data_1YZD # _entry.id 1YZD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1YZD pdb_00001yzd 10.2210/pdb1yzd/pdb NDB AR0059 ? ? RCSB RCSB032102 ? ? WWPDB D_1000032102 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-10-18 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2024-02-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_struct_conn_angle 5 5 'Structure model' struct_conn 6 5 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.value' 16 5 'Structure model' '_struct_conn.conn_type_id' 17 5 'Structure model' '_struct_conn.id' 18 5 'Structure model' '_struct_conn.pdbx_dist_value' 19 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 20 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 21 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 28 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 32 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 33 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 34 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 35 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 36 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YZD _pdbx_database_status.recvd_initial_deposition_date 2005-02-28 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YRM . unspecified PDB 1YY0 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gherghe, C.M.' 1 'Krahn, J.M.' 2 'Weeks, K.M.' 3 # _citation.id primary _citation.title ;Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 127 _citation.page_first 13622 _citation.page_last 13628 _citation.year 2005 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16190727 _citation.pdbx_database_id_DOI 10.1021/ja053647y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gherghe, C.M.' 1 ? primary 'Krahn, J.M.' 2 ? primary 'Weeks, K.M.' 3 ? # 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 ;RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3' ; 5097.094 3 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 3 water nat water 18.015 29 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GCAGA(A5M)UUAAGUCUGC' _entity_poly.pdbx_seq_one_letter_code_can GCAGACUUAAGUCUGC _entity_poly.pdbx_strand_id B,A,C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 A n 1 4 G n 1 5 A n 1 6 A5M n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 C n # _pdbx_entity_src_syn.entity_id 1 _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 ? _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 'chemically synthesized' # 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 A5M 'RNA linking' n "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H15 N4 O7 P' 322.212 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G B . n A 1 2 C 2 2 2 C C B . n A 1 3 A 3 3 3 A A B . n A 1 4 G 4 4 4 G G B . n A 1 5 A 5 5 5 A A B . n A 1 6 A5M 6 6 6 A5M A5M B . n A 1 7 U 7 7 7 U U B . n A 1 8 U 8 8 8 U U B . n A 1 9 A 9 9 9 A A B . n A 1 10 A 10 10 10 A A B . n A 1 11 G 11 11 11 G G B . n A 1 12 U 12 12 12 U U B . n A 1 13 C 13 13 13 C C B . n A 1 14 U 14 14 14 U U B . n A 1 15 G 15 15 15 G G B . n A 1 16 C 16 16 16 C C B . n B 1 1 G 1 1 1 G G A . n B 1 2 C 2 2 2 C C A . n B 1 3 A 3 3 3 A A A . n B 1 4 G 4 4 4 G G A . n B 1 5 A 5 5 5 A A A . n B 1 6 A5M 6 6 6 A5M A5M A . n B 1 7 U 7 7 7 U U A . n B 1 8 U 8 8 8 U U A . n B 1 9 A 9 9 9 A A A . n B 1 10 A 10 10 10 A A A . n B 1 11 G 11 11 11 G G A . n B 1 12 U 12 12 12 U U A . n B 1 13 C 13 13 13 C C A . n B 1 14 U 14 14 14 U U A . n B 1 15 G 15 15 15 G G A . n B 1 16 C 16 16 16 C C A . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 A 3 3 3 A A C . n C 1 4 G 4 4 4 G G C . n C 1 5 A 5 5 5 A A C . n C 1 6 A5M 6 6 6 A5M A5M C . n C 1 7 U 7 7 7 U U C . n C 1 8 U 8 8 8 U U C . n C 1 9 A 9 9 9 A A C . n C 1 10 A 10 10 10 A A C . n C 1 11 G 11 11 11 G G C . n C 1 12 U 12 12 12 U U C . n C 1 13 C 13 13 13 C C C . n C 1 14 U 14 14 14 U U C . n C 1 15 G 15 15 15 G G C . n C 1 16 C 16 16 16 C C C . 