data_4G6R # _entry.id 4G6R # _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 4G6R pdb_00004g6r 10.2210/pdb4g6r/pdb NDB NA1928 ? ? RCSB RCSB073808 ? ? WWPDB D_1000073808 ? ? # 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 2012-08-15 2 'Structure model' 1 1 2012-11-14 3 'Structure model' 1 2 2024-02-28 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' pdbx_struct_special_symmetry 6 3 'Structure model' struct_conn 7 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.value' 10 3 'Structure model' '_struct_conn.conn_type_id' 11 3 'Structure model' '_struct_conn.id' 12 3 'Structure model' '_struct_conn.pdbx_dist_value' 13 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 14 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 22 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 23 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 27 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 28 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 29 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 30 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 4G6R _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-07-19 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4G6P . unspecified PDB 4G6S . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Liberman, J.A.' 1 'Jenkins, J.L.' 2 'Krucinska, J.' 3 'Wedekind, J.E.' 4 # _citation.id primary _citation.title 'A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 134 _citation.page_first 16933 _citation.page_last 16936 _citation.year 2012 _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 22989273 _citation.pdbx_database_id_DOI 10.1021/ja3070528 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liberman, J.A.' 1 ? primary 'Guo, M.' 2 ? primary 'Jenkins, J.L.' 3 ? primary 'Krucinska, J.' 4 ? primary 'Chen, Y.' 5 ? primary 'Carey, P.R.' 6 ? primary 'Wedekind, J.E.' 7 ? # 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 'Loop A Substrate strand' 4036.471 1 ? ? ? ? 2 polymer syn 'Loop A Ribozyme strand' 3955.433 1 ? ? ? ? 3 polymer syn 'Loop B Ribozyme Strand' 5535.445 1 ? ? ? ? 4 polymer syn 'Loop B S-turn strand' 5991.568 1 ? ? ? ? 5 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 6 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 7 water nat water 18.015 6 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'UCCC(3DA)GUCCACCG' UCCCAGUCCACCG A ? 2 polyribonucleotide no no CGGUGAIAAGGG CGGUGAIAAGGG B ? 3 polyribonucleotide no no GGCAGAGAAACACACGA GGCAGAGAAACACACGA C ? 4 polyribonucleotide no no UCGUGGUACAUUACCUGCC UCGUGGUACAUUACCUGCC D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 5 'SULFATE ION' SO4 6 'MAGNESIUM ION' MG 7 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 C n 1 3 C n 1 4 C n 1 5 3DA n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 G n 2 6 A n 2 7 I n 2 8 A n 2 9 A n 2 10 G n 2 11 G n 2 12 G n 3 1 G n 3 2 G n 3 3 C n 3 4 A n 3 5 G n 3 6 A n 3 7 G n 3 8 A n 3 9 A n 3 10 A n 3 11 C n 3 12 A n 3 13 C n 3 14 A n 3 15 C n 3 16 G n 3 17 A n 4 1 U n 4 2 C n 4 3 G n 4 4 U n 4 5 G n 4 6 G n 4 7 U n 4 8 A n 4 9 C n 4 10 A n 4 11 U n 4 12 U n 4 13 A n 4 14 C n 4 15 C n 4 16 U n 4 17 G n 4 18 C n 4 19 C n # 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 3DA 'RNA linking' n "3'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 I 'RNA linking' y 'INOSINIC ACID' ? 