data_2G92 # _entry.id 2G92 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 2G92 pdb_00002g92 10.2210/pdb2g92/pdb NDB AR0068 ? ? RCSB RCSB036841 ? ? WWPDB D_1000036841 ? ? # 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 2006-04-18 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 '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' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site 7 6 'Structure model' pdbx_initial_refinement_model # 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' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2G92 _pdbx_database_status.recvd_initial_deposition_date 2006-03-04 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Li, F.' 2 # _citation.id primary _citation.title 'Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide.' _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 1 _citation.page_first 176 _citation.page_last 183 _citation.year 2006 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17163665 _citation.pdbx_database_id_DOI 10.1021/cb600063p # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Xia, J.' 1 ? primary 'Noronha, A.' 2 ? primary 'Toudjarska, I.' 3 ? primary 'Li, F.' 4 ? primary 'Akinc, A.' 5 ? primary 'Braich, R.' 6 ? primary 'Frank-Kamenetsky, M.' 7 ? primary 'Rajeev, K.G.' 8 ? primary 'Egli, M.' 9 ? primary 'Manoharan, M.' 10 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*AP*GP*CP*G)-3'" 3828.353 2 ? ? ? ? 2 water nat water 18.015 84 ? ? ? ? # _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 'CGC(NF2)AAUUAGCG' _entity_poly.pdbx_seq_one_letter_code_can CGCNAAUUAGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 NF2 n 1 5 A n 1 6 A n 1 7 U n 1 8 U n 1 9 A n 1 10 G n 1 11 C n 1 12 G n # 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 NF2 'RNA linking' . '(1S)-1,4-ANHYDRO-1-(2,4-DIFLUORO-5-METHYLPHENYL)-5-O-PHOSPHONO-D-RIBITOL' ? 'C12 H15 F2 O7 P' 340.214 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 NF2 4 4 4 NF2 D A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n B 1 1 C 1 13 13 C C B . n B 1 2 G 2 14 14 G G B . n B 1 3 C 3 15 15 C C B . n B 1 4 NF2 4 16 16 NF2 D B . n B 1 5 A 5 17 17 A A B . n B 1 6 A 6 18 18 A A B . n B 1 7 U 7 19 19 U U B . n B 1 8 U 8 20 20 U U B . n B 1 9 A 9 21 21 A A B . n B 1 10 G 10 22 22 G G B . n B 1 11 C 11 23 23 C C B . n B 1 12 G 12 24 24 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 101 HOH HOH A . C 2 HOH 2 104 104 HOH HOH A . C 2 HOH 3 105 105 HOH HOH A . C 2 HOH 4 110 110 HOH HOH A . C 2 HOH 5 113 113 HOH HOH A . C 2 HOH 6 114 114 HOH HOH A . C 2 HOH 7 117 117 HOH HOH A . C 2 HOH 8 120 120 HOH HOH A . C 2 HOH 9 129 129 HOH HOH A . C 2 HOH 10 130 130 HOH HOH A . C 2 HOH 11 135 135 HOH HOH A . C 2 HOH 12 136 136 HOH HOH A . C 2 HOH 13 140 140 HOH HOH A . C 2 HOH 14 141 141 HOH HOH A . C 2 HOH 15 145 145 HOH HOH A . C 2 HOH 16 146 146 HOH HOH A . C 2 HOH 17 150 150 HOH HOH A . C 2 HOH 18 151 151 HOH HOH A . C 2 HOH 19 152 152 HOH HOH A . C 2 HOH 20 153 153 HOH HOH A . C 2 HOH 21 155 155 HOH HOH A . C 2 HOH 22 157 157 HOH HOH A . C 2 HOH 23 158 158 HOH HOH A . C 2 HOH 24 165 165 HOH HOH A . C 2 HOH 25 166 166 HOH HOH A . C 2 HOH 26 168 168 HOH HOH A . C 2 HOH 27 171 171 HOH HOH A . C 2 HOH 28 172 172 HOH