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 D 2 CA 1 17 1 CA CA A . E 3 HOH 1 17 2 HOH HOH B . E 3 HOH 2 18 3 HOH HOH B . E 3 HOH 3 19 9 HOH HOH B . E 3 HOH 4 20 10 HOH HOH B . E 3 HOH 5 21 11 HOH HOH B . E 3 HOH 6 22 12 HOH HOH B . E 3 HOH 7 23 17 HOH HOH B . E 3 HOH 8 24 22 HOH HOH B . E 3 HOH 9 25 23 HOH HOH B . E 3 HOH 10 26 26 HOH HOH B . E 3 HOH 11 27 28 HOH HOH B . E 3 HOH 12 28 29 HOH HOH B . E 3 HOH 13 29 30 HOH HOH B . F 3 HOH 1 18 4 HOH HOH A . F 3 HOH 2 19 5 HOH HOH A . F 3 HOH 3 20 6 HOH HOH A . F 3 HOH 4 21 13 HOH HOH A . F 3 HOH 5 22 14 HOH HOH A . F 3 HOH 6 23 18 HOH HOH A . F 3 HOH 7 24 20 HOH HOH A . F 3 HOH 8 25 24 HOH HOH A . F 3 HOH 9 26 25 HOH HOH A . F 3 HOH 10 27 27 HOH HOH A . G 3 HOH 1 17 7 HOH HOH C . G 3 HOH 2 18 8 HOH HOH C . G 3 HOH 3 19 15 HOH HOH C . G 3 HOH 4 20 16 HOH HOH C . G 3 HOH 5 21 19 HOH HOH C . G 3 HOH 6 22 21 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 CrystalClear 'data reduction' '(MSC/RIGAKU)' ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _cell.entry_id 1YZD _cell.length_a 43.000 _cell.length_b 43.000 _cell.length_c 121.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YZD _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1YZD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.11 _exptl_crystal.density_percent_sol 41.76 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 273 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details 'MPD, sodium cacodylate, spermidine, magnesium chloride, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 1 spermidine ? ? ? 1 4 1 'magnesium chloride' ? ? ? 1 5 1 'calcium chloride' ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 'sodium cacodylate' ? ? ? 1 9 2 'magnesium chloride' ? ? ? 1 10 2 'calcium chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date 2004-02-24 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1YZD _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 31.7 _reflns.d_resolution_high 2.18 _reflns.number_obs 6646 _reflns.number_all 7277 _reflns.percent_possible_obs 91.4 _reflns.pdbx_Rmerge_I_obs 0.077 _reflns.pdbx_Rsym_value 0.06 _reflns.pdbx_netI_over_sigmaI 15.20 _reflns.B_iso_Wilson_estimate 28.7 _reflns.pdbx_redundancy 21.79 _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 2.18 _reflns_shell.d_res_low 2.28 _reflns_shell.percent_possible_all 57.4 _reflns_shell.Rmerge_I_obs 0.387 _reflns_shell.pdbx_Rsym_value 0.37 _reflns_shell.meanI_over_sigI_obs 3.37 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 405 _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 1YZD _refine.ls_number_reflns_obs 5556 _refine.ls_number_reflns_all 5567 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 852998.37 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.07 _refine.ls_d_res_high 2.35 _refine.ls_percent_reflns_obs 98.0 _refine.ls_R_factor_obs 0.236 _refine.ls_R_factor_all 0.265 _refine.ls_R_factor_R_work 0.236 _refine.ls_R_factor_R_free 0.292 _refine.ls_R_factor_R_free_error 0.017 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.4 _refine.ls_number_reflns_R_free 301 _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 30.5 _refine.aniso_B[1][1] 4.45 _refine.aniso_B[2][2] 4.45 _refine.aniso_B[3][3] -8.91 _refine.aniso_B[1][2] 2.19 _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 0.405429 _refine.solvent_model_param_bsol 32.0361 _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 ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _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_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1YZD _refine_analyze.Luzzati_coordinate_error_obs 0.33 _refine_analyze.Luzzati_sigma_a_obs 0.39 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.50 _refine_analyze.Luzzati_sigma_a_free 0.56 _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 1011 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 29 _refine_hist.number_atoms_total 1041 _refine_hist.d_res_high 2.35 _refine_hist.d_res_low 8.07 # 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 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 6.9 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.33 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 0.00 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 0.00 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.46 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 1.92 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.35 _refine_ls_shell.d_res_low 2.49 _refine_ls_shell.number_reflns_R_work 824 _refine_ls_shell.R_factor_R_work 0.302 _refine_ls_shell.percent_reflns_obs 92.8 _refine_ls_shell.R_factor_R_free 0.415 _refine_ls_shell.R_factor_R_free_error 0.067 _refine_ls_shell.percent_reflns_R_free 4.4 _refine_ls_shell.number_reflns_R_free 38 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 C2N.PARAM C2N.