'C10 H13 N4 O8 P' 348.206 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 U 1 1 1 U U A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 3DA 5 5 5 3DA 3DA A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n B 2 1 C 1 2 2 C C B . n B 2 2 G 2 3 3 G G B . n B 2 3 G 3 4 4 G G B . n B 2 4 U 4 5 5 U U B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 I 7 8 8 I I B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 G 11 12 12 G G B . n B 2 12 G 12 13 13 G G B . n C 3 1 G 1 15 15 G G C . n C 3 2 G 2 16 16 G G C . n C 3 3 C 3 17 17 C C C . n C 3 4 A 4 18 18 A A C . n C 3 5 G 5 19 19 G G C . n C 3 6 A 6 20 20 A A C . n C 3 7 G 7 21 21 G G C . n C 3 8 A 8 22 22 A A C . n C 3 9 A 9 23 23 A A C . n C 3 10 A 10 24 24 A A C . n C 3 11 C 11 25 25 C C C . n C 3 12 A 12 26 26 A A C . n C 3 13 C 13 27 27 C C C . n C 3 14 A 14 28 28 A A C . n C 3 15 C 15 29 29 C C C . n C 3 16 G 16 30 30 G G C . n C 3 17 A 17 31 31 A A C . n D 4 1 U 1 31 31 U U D . n D 4 2 C 2 32 32 C C D . n D 4 3 G 3 33 33 G G D . n D 4 4 U 4 34 34 U U D . n D 4 5 G 5 35 35 G G D . n D 4 6 G 6 36 36 G G D . n D 4 7 U 7 37 37 U U D . n D 4 8 A 8 38 38 A A D . n D 4 9 C 9 39 39 C C D . n D 4 10 A 10 40 40 A A D . n D 4 11 U 11 41 41 U U D . n D 4 12 U 12 42 42 U U D . n D 4 13 A 13 43 43 A A D . n D 4 14 C 14 44 44 C C D . n D 4 15 C 15 45 45 C C D . n D 4 16 U 16 46 46 U U D . n D 4 17 G 17 47 47 G G D . n D 4 18 C 18 48 48 C C D . n D 4 19 C 19 49 49 C C D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 SO4 1 101 101 SO4 SO4 A . F 6 MG 1 101 102 MG MG B . G 7 HOH 1 201 107 HOH HOH A . G 7 HOH 2 202 108 HOH HOH A . H 7 HOH 1 201 103 HOH HOH B . H 7 HOH 2 202 104 HOH HOH B . H 7 HOH 3 203 105 HOH HOH B . H 7 HOH 4 204 106 HOH HOH B . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHENIX 1.6.2_432 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 3 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 Blu-Ice . ? ? ? ? 'data collection' ? ? ? 5 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 6 PHENIX . ? ? ? ? phasing ? ? ? # _cell.length_a 93.127 _cell.length_b 93.127 _cell.length_c 128.867 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 4G6R _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _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.space_group_name_H-M 'P 61 2 2' _symmetry.entry_id 4G6R _symmetry.Int_Tables_number 178 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 4G6R _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 4.13 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 70.23 _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.pH 7.0 _exptl_crystal_grow.temp 295 _exptl_crystal_grow.pdbx_details ;22% (w/v) PEG 2000 MME, 0.1M HEPES pH=7.0, 0.25 M Lithium Sulfate, 1mM Cobalt Hexamine, 2mM spermadine, vapor diffusion, Hanging Drop, temperature 295K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date 2010-02-05 _diffrn_detector.details 'Rh coated flat mirror' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97885 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.97885 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 # _reflns.entry_id 4G6R _reflns.d_resolution_high 2.830 _reflns.d_resolution_low 35.000 _reflns.number_obs 8172 _reflns.pdbx_Rmerge_I_obs 0.059 _reflns.pdbx_netI_over_sigmaI 18.200 _reflns.pdbx_chi_squared 1.209 _reflns.pdbx_redundancy 6.700 _reflns.percent_possible_obs 97.600 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_Rsym_value ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.830 2.930 ? ? ? 