HOH A . C 2 HOH 29 179 179 HOH HOH A . C 2 HOH 30 180 180 HOH HOH A . C 2 HOH 31 182 182 HOH HOH A . C 2 HOH 32 184 184 HOH HOH A . C 2 HOH 33 185 185 HOH HOH A . D 2 HOH 1 102 102 HOH HOH B . D 2 HOH 2 103 103 HOH HOH B . D 2 HOH 3 107 107 HOH HOH B . D 2 HOH 4 108 108 HOH HOH B . D 2 HOH 5 109 109 HOH HOH B . D 2 HOH 6 111 111 HOH HOH B . D 2 HOH 7 112 112 HOH HOH B . D 2 HOH 8 115 115 HOH HOH B . D 2 HOH 9 116 116 HOH HOH B . D 2 HOH 10 118 118 HOH HOH B . D 2 HOH 11 119 119 HOH HOH B . D 2 HOH 12 121 121 HOH HOH B . D 2 HOH 13 122 122 HOH HOH B . D 2 HOH 14 123 123 HOH HOH B . D 2 HOH 15 124 124 HOH HOH B . D 2 HOH 16 125 125 HOH HOH B . D 2 HOH 17 126 126 HOH HOH B . D 2 HOH 18 127 127 HOH HOH B . D 2 HOH 19 133 133 HOH HOH B . D 2 HOH 20 134 134 HOH HOH B . D 2 HOH 21 137 137 HOH HOH B . D 2 HOH 22 138 138 HOH HOH B . D 2 HOH 23 139 139 HOH HOH B . D 2 HOH 24 142 142 HOH HOH B . D 2 HOH 25 144 144 HOH HOH B . D 2 HOH 26 147 147 HOH HOH B . D 2 HOH 27 148 148 HOH HOH B . D 2 HOH 28 149 149 HOH HOH B . D 2 HOH 29 154 154 HOH HOH B . D 2 HOH 30 156 156 HOH HOH B . D 2 HOH 31 159 159 HOH HOH B . D 2 HOH 32 160 160 HOH HOH B . D 2 HOH 33 161 161 HOH HOH B . D 2 HOH 34 162 162 HOH HOH B . D 2 HOH 35 163 163 HOH HOH B . D 2 HOH 36 164 164 HOH HOH B . D 2 HOH 37 167 167 HOH HOH B . D 2 HOH 38 169 169 HOH HOH B . D 2 HOH 39 173 173 HOH HOH B . D 2 HOH 40 174 174 HOH HOH B . D 2 HOH 41 175 175 HOH HOH B . D 2 HOH 42 176 176 HOH HOH B . D 2 HOH 43 177 177 HOH HOH B . D 2 HOH 44 178 178 HOH HOH B . D 2 HOH 45 181 181 HOH HOH B . D 2 HOH 46 183 183 HOH HOH B . D 2 HOH 47 186 186 HOH HOH B . D 2 HOH 48 188 188 HOH HOH B . D 2 HOH 49 189 189 HOH HOH B . D 2 HOH 50 190 190 HOH HOH B . D 2 HOH 51 191 191 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0003 ? 1 X-GEN 'data reduction' . ? 2 X-GEN 'data scaling' . ? 3 EPMR phasing . ? 4 # _cell.entry_id 2G92 _cell.length_a 28.614 _cell.length_b 28.614 _cell.length_c 63.171 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 2G92 _symmetry.space_group_name_H-M 'P 31' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2G92 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.95 _exptl_crystal.density_percent_sol 36.92 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pdbx_details ;Final droplet composition: 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 'cobalt hexamine' ? ? ? 1 4 1 LiCl ? ? ? 1 5 1 MgCl2 ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 'sodium cacodylate' ? ? ? 1 9 2 'cobalt hexamine' ? ? ? 1 10 2 LiCl ? ? ? 1 11 2 MgCl2 ? ? ? 1 12 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2004-11-09 _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 0.992 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.992 # _reflns.entry_id 2G92 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 24.8 _reflns.d_resolution_high 1.61 _reflns.number_obs 7538 _reflns.number_all 7538 _reflns.percent_possible_obs 0.978 _reflns.pdbx_Rmerge_I_obs 0.054 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 1.61 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 0.969 _reflns_shell.Rmerge_I_obs 0.53 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _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 2G92 _refine.ls_number_reflns_obs 7425 _refine.ls_number_reflns_all 7538 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 24.78 _refine.ls_d_res_high 1.61 _refine.ls_percent_reflns_obs 98.55 _refine.ls_R_factor_obs 0.199 _refine.ls_R_factor_all 0.199 _refine.ls_R_factor_R_work 0.196 _refine.ls_R_factor_R_free 0.231 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.5 _refine.ls_number_reflns_R_free 558 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.968 _refine.correlation_coeff_Fo_to_Fc_free 0.959 _refine.B_iso_mean 27.11 _refine.aniso_B[1][1] 1.03 _refine.aniso_B[2][2] 1.03 _refine.aniso_B[3][3] -1.55 _refine.aniso_B[1][2] 0.52 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'Model of native A-RNA' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.206 _refine.pdbx_overall_ESU_R_Free 0.113 _refine.overall_SU_ML 0.088 _refine.overall_SU_B 5.698 _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_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 506 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 590 _refine_hist.d_res_high 1.61 _refine_hist.d_res_low 24.78 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.012 0.021 ? 564 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 200 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.066 3.007 ? 860 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.504 3.000 ? 524 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.092 0.200 ? 116 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.019 0.020 ? 246 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.182 0.200 ? 89 'X-RAY DIFFRACTION' ? r_nbd_other 0.281 0.200 ? 279 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.251 0.200 ? 224 'X-RAY DIFFRACTION' ? r_nbtor_other 0.131 0.200 ? 130 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.356 0.200 ? 53 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other 0.422 0.200 ? 2 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.086 0.200 ? 14 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.177 0.200 ? 19 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.311 0.200 ? 17 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 4.323 3.000 ? 798 'X-RAY DIFFRACTION' ? r_scangle_it 5.042 4.500 ? 860 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.61 _refine_ls_shell.d_res_low 1.648 _refine_ls_shell.number_reflns_R_work 497 _refine_ls_shell.R_factor_R_work 0.232 _refine_ls_shell.percent_reflns_obs 97.12 _refine_ls_shell.R_factor_R_free 0.265 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 42 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 539 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 2G92 _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 2G92 _struct.title 'Crystal Structure Analysis of the RNA Dodecamer CGC-(NF2)-AAUUAGCG, with an Incorporated 2,4-Difluorotoluyl Residue (NF2)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2G92 _struct_keywords.pdbx_keywords RNA _struct_keywords.text '2, 4-Difluorotoluyl Nucleoside, Chemical Modification, RNA, RNA Interference, Hydrogen Bonding' # 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 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2G92 _struct_ref.pdbx_db_accession 2G92 _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 2G92 A 1 ? 