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 WATER.PARAM WATER.TOP 'X-RAY DIFFRACTION' 4 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1YZD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1YZD _struct.title ;Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YZD _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;2'-AMINE, RNA, DUPLEX ; # 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 1 ? C N N 1 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1YZD _struct_ref.pdbx_db_accession 1YZD _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1YZD B 1 ? 16 ? 1YZD 1 ? 16 ? 1 16 2 1 1YZD A 1 ? 16 ? 1YZD 1 ? 16 ? 1 16 3 1 1YZD C 1 ? 16 ? 1YZD 1 ? 16 ? 1 16 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,D,E,F 2 1,2 C,G # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 6_765 -x+2,-x+y+1,-z+1/3 -0.5000000000 -0.8660254038 0.0000000000 64.5000000000 -0.8660254038 0.5000000000 0.0000000000 37.2390923627 0.0000000000 0.0000000000 -1.0000000000 40.3333333333 # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A A 5 "O3'" ? ? ? 1_555 A A5M 6 P ? ? B A 5 B A5M 6 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale both ? A A5M 6 "O3'" ? ? ? 1_555 A U 7 P ? ? B A5M 6 B U 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? B A 5 "O3'" ? ? ? 1_555 B A5M 6 P ? ? A A 5 A A5M 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale both ? B A5M 6 "O3'" ? ? ? 1_555 B U 7 P ? ? A A5M 6 A U 7 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale both ? C A 5 "O3'" ? ? ? 1_555 C A5M 6 P ? ? C A 5 C A5M 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale6 covale both ? C A5M 6 "O3'" ? ? ? 1_555 C U 7 P ? ? C A5M 6 C U 7 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? B C 16 "O2'" ? ? ? 1_555 D CA . CA ? ? A C 16 A CA 17 1_555 ? ? ? ? ? ? ? 2.442 ? ? metalc2 metalc ? ? B C 16 "O3'" ? ? ? 1_555 D CA . CA ? ? A C 16 A CA 17 1_555 ? ? ? ? ? ? ? 2.559 ? ? metalc3 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 17 A HOH 26 1_555 ? ? ? ? ? ? ? 2.072 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? B G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? B G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? B G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 15 N1 ? ? B C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 15 O6 ? ? B C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 15 N2 ? ? B C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 14 N3 ? ? B A 3 A U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 14 O4 ? ? B A 3 A U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 13 N3 ? ? B G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 13 O2 ? ? B G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 13 N4 ? ? B G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? B A 5 A U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? B A 5 A U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A5M 6 N3 ? ? ? 1_555 B G 11 N1 ? ? B A5M 6 A G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A5M 6 N4 ? ? ? 1_555 B G 11 O6 ? ? B A5M 6 A G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A5M 6 O2 ? ? ? 