0.656 ? ? 0.850 6.700 ? 771 95.100 1 1 2.930 3.050 ? ? ? 0.325 ? ? 0.986 7.000 ? 790 98.000 2 1 3.050 3.190 ? ? ? 0.147 ? ? 1.191 7.100 ? 797 98.600 3 1 3.190 3.350 ? ? ? 0.098 ? ? 1.282 7.100 ? 803 98.500 4 1 3.350 3.560 ? ? ? 0.090 ? ? 1.376 7.000 ? 809 98.500 5 1 3.560 3.840 ? ? ? 0.074 ? ? 1.511 6.900 ? 818 98.800 6 1 3.840 4.230 ? ? ? 0.061 ? ? 1.345 6.700 ? 822 98.300 7 1 4.230 4.840 ? ? ? 0.058 ? ? 1.175 6.600 ? 821 98.200 8 1 4.840 6.090 ? ? ? 0.049 ? ? 1.263 6.400 ? 853 98.500 9 1 6.090 35.000 ? ? ? 0.041 ? ? 1.073 6.100 ? 888 93.800 10 1 # _refine.entry_id 4G6R _refine.ls_d_res_high 2.8320 _refine.ls_d_res_low 25.1700 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 93.8900 _refine.ls_number_reflns_obs 7821 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details 'Copied from PDB ID 2P7F' _refine.details ? _refine.ls_R_factor_obs 0.1788 _refine.ls_R_factor_R_work 0.1765 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2202 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_number_reflns_R_free 399 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 90.8369 _refine.solvent_model_param_bsol 53.0560 _refine.solvent_model_param_ksol 0.3080 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -20.7450 _refine.aniso_B[2][2] -20.7450 _refine.aniso_B[3][3] 41.4901 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.2900 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.0000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.7200 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 138.680 _refine.B_iso_min 64.380 _refine.pdbx_overall_phase_error 29.6400 _refine.occupancy_max 1.000 _refine.occupancy_min 0.450 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_R_factor_all ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 1292 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 1304 _refine_hist.d_res_high 2.8320 _refine_hist.d_res_low 25.1700 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 1477 0.008 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 2292 0.881 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 303 0.056 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 62 0.010 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 747 16.994 ? ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.832 3.2413 3 87.0000 2208 . 0.3187 0.4218 . 126 . 2334 . . 'X-RAY DIFFRACTION' 3.2413 4.0808 3 97.0000 2522 . 0.1953 0.2304 . 122 . 2644 . . 'X-RAY DIFFRACTION' 4.0808 25.17 3 98.0000 2692 . 0.1425 0.1767 . 151 . 2843 . . 'X-RAY DIFFRACTION' # _struct.entry_id 4G6R _struct.title 'Minimal Hairpin Ribozyme in the Transition State with G8I Variation' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4G6R _struct_keywords.text 'RNA, Structure-activity relationship, Nucleic Acid Conformation' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? G N N 7 ? H N N 7 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 PDB 4G6R 4G6R 1 UCCCAGUCCACCG ? ? 2 PDB 4G6R 4G6R 2 CGGUGAIAAGGG ? ? 