12 ? 2G92 1 ? 12 ? 1 12 2 1 2G92 B 1 ? 12 ? 2G92 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a duplex and corresponds to the crystallographic asymmetric unit, hence no symmetry operators are needed' _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 ? A C 3 "O3'" ? ? ? 1_555 A NF2 4 P ? ? A C 3 A NF2 4 1_555 ? ? ? ? ? ? ? 1.584 ? ? covale2 covale both ? A NF2 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A NF2 4 A A 5 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale3 covale both ? B C 3 "O3'" ? ? ? 1_555 B NF2 4 P ? ? B C 15 B NF2 16 1_555 ? ? ? ? ? ? ? 1.571 ? ? covale4 covale both ? B NF2 4 "O3'" ? ? ? 1_555 B A 5 P ? ? B NF2 16 B A 17 1_555 ? ? ? ? ? ? ? 1.588 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 1 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 1 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 1 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 5 B U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 5 B U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 6 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 6 B U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 6 B U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 7 B A 18 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog15 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 8 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 8 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 NF2 4 ? 2 'BINDING SITE FOR RESIDUE NF2 A 4' AC2 Software B NF2 16 ? 2 'BINDING SITE FOR RESIDUE NF2 B 16' # 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 HOH C . ? HOH A 105 . ? 1_555 ? 2 AC1 2 HOH C . ? HOH A 158 . ? 1_555 ? 3 AC2 2 HOH D . ? HOH B 138 . ? 1_555 ? 4 AC2 2 HOH D . ? HOH B 163 . ? 1_555 ? # 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 C5 A G 2 ? ? C6 A G 2 ? ? O6 A G 2 ? ? 124.16 128.60 -4.44 0.60 N 2 1 "O5'" A U 7 ? ? "C5'" A U 7 ? ? "C4'" A U 7 ? ? 104.16 109.40 -5.24 0.80 N 3 1 N1 A U 8 ? ? C2 A U 8 ? ? O2 A U 8 ? ? 127.10 122.80 4.30 0.70 N 4 1 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 113.05 108.50 4.55 0.70 N 5 1 "O3'" B NF2 16 ? ? P B A 17 ? ? OP1 B A 17 ? ? 118.14 110.50 7.64 1.10 Y 6 1 N9 B A 17 ? ? C4 B A 17 ? ? C5 B A 17 ? ? 108.59 105.80 2.79 0.40 N 7 1 N1 B A 17 ? ? C6 B A 17 ? ? N6 B A 17 ? ? 114.75 118.60 -3.85 0.60 N 8 1 "O5'" B U 19 ? ? "C5'" B U 19 ? ? "C4'" B U 19 ? ? 104.50 109.40 -4.90 0.80 N 9 1 "C4'" B U 19 ? ? "C3'" B U 19 ? ? "C2'" B U 19 ? ? 95.93 102.60 -6.67 1.00 N 10 1 "O4'" B G 24 ? ? "C1'" B G 24 ? ? N9 B G 24 ? ? 112.90 108.50 4.40 0.70 N # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 4.4067 _pdbx_refine_tls.origin_y 12.3175 _pdbx_refine_tls.origin_z 14.3016 _pdbx_refine_tls.T[1][1] 0.0125 _pdbx_refine_tls.T[2][2] 0.0292 _pdbx_refine_tls.T[3][3] 0.0001 _pdbx_refine_tls.T[1][2] 0.0032 _pdbx_refine_tls.T[1][3] -0.0050 _pdbx_refine_tls.T[2][3] 0.0119 _pdbx_refine_tls.L[1][1] 0.0146 _pdbx_refine_tls.L[2][2] 0.3351 _pdbx_refine_tls.L[3][3] 0.2382 _pdbx_refine_tls.L[1][2] -0.0044 _pdbx_refine_tls.L[1][3] 0.0585 _pdbx_refine_tls.L[2][3] 0.0179 _pdbx_refine_tls.S[1][1] -0.0252 _pdbx_refine_tls.S[1][2] 0.0302 _pdbx_refine_tls.S[1][3] 0.0025 _pdbx_refine_tls.S[2][1] 0.0317 _pdbx_refine_tls.S[2][2] -0.0130 _pdbx_refine_tls.S[2][3] 0.0001 _pdbx_refine_tls.S[3][1] -0.0414 _pdbx_refine_tls.S[3][2] 0.0376 _pdbx_refine_tls.S[3][3] 0.0382 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 1 A 1 A 12 A 12 ? 