 17.489 1.482 34.807 1 AA_C2C3:G12G13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A C 3 1_555 B G 11 1_555 A C 4 1_555 B G 10 1_555 0.550 -1.670 3.277 0.803 8.810 26.717 -5.351 -0.958 2.618 18.435 -1.681 28.118 2 AA_C3C4:G11G12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A C 4 1_555 B G 10 1_555 A A 5 1_555 B A 8 1_555 -0.015 -1.214 5.310 -3.538 26.638 74.223 -2.144 -0.145 4.723 21.413 2.844 78.275 3 AA_C4A5:A9G11_BB A 4 ? B 11 ? A 5 ? B 9 ? 1 A A 5 1_555 B A 8 1_555 E U 2 1_555 B G 7 1_555 -0.234 0.476 3.485 12.576 -1.391 10.962 2.593 9.450 2.074 -5.415 -48.954 16.726 4 AP_A5U7:G8A9_BB A 5 ? B 9 ? P 7 ? B 8 ? 1 E U 2 1_555 B G 7 1_555 E C 3 1_555 B A 6 1_555 -0.052 -0.449 2.965 -2.783 16.698 54.147 -1.311 -0.085 2.729 17.859 2.976 56.540 5 PP_U7C8:A7G8_BB P 7 ? B 8 ? P 8 ? B 7 ? 1 E C 3 1_555 B A 6 1_555 E C 4 1_555 B G 5 1_555 -0.127 -1.335 3.550 -5.312 7.481 36.229 -3.122 -0.538 3.208 11.799 8.377 37.335 6 PP_C8C9:G6A7_BB P 8 ? B 7 ? P 9 ? B 6 ? 1 E C 4 1_555 B G 5 1_555 E A 5 1_555 B U 4 1_555 -0.498 -1.829 3.224 -5.612 14.321 33.877 -4.583 0.113 2.340 23.153 9.073 37.112 7 PP_C9A10:U5G6_BB P 9 ? B 6 ? P 10 ? B 5 ? 1 E A 5 1_555 B U 4 1_555 E C 6 1_555 B G 3 1_555 -0.314 -1.608 3.509 -0.281 2.578 28.566 -3.858 0.567 3.357 5.210 0.568 28.681 8 PP_A10C11:G4U5_BB P 10 ? B 5 ? P 11 ? B 4 ? 1 E C 6 1_555 B G 3 1_555 E C 7 1_555 B G 2 1_555 -0.015 -2.160 3.120 -0.489 6.104 31.409 -4.904 -0.052 2.664 11.142 0.893 31.985 9 PP_C11C12:G3G4_BB P 11 ? B 4 ? P 12 ? B 3 ? 1 E C 7 1_555 B G 2 1_555 E G 8 1_555 B C 1 1_555 0.224 -1.773 3.188 3.675 10.240 32.997 -4.386 0.132 2.550 17.448 -6.262 34.697 10 PP_C12G13:C2G3_BB P 12 ? B 3 ? P 13 ? B 2 ? 1 C G 1 1_555 D C 19 1_555 C G 2 1_555 D C 18 1_555 -0.791 -1.069 2.821 -7.231 4.332 32.696 -2.453 0.344 2.768 7.539 12.586 33.737 11 CC_G15G16:C48C49_DD C 15 ? D 49 ? C 16 ? D 48 ? 1 C G 2 1_555 D C 18 1_555 C C 3 1_555 D G 17 1_555 0.279 -1.401 3.440 2.203 7.140 35.458 -3.271 -0.135 3.120 11.565 -3.569 36.212 12 CC_G16C17:G47C48_DD C 16 ? D 48 ? C 17 ? D 47 ? 1 C C 3 1_555 D G 17 1_555 C A 4 1_555 D U 16 1_555 0.430 -1.717 3.392 1.955 11.672 31.611 -4.769 -0.440 2.632 20.546 -3.441 33.701 13 CC_C17A18:U46G47_DD C 17 ? D 47 ? C 18 ? D 46 ? 1 C A 4 1_555 D U 16 1_555 C G 5 1_555 D C 15 1_555 0.208 -1.950 3.513 -0.106 7.471 28.619 -5.408 -0.430 2.921 14.796 0.210 29.558 14 CC_A18G19:C45U46_DD C 18 ? D 46 ? C 19 ? D 45 ? 