3 PDB 4G6R 4G6R 3 GGCAGAGAAACACACGA ? ? 4 PDB 4G6R 4G6R 4 UCGUGGUACAUUACCUGCC ? ? # 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 4G6R A 1 ? 13 ? 4G6R 1 ? 13 ? 1 13 2 2 4G6R B 1 ? 12 ? 4G6R 2 ? 13 ? 2 13 3 3 4G6R C 1 ? 17 ? 4G6R 15 ? 31 ? 15 31 4 4 4G6R D 1 ? 19 ? 4G6R 31 ? 49 ? 31 49 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 5560 ? 1 MORE -23 ? 1 'SSA (A^2)' 9220 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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 ? # 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 4 "O3'" ? ? ? 1_555 A 3DA 5 P ? ? A C 4 A 3DA 5 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale2 covale one ? A 3DA 5 "O2'" ? ? ? 1_555 A G 6 P ? ? A 3DA 5 A G 6 1_555 ? ? ? ? ? ? ? 1.616 ? ? metalc1 metalc ? ? G HOH . O ? ? ? 1_555 F MG . MG ? ? A HOH 201 B MG 101 1_555 ? ? ? ? ? ? ? 2.141 ? ? metalc2 metalc ? ? G HOH . O ? ? ? 1_555 F MG . MG ? ? A HOH 202 B MG 101 1_555 ? ? ? ? ? ? ? 2.096 ? ? metalc3 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 101 B HOH 201 1_555 ? ? ? ? ? ? ? 2.132 ? ? metalc4 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 101 B HOH 202 1_555 ? ? ? ? ? ? ? 2.179 ? ? metalc5 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 101 B HOH 203 1_555 ? ? ? ? ? ? ? 2.018 ? ? metalc6 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 101 B HOH 204 1_555 ? ? ? ? ? ? ? 2.188 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 3DA 5 N3 ? ? ? 1_555 B A 8 N6 ? ? A 3DA 5 B A 9 1_555 ? ? ? ? ? ? '3DA-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A 3DA 5 N3 ? ? ? 1_555 B A 9 N6 ? ? A 3DA 5 B A 10 1_555 ? ? ? ? ? ? '3DA-A MISPAIR' ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 11 N3 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 11 O2 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 11 N4 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 8 N4 ? ? ? 1_555 B A 6 N1 ? ? A C 8 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 19 N3 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 19 O2 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 19 N4 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 18 N3 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog34 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 17 N1 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 17 O6 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 17 N2 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C A 4 N1 ? ? ? 1_555 D U 16 N3 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C A 4 N6 ? ? ? 1_555 D U 16 O4 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C A 6 N1 ? ? ? 1_555 D C 14 N4 ? ? C A 20 D C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog43 hydrog ? ? C G 7 N2 ? ? ? 1_555 D A 13 N7 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog44 hydrog ? ? C A 8 N6 ? ? ? 1_555 D U 11 O2 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog45 hydrog ? ? C A 8 N7 ? ? ? 1_555 D U 11 N3 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog46 hydrog ? ? C A 9 N6 ? ? ? 1_555 D A 10 N1 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog47 hydrog ? ? C A 10 N6 ? ? ? 1_555 D A 8 N7 ? ? C A 24 D A 38 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog48 hydrog ? ? C A 12 N1 ? ? ? 