'X-RAY DIFFRACTION' ? 2 1 B 13 B 1 B 24 B 12 ? 'X-RAY DIFFRACTION' ? # 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 NF2 F2 F N N 114 NF2 C2 C Y N 115 NF2 C3 C Y N 116 NF2 C4 C Y N 117 NF2 F4 F N N 118 NF2 C1 C Y N 119 NF2 C6 C Y N 120 NF2 C5 C Y N 121 NF2 CM C N N 122 NF2 "C1'" C N S 123 NF2 "O4'" O N N 124 NF2 "C2'" C N R 125 NF2 "O2'" O N N 126 NF2 "C3'" C N S 127 NF2 "O3'" O N N 128 NF2 "C4'" C N R 129 NF2 "C5'" C N N 130 NF2 "O5'" O N N 131 NF2 P P N N 132 NF2 OP1 O N N 133 NF2 OP2 O N N 134 NF2 OP3 O N N 135 NF2 H3 H N N 136 NF2 H6 H N N 137 NF2 HM1 H N N 138 NF2 HM2 H N N 139 NF2 HM3 H N N 140 NF2 "H1'" H N N 141 NF2 "H2'" H N N 142 NF2 "HO2'" H N N 143 NF2 "H3'" H N N 144 NF2 "HO3'" H N N 145 NF2 "H4'" H N N 146 NF2 "H5'" H N N 147 NF2 "H5''" H N N 148 NF2 HOP2 H N N 149 NF2 HOP3 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 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 NF2 F2 C2 sing N N 118 NF2 C2 C3 doub Y N 119 NF2 C2 C1 sing Y N 120 NF2 C3 C4 sing Y N 121 NF2 C3 H3 sing N N 122 NF2 C4 F4 sing N N 123 NF2 C4 C5 doub Y N 124 NF2 C1 C6 doub Y N 125 NF2 C1 "C1'" sing N N 126 NF2 C6 C5 sing Y N 127 NF2 C6 H6 sing N N 128 NF2 C5 CM sing N N 129 NF2 CM HM1 sing N N 130 NF2 CM HM2 sing N N 131 NF2 CM HM3 sing N N 132 NF2 "C1'" "O4'" sing N N 133 NF2 "C1'" "C2'" sing N N 134 NF2 "C1'" "H1'" sing N N 135 NF2 "O4'" "C4'" sing N N 136 NF2 "C2'" "O2'" sing N N 137 NF2 "C2'" "C3'" sing N N 138 NF2 "C2'" "H2'" sing N N 139 NF2 "O2'" "HO2'" sing N N 140 NF2 "C3'" "O3'" sing N N 141 NF2 "C3'" "C4'" sing N N 142 NF2 "C3'" "H3'" sing N N 143 NF2 "O3'" "HO3'" sing N N 144 NF2 "C4'" "C5'" sing N N 145 NF2 "C4'" "H4'" sing N N 146 NF2 "C5'" "O5'" sing N N 147 NF2 "C5'" "H5'" sing N N 148 NF2 "C5'" "H5''" sing N N 149 NF2 "O5'" P sing N N 150 NF2 P OP1 doub N N 151 NF2 P OP2 sing N N 152 NF2 P OP3 sing N N 153 NF2 OP2 HOP2 sing N N 154 NF2 OP3 HOP3 sing N N 155 U OP3 P sing N N 156 U OP3 HOP3 sing N N 157 U P OP1 doub N N 158 U P OP2 sing N N 159 U P "O5'" sing N N 160 U OP2 HOP2 sing N N 161 U "O5'" "C5'" sing N N 162 U "C5'" "C4'" sing N N 163 U "C5'" "H5'" sing N N 164 U "C5'" "H5''" sing N N 165 U "C4'" "O4'" sing N N 166 U "C4'" "C3'" sing N N 167 U "C4'" "H4'" sing N N 168 U "O4'" "C1'" sing N N 169 U "C3'" "O3'" sing N N 170 U "C3'" "C2'" sing N N 171 U "C3'" "H3'" sing N N 172 U "O3'" "HO3'" sing N N 173 U "C2'" "O2'" sing N N 174 U "C2'" "C1'" sing N N 175 U "C2'" "H2'" sing N N 176 U "O2'" "HO2'" sing N N 177 U "C1'" N1 sing N N 178 U "C1'" "H1'" sing N N 179 U N1 C2 sing N N 180 U N1 C6 sing N N 181 U C2 O2 doub N N 182 U C2 N3 sing N N 183 U N3 C4 sing N N 184 U N3 H3 sing N N 185 U C4 O4 doub N N 186 U C4 C5 sing N N 187 U C5 C6 doub N N 188 U C5 H5 sing N N 189 U C6 H6 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2G92 'double helix' 2G92 'a-form double helix' 2G92 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 B G 12 1_555 0.201 -0.212 0.067 9.728 -16.884 -1.199 1 A_C1:G24_B A 1 ? B 24 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.389 -0.231 -0.126 -5.522 -13.522 -0.225 2 A_G2:C23_B A 2 ? B 23 ? 