1_555 B G 11 N2 ? ? B A5M 6 A G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? B U 7 A A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? B U 7 A A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? B U 8 A A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 9 N6 ? ? B U 8 A A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? B A 9 A U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? B A 9 A U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? B A 10 A U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? B A 10 A U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 B A5M 6 N3 ? ? B G 11 A A5M 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 N2 ? ? ? 1_555 B A5M 6 O2 ? ? B G 11 A A5M 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 O6 ? ? ? 1_555 B A5M 6 N4 ? ? B G 11 A A5M 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? B U 12 A A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? B U 12 A A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 4 N1 ? ? B C 13 A G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 4 O6 ? ? B C 13 A G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 4 N2 ? ? B C 13 A G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 3 N1 ? ? B U 14 A A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 3 N6 ? ? B U 14 A A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 2 N3 ? ? B G 15 A C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 2 O2 ? ? B G 15 A C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 2 N4 ? ? B G 15 A C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 1 N1 ? ? B C 16 A G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 1 O6 ? ? B C 16 A G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 1 N2 ? ? B C 16 A G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 1 N1 ? ? ? 1_555 C C 16 N3 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 1 N2 ? ? ? 1_555 C C 16 O2 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C G 1 O6 ? ? ? 1_555 C C 16 N4 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C C 2 N3 ? ? ? 1_555 C G 15 N1 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C C 2 N4 ? ? ? 1_555 C G 15 O6 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C C 2 O2 ? ? ? 1_555 C G 15 N2 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C A 3 N1 ? ? ? 1_555 C U 14 N3 ? ? C A 3 C U 14 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C A 3 N6 ? ? ? 1_555 C U 14 O4 ? ? C A 3 C U 14 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 4 N1 ? ? ? 1_555 C C 13 N3 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C G 4 N2 ? ? ? 1_555 C C 13 O2 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C G 4 O6 ? ? ? 1_555 C C 13 N4 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C A 5 N1 ? ? ? 1_555 C U 12 N3 ? ? C A 5 C U 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C A 5 N6 ? ? ? 1_555 C U 12 O4 ? ? C A 5 C U 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C A5M 6 N3 ? ? ? 1_555 C G 11 N1 ? ? C A5M 6 C G 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C A5M 6 N4 ? ? ? 1_555 C G 11 O6 ? ? C A5M 6 C G 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C A5M 6 O2 ? ? ? 1_555 C G 11 N2 ? ? C A5M 6 C G 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C U 7 N3 ? ? ? 1_555 C A 10 N1 ? ? C U 7 C A 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C U 7 O4 ? ? ? 1_555 C A 10 N6 ? ? C U 7 C A 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C U 8 N3 ? ? ? 1_555 C A 9 N1 ? ? C U 8 C A 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C U 8 O4 ? ? ? 1_555 C A 9 N6 ? ? C U 8 C A 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C A 9 N1 ? ? ? 1_555 C U 8 N3 ? ? C A 9 C U 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C A 9 N6 ? ? ? 1_555 C U 8 O4 ? ? C A 9 C U 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C A 10 N1 ? ? ? 1_555 C U 7 N3 ? ? C A 10 C U 7 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C A 10 N6 ? ? ? 1_555 C U 7 O4 ? ? C A 10 C U 7 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C G 11 N1 ? ? ? 1_555 C A5M 6 N3 ? ? C G 11 C A5M 6 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C G 11 N2 ? ? ? 1_555 C A5M 6 O2 ? ? C G 11 C A5M 6 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C G 11 O6 ? ? ? 1_555 C A5M 6 N4 ? ? C G 11 C A5M 6 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? C U 12 N3 ? ? ? 