1 C G 5 1_555 D C 15 1_555 C A 6 1_555 D C 14 1_555 0.851 -1.498 3.522 3.788 9.046 39.554 -3.196 -0.787 3.183 13.124 -5.496 40.705 15 CC_G19A20:C44C45_DD C 19 ? D 45 ? C 20 ? D 44 ? 1 C A 6 1_555 D C 14 1_555 C G 7 1_555 D A 13 1_555 -0.567 -1.008 3.106 5.042 6.538 57.552 -1.360 0.832 2.930 6.753 -5.207 58.091 16 CC_A20G21:A43C44_DD C 20 ? D 44 ? C 21 ? D 43 ? 1 C G 7 1_555 D A 13 1_555 C A 8 1_555 D U 11 1_555 -2.284 -0.508 3.391 2.207 -1.593 12.155 -0.450 13.148 2.971 -7.402 -10.253 12.454 17 CC_G21A22:U41A43_DD C 21 ? D 43 ? C 22 ? D 41 ? 1 C A 8 1_555 D U 11 1_555 C A 9 1_555 D A 10 1_555 -0.162 -2.452 3.571 -10.107 5.054 46.284 -3.471 -0.661 3.266 6.319 12.638 47.569 18 CC_A22A23:A40U41_DD C 22 ? D 41 ? C 23 ? D 40 ? 1 C A 9 1_555 D A 10 1_555 C A 10 1_555 D A 8 1_555 -3.427 -3.217 3.551 -6.677 -1.002 72.757 -2.666 2.634 3.847 -0.843 5.616 73.027 19 CC_A23A24:A38A40_DD C 23 ? D 40 ? C 24 ? D 38 ? 1 C A 10 1_555 D A 8 1_555 C C 11 1_555 E G 1 1_555 2.644 -0.137 2.854 2.960 2.933 -30.424 -0.223 5.481 2.593 -5.556 5.607 -30.702 20 CC_A24C25:G6A38_PD C 24 ? D 38 ? C 25 ? P 6 ? 1 C C 11 1_555 E G 1 1_555 C A 12 1_555 D G 6 1_555 0.379 -2.018 3.877 5.874 6.727 47.618 -3.063 0.062 3.597 8.247 -7.201 48.400 21 CC_C25A26:G36G6_DP C 25 ? P 6 ? C 26 ? D 36 ? 1 C A 12 1_555 D G 6 1_555 C C 13 1_555 D G 5 1_555 1.122 -0.624 2.897 -4.668 4.297 28.696 -2.011 -3.061 2.567 8.539 9.275 29.375 22 CC_A26C27:G35G36_DD C 26 ? D 36 ? C 27 ? D 35 ? 1 C C 13 1_555 D G 5 1_555 C A 14 1_555 D U 4 1_555 0.066 -1.167 3.319 -0.846 10.893 36.243 -3.157 -0.207 2.860 17.040 1.324 37.801 23 CC_C27A28:U34G35_DD C 27 ? D 35 ? C 28 ? D 34 ? 1 C A 14 1_555 D U 4 1_555 C C 15 1_555 D G 3 1_555 0.396 -1.017 3.275 2.727 -1.257 32.102 -1.606 -0.222 3.333 -2.267 -4.917 32.238 24 CC_A28C29:G33U34_DD C 28 ? D 34 ? C 29 ? D 33 ? 1 C C 15 1_555 D G 3 1_555 C G 16 1_555 D C 2 1_555 0.114 -1.509 3.500 0.975 14.039 33.331 -4.389 -0.048 2.672 23.231 -1.613 36.102 25 CC_C29G30:C32G33_DD C 29 ? D 33 ? C 30 ? D 32 ? 1 C G 16 1_555 D C 2 1_555 C A 17 1_555 D U 1 1_555 0.754 -1.585 2.958 2.027 1.849 34.141 -2.953 -0.993 2.909 3.142 -3.446 34.248 26 CC_G30A31:U31C32_DD C 30 ? D 32 ? C 31 ? D 31 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 6 'SULFATE ION' SO4 7 'SODIUM ION' NA 8 'COBALT HEXAMMINE(III)' NCO 9 water HOH # _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 1ZFR _pdbx_initial_refinement_model.details 'PDB ENTRY 1ZFR' #