19 1 1 A C 3 1_555 B G 10 1_555 0.001 -0.154 0.121 -4.590 -12.355 -0.844 3 A_C3:G22_B A 3 ? B 22 ? 19 1 1 A A 5 1_555 B U 8 1_555 0.112 -0.115 0.028 -0.442 -13.202 1.293 4 A_A5:U20_B A 5 ? B 20 ? 20 1 1 A A 6 1_555 B U 7 1_555 -0.013 -0.183 -0.020 2.795 -15.556 -1.255 5 A_A6:U19_B A 6 ? B 19 ? 20 1 1 A U 7 1_555 B A 6 1_555 -0.791 0.009 0.374 -0.908 -19.427 12.032 6 A_U7:A18_B A 7 ? B 18 ? ? ? 1 A U 8 1_555 B A 5 1_555 0.512 -0.435 -0.521 4.364 -16.138 -3.753 7 A_U8:A17_B A 8 ? B 17 ? 20 1 1 A G 10 1_555 B C 3 1_555 -0.346 -0.255 -0.069 -0.218 -12.920 -1.994 8 A_G10:C15_B A 10 ? B 15 ? 19 1 1 A C 11 1_555 B G 2 1_555 0.207 -0.180 0.011 1.754 -12.237 2.770 9 A_C11:G14_B A 11 ? B 14 ? 19 1 1 A G 12 1_555 B C 1 1_555 -0.275 -0.185 0.057 -4.618 -16.104 -0.390 10 A_G12:C13_B A 12 ? B 13 ? 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 C 1 1_555 B G 12 1_555 A G 2 1_555 B C 11 1_555 -0.737 -1.943 3.428 -2.883 15.882 32.009 -5.290 0.815 2.296 26.780 4.861 35.754 1 AA_C1G2:C23G24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A G 2 1_555 B C 11 1_555 A C 3 1_555 B G 10 1_555 -0.338 -1.247 3.195 -2.868 6.107 33.426 -3.048 0.145 2.946 10.485 4.925 34.081 2 AA_G2C3:G22C23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A C 3 1_555 B G 10 1_555 A A 5 1_555 B U 8 1_555 0.489 -3.528 6.143 -0.245 26.205 59.266 -5.214 -0.477 4.399 25.208 0.235 64.317 3 AA_C3A5:U20G22_BB A 3 ? B 22 ? A 5 ? B 20 ? 1 A A 5 1_555 B U 8 1_555 A A 6 1_555 B U 7 1_555 -0.266 -0.964 3.177 0.592 9.943 33.411 -3.019 0.528 2.780 16.835 -1.002 34.824 4 AA_A5A6:U19U20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A A 6 1_555 B U 7 1_555 A U 7 1_555 B A 6 1_555 0.977 -1.468 3.438 -1.296 19.189 19.513 -7.252 -2.347 1.399 44.893 3.031 27.332 5 AA_A6U7:A18U19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A U 7 1_555 B A 6 1_555 A U 8 1_555 B A 5 1_555 -0.896 -0.351 3.154 2.993 6.256 37.158 -1.306 1.749 2.980 9.714 -4.647 37.777 6 AA_U7U8:A17A18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A U 8 1_555 B A 5 1_555 A G 10 1_555 B C 3 1_555 -0.592 -3.496 6.113 -5.186 28.986 57.016 -5.443 0.181 4.122 28.385 5.078 63.599 7 AA_U8G10:C15A17_BB A 8 ? B 17 ? A 10 ? B 15 ? 1 A G 10 1_555 B C 3 1_555 A C 11 1_555 B G 2 1_555 0.370 -1.374 3.201 -0.140 11.403 35.620 -3.526 -0.595 2.651 18.077 0.222 37.345 8 AA_G10C11:G14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A C 11 1_555 B G 2 1_555 A G 12 1_555 B C 1 1_555 0.396 -1.695 3.224 2.844 12.840 30.733 -4.855 -0.268 2.372 22.953 -5.085 33.366 9 AA_C11G12:C13G14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_initial_refinement_model.accession_code ? _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 Other _pdbx_initial_refinement_model.details 'Model of native A-RNA' # _atom_sites.entry_id 2G92 _atom_sites.fract_transf_matrix[1][1] 0.034948 _atom_sites.fract_transf_matrix[1][2] 0.020177 _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] 0.040354 _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] 0.015830 _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 F N O P # loop_