1_555 C A 5 N1 ? ? C U 12 C A 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? C U 12 O4 ? ? ? 1_555 C A 5 N6 ? ? C U 12 C A 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? C C 13 N3 ? ? ? 1_555 C G 4 N1 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C C 13 N4 ? ? ? 1_555 C G 4 O6 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? C C 13 O2 ? ? ? 1_555 C G 4 N2 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? C U 14 N3 ? ? ? 1_555 C A 3 N1 ? ? C U 14 C A 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? C U 14 O4 ? ? ? 1_555 C A 3 N6 ? ? C U 14 C A 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? C G 15 N1 ? ? ? 1_555 C C 2 N3 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? C G 15 N2 ? ? ? 1_555 C C 2 O2 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? C G 15 O6 ? ? ? 1_555 C C 2 N4 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? C C 16 N3 ? ? ? 1_555 C G 1 N1 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? C C 16 N4 ? ? ? 1_555 C G 1 O6 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? C C 16 O2 ? ? ? 1_555 C G 1 N2 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 "O2'" ? B C 16 ? A C 16 ? 1_555 CA ? D CA . ? A CA 17 ? 1_555 "O3'" ? B C 16 ? A C 16 ? 1_555 70.9 ? 2 "O2'" ? B C 16 ? A C 16 ? 1_555 CA ? D CA . ? A CA 17 ? 1_555 O ? F HOH . ? A HOH 26 ? 1_555 68.7 ? 3 "O3'" ? B C 16 ? A C 16 ? 1_555 CA ? D CA . ? A CA 17 ? 1_555 O ? F HOH . ? A HOH 26 ? 1_555 130.0 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id CA _struct_site.pdbx_auth_seq_id 17 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE CA A 17' # 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 C B 16 ? C A 16 . ? 1_555 ? 2 AC1 2 HOH F . ? HOH A 26 . ? 1_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A A5M 6 B A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" 2 B A5M 6 A A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" 3 C A5M 6 C A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id C _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 19 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 A5M P P N N 38 A5M OP1 O N N 39 A5M OP2 O N N 40 A5M "O5'" O N N 41 A5M "C5'" C N N 42 A5M "C4'" C N R 43 A5M "O4'" O N N 44 A5M "C1'" C N R 45 A5M N1 N N N 46 A5M C6 C N N 47 A5M C2 C N N 48 A5M O2 O N N 49 A5M N3 N N N 50 A5M C4 C N N 51 A5M N4 N N N 52 A5M C5 C N N 53 A5M "C2'" C N R 54 A5M "N2'" N N N 55 A5M "C3'" C N S 56 A5M "O3'" O N N 57 A5M OP3 O N N 58 A5M HOP2 H N N 59 A5M "H5'" H N N 60 A5M "H5''" H N N 61 A5M "H4'" H N N 62 A5M "H1'" H N N 63 A5M H6 H N N 64 A5M H41 H N N 65 A5M H42 H N N 66 A5M H5 H N N 67 A5M "H2'" H N N 68 A5M "H'1N" H N N 69 A5M "H'2N" H N N 70 A5M "H3'" H N N 71 A5M "HO3'" H N N 72 A5M HOP3 H N N 73 C OP3 O N N 74 C P P N N 75 C OP1 O N N 76 C OP2 O N N 77 C "O5'" O N N 78 C "C5'" C N N 79 C "C4'" C N R 80 C "O4'" O N N 81 C "C3'" C N S 82 C "O3'" O N N 83 C "C2'" C N R 84 C "O2'" O N N 85 C "C1'" C N R 86 C N1 N N N 87 C C2 C N N 88 C O2 O N N 89 C N3 N N N 90 C C4 C N N 91 C N4 N N N 92 C C5 C N N 93 C C6 C N N 94 C HOP3 H N N 95 C HOP2 H N N 96 C "H5'" H N N 97 C "H5''" H N N 98 C "H4'" H N N 99 C "H3'" H N N 100 C "HO3'" H N N 101 C "H2'" H N N 102 C "HO2'" H N N 103 C "H1'" H N N 104 C H41 H N N 105 C H42 H N N 106 C H5 H N N 107 C H6 H N N 108 CA CA CA N N 109 G OP3 O N N 110 G P P N N 111 G OP1 O N N 112 G OP2 O N N 113 G "O5'" O N N 114 G "C5'" C N N 115 G "C4'" C N R 116 G "O4'" O N N 117 G "C3'" C N S 118 G "O3'" O N N 119 G "C2'" C N R 120 G "O2'" O N N 121 G "C1'" C N R 122 G N9 N Y N 123 G C8 C Y N 124 G N7 N Y N 125 G C5 C Y N 126 G C6 C N N 127 G O6 O N N 128 G N1 N N N 129 G C2 C N N 130 G N2 N N N 131 G N3 N N N 132 G C4 C Y N 133 G HOP3 H N N 134 G HOP2 H N N 135 G "H5'" H N N 136 G "H5''" H N N 137 G "H4'" H N N 138 G "H3'" H N N 139 G "HO3'" H N N 140 G "H2'" H N N 141 G "HO2'" H N N 142 G "H1'" H N N 143 G H8 H N N 144 G H1 H N N 145 G H21 H N N 146 G H22 H N N 147 HOH O O N N 148 HOH H1 H N N 149 HOH H2 H N N 150 U OP3 O N N 151 U P P N N 152 U OP1 O N N 153 U OP2 O N N 154 U "O5'" O N N 155 U "C5'" C N N 