1_555 D G 6 N1 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog49 hydrog ? ? C A 12 N6 ? ? ? 1_555 D G 6 O6 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog50 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C A 17 N1 ? ? ? 1_555 D U 1 N3 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C A 17 N6 ? ? ? 1_555 D U 1 O4 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _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 O ? G HOH . ? A HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? G HOH . ? A HOH 202 ? 1_555 88.8 ? 2 O ? G HOH . ? A HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 90.9 ? 3 O ? G HOH . ? A HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 89.2 ? 4 O ? G HOH . ? A HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 91.1 ? 5 O ? G HOH . ? A HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 179.7 ? 6 O ? H HOH . ? B HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 90.5 ? 7 O ? G HOH . ? A HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 179.6 ? 8 O ? G HOH . ? A HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 91.3 ? 9 O ? H HOH . ? B HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 88.7 ? 10 O ? H HOH . ? B HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 88.9 ? 11 O ? G HOH . ? A HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 90.8 ? 12 O ? G HOH . ? A HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 89.8 ? 13 O ? H HOH . ? B HOH 201 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 178.0 ? 14 O ? H HOH . ? B HOH 202 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 90.5 ? 15 O ? H HOH . ? B HOH 203 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 89.6 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 101 ? 3 'BINDING SITE FOR RESIDUE SO4 A 101' AC2 Software B MG 101 ? 6 'BINDING SITE FOR RESIDUE MG B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 C A 2 ? C A 2 . ? 1_555 ? 2 AC1 3 C A 3 ? C A 3 . ? 1_555 ? 3 AC1 3 HOH G . ? HOH A 202 . ? 1_555 ? 4 AC2 6 HOH G . ? HOH A 201 . ? 1_555 ? 5 AC2 6 HOH G . ? HOH A 202 . ? 1_555 ? 6 AC2 6 HOH H . ? HOH B 201 . ? 1_555 ? 7 AC2 6 HOH H . ? HOH B 202 . ? 1_555 ? 8 AC2 6 HOH H . ? HOH B 203 . ? 1_555 ? 9 AC2 6 HOH H . ? HOH B 204 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 I _pdbx_validate_rmsd_bond.auth_seq_id_1 8 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 OP1 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 I _pdbx_validate_rmsd_bond.auth_seq_id_2 8 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.609 _pdbx_validate_rmsd_bond.bond_target_value 1.480 _pdbx_validate_rmsd_bond.bond_deviation 0.129 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.020 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id I _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 8 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.051 _pdbx_validate_planes.type 'SIDE CHAIN' # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 3DA _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 3DA _pdbx_struct_mod_residue.auth_seq_id 5 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DA _pdbx_struct_mod_residue.details "3'-DEOXYADENOSINE-5'-MONOPHOSPHATE" # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id U _pdbx_struct_special_symmetry.auth_seq_id 