156 U "C4'" C N R 157 U "O4'" O N N 158 U "C3'" C N S 159 U "O3'" O N N 160 U "C2'" C N R 161 U "O2'" O N N 162 U "C1'" C N R 163 U N1 N N N 164 U C2 C N N 165 U O2 O N N 166 U N3 N N N 167 U C4 C N N 168 U O4 O N N 169 U C5 C N N 170 U C6 C N N 171 U HOP3 H N N 172 U HOP2 H N N 173 U "H5'" H N N 174 U "H5''" H N N 175 U "H4'" H N N 176 U "H3'" H N N 177 U "HO3'" H N N 178 U "H2'" H N N 179 U "HO2'" H N N 180 U "H1'" H N N 181 U H3 H N N 182 U H5 H N N 183 U H6 H N N 184 # 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 A5M P OP1 doub N N 40 A5M P OP2 sing N N 41 A5M P "O5'" sing N N 42 A5M P OP3 sing N N 43 A5M OP2 HOP2 sing N N 44 A5M "O5'" "C5'" sing N N 45 A5M "C5'" "C4'" sing N N 46 A5M "C5'" "H5'" sing N N 47 A5M "C5'" "H5''" sing N N 48 A5M "C4'" "O4'" sing N N 49 A5M "C4'" "C3'" sing N N 50 A5M "C4'" "H4'" sing N N 51 A5M "O4'" "C1'" sing N N 52 A5M "C1'" N1 sing N N 53 A5M "C1'" "C2'" sing N N 54 A5M "C1'" "H1'" sing N N 55 A5M N1 C6 sing N N 56 A5M N1 C2 sing N N 57 A5M C6 C5 doub N N 58 A5M C6 H6 sing N N 59 A5M C2 O2 doub N N 60 A5M C2 N3 sing N N 61 A5M N3 C4 doub N N 62 A5M C4 N4 sing N N 63 A5M C4 C5 sing N N 64 A5M N4 H41 sing N N 65 A5M N4 H42 sing N N 66 A5M C5 H5 sing N N 67 A5M "C2'" "N2'" sing N N 68 A5M "C2'" "C3'" sing N N 69 A5M "C2'" "H2'" sing N N 70 A5M "N2'" "H'1N" sing N N 71 A5M "N2'" "H'2N" sing N N 72 A5M "C3'" "O3'" sing N N 73 A5M "C3'" "H3'" sing N N 74 A5M "O3'" "HO3'" sing N N 75 A5M OP3 HOP3 sing N N 76 C OP3 P sing N N 77 C OP3 HOP3 sing N N 78 C P OP1 doub N N 79 C P OP2 sing N N 80 C P "O5'" sing N N 81 C OP2 HOP2 sing N N 82 C "O5'" "C5'" sing N N 83 C "C5'" "C4'" sing N N 84 C "C5'" "H5'" sing N N 85 C "C5'" "H5''" sing N N 86 C "C4'" "O4'" sing N N 87 C "C4'" "C3'" sing N N 88 C "C4'" "H4'" sing N N 89 C "O4'" "C1'" sing N N 90 C "C3'" "O3'" sing N N 91 C "C3'" "C2'" sing N N 92 C "C3'" "H3'" sing N N 93 C "O3'" "HO3'" sing N N 94 C "C2'" "O2'" sing N N 95 C "C2'" "C1'" sing N N 96 C "C2'" "H2'" sing N N 97 C "O2'" "HO2'" sing N N 98 C "C1'" N1 sing N N 99 C "C1'" "H1'" sing N N 100 C N1 C2 sing N N 101 C N1 C6 sing N N 102 C C2 O2 doub N N 103 C C2 N3 sing N N 104 C N3 C4 doub N N 105 C C4 N4 sing N N 106 C C4 C5 sing N N 107 C N4 H41 sing N N 108 C N4 H42 sing N N 109 C C5 C6 doub N N 110 C C5 H5 sing N N 111 C C6 H6 sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 U OP3 P sing N N 155 U OP3 HOP3 sing N N 156 U P OP1 doub N N 157 U P OP2 sing N N 158 U P "O5'" sing N N 159 U OP2 HOP2 sing N N 160 U "O5'" "C5'" sing N N 161 U "C5'" "C4'" sing N N 162 U "C5'" "H5'" sing N N 163 U "C5'" "H5''" sing N N 164 U "C4'" "O4'" sing N N 165 U "C4'" "C3'" sing N N 166 U "C4'" "H4'" sing N N 167 U "O4'" "C1'" sing N N 168 U "C3'" "O3'" sing N N 169 U "C3'" "C2'" sing N N 170 U "C3'" "H3'" sing N N 171 U "O3'" "HO3'" sing N N 172 U "C2'" "O2'" sing N N 173 U "C2'" "C1'" sing N N 174 U "C2'" "H2'" sing N N 175 U "O2'" "HO2'" sing N N 176 U "C1'" N1 sing N N 177 U "C1'" "H1'" sing N N 178 U N1 C2 sing N N 179 U N1 C6 sing N N 180 U C2 O2 doub N N 181 U C2 N3 sing N N 182 U N3 C4 sing N N 183 U N3 H3 sing N N 184 U C4 O4 doub N N 185 U C4 C5 sing N N 186 U C5 C6 doub N N 187 U C5 H5 sing N N 188 U C6 H6 sing N N 189 # _ndb_struct_conf_na.entry_id 1YZD _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 16 1_555 -0.428 -0.301 -0.070 -3.546 -6.358 1.514 1 B_G1:C16_A B 1 ? A 16 ? 19 1 1 A C 2 1_555 B G 15 1_555 0.374 -0.330 -0.383 5.674 -18.494 2.445 2 B_C2:G15_A B 2 ? A 15 ? 19 1 1 A A 3 1_555 B U 14 1_555 -0.056 -0.172 0.006 -5.406 -15.657 6.243 3 B_A3:U14_A B 3 ? A 14 ? 20 1 1 A G 4 1_555 B C 13 1_555 -0.407 -0.312 0.104 -2.711 -16.396 0.623 4 B_G4:C13_A B 4 ? A 13 ? 19 1 1 A A 5 1_555 B U 12 1_555 0.152 -0.324 -0.210 -6.361 -15.487 4.330 5 B_A5:U12_A B 5 ? A 12 ? 20 1 1 A A5M 6 1_555 B G 11 1_555 0.346 -0.360 -0.135 3.939 -16.521 3.611 6 B_A5M6:G11_A B 6 ? A 11 ? 19 1 1 A U 7 1_555 B A 10 1_555 -0.246 -0.220 -0.208 0.489 -15.681 -0.107 7 B_U7:A10_A B 7 ? A 10 ? 20 1 1 A U 8 1_555 B A 9 1_555 -0.013 -0.187 0.153 6.649 -11.798 8.087 8 B_U8:A9_A B 8 ? A 9 ? 20 1 1 A A 9 1_555 B U 8 1_555 -0.009 -0.176 0.203 0.369 -21.318 7.383 9 B_A9:U8_A B 9 ? A 8 ? 20 1 1 A A 10 1_555 B U 7 1_555 0.241 -0.349 -0.247 -4.805 -16.153 -3.264 10 B_A10:U7_A B 10 ? A 7 ? 20 1 1 A G 11 1_555 B A5M 6 1_555 -0.475 -0.209 -0.062 -8.215 -20.955 6.884 11 B_G11:A5M6_A B 11 ? A 6 ? 19 1 1 A U 12 1_555 B A 5 1_555 -0.068 -0.194 0.087 -4.605 -9.562 -4.777 12 B_U12:A5_A B 12 ? A 5 ? 20 1 1 A C 13 1_555 B G 4 1_555 -0.195 -0.153 0.058 -0.668 -16.932 1.599 13 B_C13:G4_A B 13 ? A 4 ? 19 1 1 A U 14 1_555 B A 3 1_555 0.138 -0.223 0.136 -6.244 -11.794 6.634 14 B_U14:A3_A B 14 ? A 3 ? 20 1 1 A G 15 1_555 B C 2 1_555 -0.367 -0.341 -0.014 -4.982 -12.275 4.361 15 B_G15:C2_A B 15 ? A 2 ? 19 1 1 A C 16 1_555 B G 1 1_555 1.067 -0.471 -0.044 2.223 -16.280 2.155 16 B_C16:G1_A B 16 ? A 1 ? 19 1 1 C G 1 1_555 C C 16 6_765 0.033 -0.128 -0.261 -4.023 -7.465 0.129 17 C_G1:C16_C C 1 ? C 16 ? 19 1 1 C C 2 1_555 C G 15 6_765 0.193 -0.324 -0.056 3.708 -14.363 4.026 18 C_C2:G15_C C 2 ? C 15 ? 19 1 1 C A 3 1_555 C U 14 6_765 -0.381 -0.249 0.087 1.338 -11.965 5.925 19 C_A3:U14_C C 3 ? C 14 ? 20 1 1 C G 4 1_555 C C 13 6_765 -0.231 -0.322 -0.146 -1.248 -12.887 1.203 20 C_G4:C13_C C 4 ? C 13 ? 19 1 1 C A 5 1_555 C U 12 6_765 -0.219 -0.399 -0.305 1.855 -10.431 -0.888 21 C_A5:U12_C C 5 ? C 12 ? 20 1 1 C A5M 6 1_555 C G 11 6_765 0.108 -0.003 0.432 -2.190 -15.622 6.884 22 C_A5M6:G11_C C 6 ? C 11 ? 19 1 1 C U 7 1_555 C A 10 6_765 0.452 -0.206 -0.138 3.468 -12.001 -0.900 23 C_U7:A10_C C 7 ? C 10 ? 20 1 1 C U 8 1_555 C A 9 6_765 0.029 -0.200 -0.256 4.723 -14.772 6.253 24 C_U8:A9_C C 8 ? C 9 ? 20 1 1 C A 9 1_555 C U 8 6_765 -0.029 -0.200 -0.256 -4.723 -14.772 6.253 25 C_A9:U8_C C 9 ? C 8 ? 20 1 1 C A 10 1_555 C U 7 6_765 -0.452 -0.206 -0.138 -3.468 -12.001 -0.900 26 C_A10:U7_C C 10 ? C 7 ? 20 1 1 C G 11 1_555 C A5M 6 6_765 -0.108 -0.003 0.432 2.190 -15.622 6.884 27 C_G11:A5M6_C C 11 ? C 6 ? 19 1 1 C U 12 1_555 C A 5 6_765 0.219 -0.399 -0.305 -1.855 -10.431 -0.888 28 C_U12:A5_C C 12 ? C 5 ? 20 1 1 C C 13 1_555 C G 4 6_765 0.231 -0.322 -0.146 1.248 -12.887 1.203 29 C_C13:G4_C C 13 ? C 4 ? 19 1 1 C U 14 1_555 C A 3 6_765 0.381 -0.249 0.087 -1.338 -11.965 5.925 30 C_U14:A3_C C 14 ? C 3 ? 20 1 1 C G 15 1_555 C C 2 6_765 -0.193 -0.324 -0.056 -3.708 -14.363 4.026 31 C_G15:C2_C C 15 ? C 2 ? 19 1 1 C C 16 1_555 C G 1 6_765 -0.033 -0.128 -0.261 4.023 -7.465 0.129 32 C_C16:G1_C C 16 ? C 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 G 1 1_555 B C 16 1_555 A C 2 1_555 B G 15 1_555 -0.621 -1.177 2.999 0.626 6.846 37.013 -2.612 1.035 2.736 10.670 -0.975 37.624 1 BB_G1C2:G15C16_AA B 1 ? A 16 ? B 2 ? A 15 ? 1 A C 2 1_555 B G 15 1_555 A A 3 1_555 B U 14 1_555 0.643 -1.474 3.471 -1.722 15.703 29.384 -5.065 -1.397 2.362 28.509 3.126 33.279 2 BB_C2A3:U14G15_AA B 2 ? A 15 ? B 3 ? A 14 ? 1 A A 3 1_555 B U 14 1_555 A G 4 1_555 B C 13 1_555 -0.268 -1.716 3.053 0.274 13.736 29.565 -5.038 0.517 2.070 25.269 -0.503 32.537 3 BB_A3G4:C13U14_AA B 3 ? A 14 ? B 4 ? A 13 ? 1 A G 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 0.654 -1.243 3.324 4.989 9.719 32.479 -3.614 -0.341 2.909 16.794 -8.621 34.220 4 BB_G4A5:U12C13_AA B 4 ? A 13 ? B 5 ? A 12 ? 1 A A 5 1_555 B U 12 1_555 A A5M 6 1_555 B G 11 1_555 0.424 -1.266 2.963 3.162 4.131 35.727 -2.564 -0.287 2.829 6.690 -5.120 36.091 5 BB_A5A5M6:G11U12_AA B 5 ? A 12 ? B 6 ? A 11 ? 1 A A5M 6 1_555 B G 11 1_555 A U 7 1_555 B A 10 1_555 -0.376 -2.230 3.398 0.272 9.227 19.810 -9.096 1.086 2.149 25.132 -0.740 21.836 6 BB_A5M6U7:A10G11_AA B 6 ? A 11 ? B 7 ? A 10 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 0.271 -1.011 3.111 -4.525 4.493 35.623 -2.216 -1.028 2.911 7.273 7.324 36.171 7 BB_U7U8:A9A10_AA B 7 ? A 10 ? B 8 ? A 9 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 -0.058 -1.480 3.131 0.293 16.483 32.264 -4.379 0.130 2.147 27.532 -0.490 36.132 8 BB_U8A9:U8A9_AA B 8 ? A 9 ? B 9 ? A 8 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 -0.819 -1.364 3.329 1.391 14.861 33.639 -4.059 1.477 2.492 24.251 -2.270 36.714 9 BB_A9A10:U7U8_AA B 9 ? A 8 ? B 10 ? A 7 ? 