1 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id A _pdbx_struct_special_symmetry.label_comp_id U _pdbx_struct_special_symmetry.label_seq_id 1 # 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 3DA P P N N 1 3DA O1P O N N 2 3DA O2P O N N 3 3DA "O5'" O N N 4 3DA "C5'" C N N 5 3DA "C4'" C N S 6 3DA "O4'" O N N 7 3DA "C1'" C N R 8 3DA N9 N Y N 9 3DA C4 C Y N 10 3DA N3 N Y N 11 3DA C2 C Y N 12 3DA N1 N Y N 13 3DA C6 C Y N 14 3DA N6 N N N 15 3DA C5 C Y N 16 3DA N7 N Y N 17 3DA C8 C Y N 18 3DA "C2'" C N R 19 3DA "O2'" O N N 20 3DA "C3'" C N N 21 3DA O3P O N N 22 3DA HOP2 H N N 23 3DA "H5'1" H N N 24 3DA "H5'2" H N N 25 3DA "H4'" H N N 26 3DA "H1'" H N N 27 3DA H2 H N N 28 3DA HN61 H N N 29 3DA HN62 H N N 30 3DA H8 H N N 31 3DA "H2'1" H N N 32 3DA "HO'2" H N N 33 3DA "H3'1" H N N 34 3DA "H3'2" H N N 35 3DA HOP3 H N N 36 A OP3 O N N 37 A P P N N 38 A OP1 O N N 39 A OP2 O N N 40 A "O5'" O N N 41 A "C5'" C N N 42 A "C4'" C N R 43 A "O4'" O N N 44 A "C3'" C N S 45 A "O3'" O N N 46 A "C2'" C N R 47 A "O2'" O N N 48 A "C1'" C N R 49 A N9 N Y N 50 A C8 C Y N 51 A N7 N Y N 52 A C5 C Y N 53 A C6 C Y N 54 A N6 N N N 55 A N1 N Y N 56 A C2 C Y N 57 A N3 N Y N 58 A C4 C Y N 59 A HOP3 H N N 60 A HOP2 H N N 61 A "H5'" H N N 62 A "H5''" H N N 63 A "H4'" H N N 64 A "H3'" H N N 65 A "HO3'" H N N 66 A "H2'" H N N 67 A "HO2'" H N N 68 A "H1'" H N N 69 A H8 H N N 70 A H61 H N N 71 A H62 H N N 72 A H2 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 G OP3 O N N 109 G P P N N 110 G OP1 O N N 111 G OP2 O N N 112 G "O5'" O N N 113 G "C5'" C N N 114 G "C4'" C N R 115 G "O4'" O N N 116 G "C3'" C N S 117 G "O3'" O N N 118 G "C2'" C N R 119 G "O2'" O N N 120 G "C1'" C N R 121 G N9 N Y N 122 G C8 C Y N 123 G N7 N Y N 124 G C5 C Y N 125 G C6 C N N 126 G O6 O N N 127 G N1 N N N 128 G C2 C N N 129 G N2 N N N 130 G N3 N N N 131 G C4 C Y N 132 G HOP3 H N N 133 G HOP2 H N N 134 G "H5'" H N N 135 G "H5''" H N N 136 G "H4'" H N N 137 G "H3'" H N N 138 G "HO3'" H N N 139 G "H2'" H N N 140 G "HO2'" H N N 141 G "H1'" H N N 142 G H8 H N N 143 G H1 H N N 144 G H21 H N N 145 G H22 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 I OP3 O N N 150 I P P N N 151 I OP1 O N N 152 I OP2 O N N 153 I "O5'" O N N 154 I "C5'" C N N 155 I "C4'" C N R 156 I "O4'" O N N 157 I "C3'" C N S 158 I "O3'" O N N 159 I "C2'" C N R 160 I "O2'" O N N 161 I "C1'" C N R 162 I N9 N Y N 163 I C8 C Y N 164 I N7 N Y N 165 I C5 C Y N 166 I C6 C N N 167 I O6 O N N 168 I N1 N N N 169 I C2 C N N 170 I N3 N N N 171 I C4 C Y N 172 I HOP3 H N N 173 I HOP2 H N N 174 I "H5'" H N N 175 I "H5''" H N N 176 I "H4'" H N N 177 I "H3'" H N N 178 I "HO3'" H N N 179 I "H2'" H N N 180 I "HO2'" H N N 181 I "H1'" H N N 182 I H8 H N N 183 I H1 H N N 184 I H2 H N N 185 MG MG MG N N 186 SO4 S S N N 187 SO4 O1 O N N 188 SO4 O2 O N N 189 SO4 O3 O N N 190 SO4 O4 O N N 191 U OP3 O N N 192 U P P N N 193 U OP1 O N N 194 U OP2 O N N 195 U "O5'" O N N 196 U "C5'" C N N 197 U "C4'" C N R 198 U "O4'" O N N 199 U "C3'" C N S 200 U "O3'" O N N 201 U "C2'" C N R 202 U "O2'" O N N 203 U "C1'" C N R 204 U N1 N N N 205 U C2 C N N 206 U O2 O N N 207 U N3 N N N 208 U C4 C N N 209 U O4 O N N 210 U C5 C N N 211 U C6 C N N 212 U HOP3 H N N 213 U HOP2 H N N 214 U "H5'" H N N 215 U "H5''" H N N 216 U "H4'" H N N 217 U "H3'" H N N 218 U "HO3'" H N N 219 U "H2'" H N N 220 U "HO2'" H N N 221 U "H1'" H N N 222 U H3 H N N 223 U H5 H N N 224 U H6 H N N 225 # 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 3DA P O1P doub N N 1 3DA P O2P sing N N 2 3DA P "O5'" sing N N 3 3DA P O3P sing N N 4 3DA O2P HOP2 sing N N 5 3DA "O5'" "C5'" sing N N 6 3DA "C5'" "C4'" sing N N 7 3DA "C5'" "H5'1" sing N N 8 3DA "C5'" "H5'2" sing N N 9 3DA "C4'" "O4'" sing N N 10 3DA "C4'" "C3'" sing N N 11 3DA "C4'" "H4'" sing N N 12 3DA "O4'" "C1'" sing N N 13 3DA "C1'" N9 sing N N 14 3DA "C1'" "C2'" sing N N 15 3DA "C1'" "H1'" sing N N 16 3DA N9 C4 sing Y N 17 3DA N9 C8 sing Y N 18 3DA C4 N3 sing Y N 19 3DA C4 C5 doub Y N 20 3DA N3 C2 doub Y N 21 3DA C2 N1 sing Y N 22 3DA C2 H2 sing N N 23 3DA N1 C6 doub Y N 24 3DA C6 N6 sing N N 25 3DA C6 C5 sing Y N 26 3DA N6 HN61 sing N N 27 3DA N6 HN62 sing N N 28 3DA C5 N7 sing Y N 29 3DA N7 C8 doub Y N 30 3DA C8 H8 sing N N 31 3DA "C2'" "O2'" sing N N 32 3DA "C2'" "C3'" sing N N 33 3DA "C2'" "H2'1" sing N N 34 3DA "O2'" "HO'2" sing N N 35 3DA "C3'" "H3'1" sing N N 36 3DA "C3'" "H3'2" sing N N 37 3DA O3P HOP3 sing N N 38 A OP3 P sing N N 39 A OP3 HOP3 sing N N 40 A P OP1 doub N N 41 A P OP2 sing N N 42 A P "O5'" sing N N 43 A OP2 HOP2 sing N N 44 A "O5'" "C5'" sing N N 45 A "C5'" "C4'" sing N N 46 A "C5'" "H5'" sing N N 47 A "C5'" "H5''" sing N N 48 A "C4'" "O4'" sing N N 49 A "C4'" "C3'" sing N N 50 A "C4'" "H4'" sing N N 51 A "O4'" "C1'" sing N N 52 A "C3'" "O3'" sing N N 53 A "C3'" "C2'" sing N N 54 A "C3'" "H3'" sing N N 55 A "O3'" "HO3'" sing N N 56 A "C2'" "O2'" sing N N 57 A "C2'" "C1'" sing N N 58 A "C2'" "H2'" sing N N 59 A "O2'" "HO2'" sing N N 60 A "C1'" N9 sing N N 61 A "C1'" "H1'" sing N N 62 A N9 C8 sing Y N 63 A N9 C4 sing Y N 64 A C8 N7 doub Y N 65 A C8 H8 sing N N 66 A N7 C5 sing Y N 67 A C5 C6 sing Y N 68 A C5 C4 doub Y N 69 A C6 N6 sing N N 70 A C6 N1 doub Y N 71 A N6 H61 sing N N 72 A N6 H62 sing N N 73 A N1 C2 sing Y N 74 A C2 N3 doub Y N 75 A C2 H2 sing N N 76 A N3 C4 sing Y N 77 C OP3 P sing N N 78 C OP3 HOP3 sing N N 79 C P OP1 doub N N 80 C P OP2 sing N N 81 C P "O5'" sing N N 82 C OP2 HOP2 sing N N 83 C "O5'" "C5'" sing N N 84 C "C5'" "C4'" sing N N 85 C "C5'" "H5'" sing N N 86 C "C5'" "H5''" sing N N 87 C "C4'" "O4'" sing N N 88 C "C4'" "C3'" sing N N 89 C "C4'" "H4'" sing N N 90 C "O4'" "C1'" sing N N 91 C "C3'" "O3'" sing N N 92 C "C3'" "C2'" sing N N 93 C "C3'" "H3'" sing N N 94 C "O3'" "HO3'" sing N N 95 C "C2'" "O2'" sing N N 96 C "C2'" "C1'" sing N N 97 C "C2'" "H2'" sing N N 98 C "O2'" "HO2'" sing N N 99 C "C1'" N1 sing N N 100 C "C1'" "H1'" sing N N 101 C N1 C2 sing N N 102 C N1 C6 sing N N 103 C C2 O2 doub N N 104 C C2 N3 sing N N 105 C N3 C4 doub N N 106 C C4 N4 sing N N 107 C C4 C5 sing N N 108 C N4 H41 sing N N 109 C N4 H42 sing N N 110 C C5 C6 doub N N 111 C C5 H5 sing N N 112 C C6 H6 sing N N 113 G OP3 P sing N N 114 G OP3 HOP3 sing N N 115 G P OP1 doub N N 116 G P OP2 sing N N 117 G P "O5'" sing N N 118 G OP2 HOP2 sing N N 119 G "O5'" "C5'" sing N N 120 G "C5'" "C4'" sing N N 121 G "C5'" "H5'" sing N N 122 G "C5'" "H5''" sing N N 123 G "C4'" "O4'" sing N N 124 G "C4'" "C3'" sing N N 125 G "C4'" "H4'" sing N N 126 G "O4'" "C1'" sing N N 127 G "C3'" "O3'" sing N N 128 G "C3'" "C2'" sing N