1 A A 10 1_555 B U 7 1_555 A G 11 1_555 B A5M 6 1_555 1.597 -1.632 3.304 2.534 18.602 25.031 -6.137 -2.547 1.833 36.997 -5.040 31.199 10 BB_A10G11:A5M6U7_AA B 10 ? A 7 ? B 11 ? A 6 ? 1 A G 11 1_555 B A5M 6 1_555 A U 12 1_555 B A 5 1_555 -1.097 -1.795 3.082 -5.566 5.501 30.257 -4.299 1.061 2.871 10.323 10.444 31.230 11 BB_G11U12:A5A5M6_AA B 11 ? A 6 ? B 12 ? A 5 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B G 4 1_555 0.062 -1.410 2.923 -0.135 3.979 33.447 -2.997 -0.127 2.742 6.884 0.233 33.677 12 BB_U12C13:G4A5_AA B 12 ? A 5 ? B 13 ? A 4 ? 1 A C 13 1_555 B G 4 1_555 A U 14 1_555 B A 3 1_555 0.348 -1.159 3.369 0.183 6.774 33.601 -3.030 -0.562 3.086 11.571 -0.313 34.258 13 BB_C13U14:A3G4_AA B 13 ? A 4 ? B 14 ? A 3 ? 1 A U 14 1_555 B A 3 1_555 A G 15 1_555 B C 2 1_555 -0.452 -1.370 3.046 0.256 11.212 30.853 -4.089 0.838 2.410 20.255 -0.462 32.781 14 BB_U14G15:C2A3_AA B 14 ? A 3 ? B 15 ? A 2 ? 1 A G 15 1_555 B C 2 1_555 A C 16 1_555 B G 1 1_555 0.664 -1.037 3.107 1.933 -0.334 39.974 -1.479 -0.759 3.143 -0.488 -2.826 40.021 15 BB_G15C16:G1C2_AA B 15 ? A 2 ? B 16 ? A 1 ? 1 C G 1 1_555 C C 16 6_765 C C 2 1_555 C G 15 6_765 0.191 -1.284 3.093 -1.354 1.250 31.775 -2.556 -0.579 3.031 2.280 2.471 31.827 16 CC_G1C2:G15C16_CC C 1 ? C 16 ? C 2 ? C 15 ? 1 C C 2 1_555 C G 15 6_765 C A 3 1_555 C U 14 6_765 -0.105 -1.478 3.296 -1.033 10.144 29.320 -4.593 0.011 2.651 19.318 1.968 31.006 17 CC_C2A3:U14G15_CC C 2 ? C 15 ? C 3 ? C 14 ? 1 C A 3 1_555 C U 14 6_765 C G 4 1_555 C C 13 6_765 -0.687 -1.553 3.182 -1.830 13.760 31.281 -4.573 0.913 2.347 24.088 3.203 34.152 18 CC_A3G4:C13U14_CC C 3 ? C 14 ? C 4 ? C 13 ? 1 C G 4 1_555 C C 13 6_765 C A 5 1_555 C U 12 6_765 -0.386 -1.334 3.150 0.361 11.390 31.783 -3.959 0.718 2.531 20.011 -0.634 33.714 19 CC_G4A5:U12C13_CC C 4 ? C 13 ? C 5 ? C 12 ? 1 C A 5 1_555 C U 12 6_765 C A5M 6 1_555 C G 11 6_765 1.091 -1.336 3.270 -1.976 10.351 33.982 -3.600 -2.057 2.695 17.205 3.284 35.533 20 CC_A5A5M6:G11U12_CC C 5 ? C 12 ? C 6 ? C 11 ? 1 C A5M 6 1_555 C G 11 6_765 C U 7 1_555 C A 10 6_765 -0.949 -1.672 2.906 2.103 10.351 30.754 -4.441 1.992 2.176 18.834 -3.826 32.475 21 CC_A5M6U7:A10G11_CC C 6 ? C 11 ? C 7 ? C 10 ? 1 C U 7 1_555 C A 10 6_765 C U 8 1_555 C A 9 6_765 0.208 -1.270 3.195 0.894 7.399 30.744 -3.610 -0.228 2.825 13.704 -1.656 31.613 22 CC_U7U8:A9A10_CC C 7 ? C 10 ? C 8 ? C 9 ? 1 C U 8 1_555 C A 9 6_765 C A 9 1_555 C U 8 6_765 0.000 -1.208 3.344 0.000 17.930 32.388 -4.180 0.000 2.375 29.495 0.000 36.903 23 CC_U8A9:U8A9_CC C 8 ? C 9 ? C 9 ? C 8 ? 1 C A 9 1_555 C U 8 6_765 C A 10 1_555 C U 7 6_765 -0.208 -1.270 3.195 -0.894 7.399 30.744 -3.610 0.228 2.825 13.704 1.656 31.613 24 CC_A9A10:U7U8_CC C 9 ? C 8 ? C 10 ? C 7 ? 1 C A 10 1_555 C U 7 6_765 C G 11 1_555 C A5M 6 6_765 0.949 -1.672 2.906 -2.103 10.351 30.754 -4.441 -1.992 2.176 18.834 3.826 32.475 25 CC_A10G11:A5M6U7_CC C 10 ? C 7 ? C 11 ? C 6 ? 1 C G 11 1_555 C A5M 6 6_765 C U 12 1_555 C A 5 6_765 -1.091 -1.336 3.270 1.976 10.351 33.982 -3.600 2.057 2.695 17.205 -3.284 35.533 26 CC_G11U12:A5A5M6_CC C 11 ? C 6 ? C 12 ? C 5 ? 1 C U 12 1_555 C A 5 6_765 C C 13 1_555 C G 4 6_765 0.386 -1.334 3.150 -0.361 11.390 31.783 -3.959 -0.718 2.531 20.011 0.634 33.714 27 CC_U12C13:G4A5_CC C 12 ? C 5 ? C 13 ? C 4 ? 1 C C 13 1_555 C G 4 6_765 C U 14 1_555 C A 3 6_765 0.687 -1.553 3.182 1.830 13.760 31.281 -4.573 -0.913 2.347 24.088 -3.203 34.152 28 CC_C13U14:A3G4_CC C 13 ? C 4 ? C 14 ? C 3 ? 1 C U 14 1_555 C A 3 6_765 C G 15 1_555 C C 2 6_765 0.105 -1.478 3.296 1.033 10.144 29.320 -4.593 -0.011 2.651 19.318 -1.968 31.006 29 CC_U14G15:C2A3_CC C 14 ? C 3 ? C 15 ? C 2 ? 1 C G 15 1_555 C C 2 6_765 C C 16 1_555 C G 1 6_765 -0.191 -1.284 3.093 1.354 1.250 31.775 -2.556 0.579 3.031 2.280 -2.471 31.827 30 CC_G15C16:G1C2_CC C 15 ? C 2 ? C 16 ? C 1 ? # _atom_sites.entry_id 1YZD _atom_sites.fract_transf_matrix[1][1] 0.023256 _atom_sites.fract_transf_matrix[1][2] 0.013427 _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] 0.026854 _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] 0.008264 _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 CA N O P # loop_