N 129 G "C3'" "H3'" sing N N 130 G "O3'" "HO3'" sing N N 131 G "C2'" "O2'" sing N N 132 G "C2'" "C1'" sing N N 133 G "C2'" "H2'" sing N N 134 G "O2'" "HO2'" sing N N 135 G "C1'" N9 sing N N 136 G "C1'" "H1'" sing N N 137 G N9 C8 sing Y N 138 G N9 C4 sing Y N 139 G C8 N7 doub Y N 140 G C8 H8 sing N N 141 G N7 C5 sing Y N 142 G C5 C6 sing N N 143 G C5 C4 doub Y N 144 G C6 O6 doub N N 145 G C6 N1 sing N N 146 G N1 C2 sing N N 147 G N1 H1 sing N N 148 G C2 N2 sing N N 149 G C2 N3 doub N N 150 G N2 H21 sing N N 151 G N2 H22 sing N N 152 G N3 C4 sing N N 153 HOH O H1 sing N N 154 HOH O H2 sing N N 155 I OP3 P sing N N 156 I OP3 HOP3 sing N N 157 I P OP1 doub N N 158 I P OP2 sing N N 159 I P "O5'" sing N N 160 I OP2 HOP2 sing N N 161 I "O5'" "C5'" sing N N 162 I "C5'" "C4'" sing N N 163 I "C5'" "H5'" sing N N 164 I "C5'" "H5''" sing N N 165 I "C4'" "O4'" sing N N 166 I "C4'" "C3'" sing N N 167 I "C4'" "H4'" sing N N 168 I "O4'" "C1'" sing N N 169 I "C3'" "O3'" sing N N 170 I "C3'" "C2'" sing N N 171 I "C3'" "H3'" sing N N 172 I "O3'" "HO3'" sing N N 173 I "C2'" "O2'" sing N N 174 I "C2'" "C1'" sing N N 175 I "C2'" "H2'" sing N N 176 I "O2'" "HO2'" sing N N 177 I "C1'" N9 sing N N 178 I "C1'" "H1'" sing N N 179 I N9 C8 sing Y N 180 I N9 C4 sing Y N 181 I C8 N7 doub Y N 182 I C8 H8 sing N N 183 I N7 C5 sing Y N 184 I C5 C6 sing N N 185 I C5 C4 doub Y N 186 I C6 O6 doub N N 187 I C6 N1 sing N N 188 I N1 C2 sing N N 189 I N1 H1 sing N N 190 I C2 N3 doub N N 191 I C2 H2 sing N N 192 I N3 C4 sing N N 193 SO4 S O1 doub N N 194 SO4 S O2 doub N N 195 SO4 S O3 sing N N 196 SO4 S O4 sing N N 197 U OP3 P sing N N 198 U OP3 HOP3 sing N N 199 U P OP1 doub N N 200 U P OP2 sing N N 201 U P "O5'" sing N N 202 U OP2 HOP2 sing N N 203 U "O5'" "C5'" sing N N 204 U "C5'" "C4'" sing N N 205 U "C5'" "H5'" sing N N 206 U "C5'" "H5''" sing N N 207 U "C4'" "O4'" sing N N 208 U "C4'" "C3'" sing N N 209 U "C4'" "H4'" sing N N 210 U "O4'" "C1'" sing N N 211 U "C3'" "O3'" sing N N 212 U "C3'" "C2'" sing N N 213 U "C3'" "H3'" sing N N 214 U "O3'" "HO3'" sing N N 215 U "C2'" "O2'" sing N N 216 U "C2'" "C1'" sing N N 217 U "C2'" "H2'" sing N N 218 U "O2'" "HO2'" sing N N 219 U "C1'" N1 sing N N 220 U "C1'" "H1'" sing N N 221 U N1 C2 sing N N 222 U N1 C6 sing N N 223 U C2 O2 doub N N 224 U C2 N3 sing N N 225 U N3 C4 sing N N 226 U N3 H3 sing N N 227 U C4 O4 doub N N 228 U C4 C5 sing N N 229 U C5 C6 doub N N 230 U C5 H5 sing N N 231 U C6 H6 sing N N 232 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4G6R 'double helix' 4G6R 'a-form double helix' 4G6R 'bulge loop' 4G6R 'mismatched base pair' 4G6R 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 2 1_555 B G 12 1_555 0.635 -0.194 -0.149 3.293 -17.247 2.499 1 A_C2:G13_B A 2 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 0.555 -0.142 0.010 -1.906 -5.670 1.759 2 A_C3:G12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 0.321 0.014 0.041 4.184 0.464 6.786 3 A_C4:G11_B A 4 ? B 11 ? 19 1 1 A 3DA 5 1_555 B A 8 1_555 6.725 -3.859 -0.442 9.406 -4.104 -22.439 4 A_3DA5:A9_B A 5 ? B 9 ? ? ? 1 A C 8 1_555 B A 6 1_555 -2.897 0.601 -0.967 25.688 -14.519 3.835 5 A_C8:A7_B A 8 ? B 7 ? ? ? 1 A C 9 1_555 B G 5 1_555 0.063 0.111 0.250 1.710 -10.300 2.680 6 A_C9:G6_B A 9 ? B 6 ? 19 1 1 A A 10 1_555 B U 4 1_555 -0.416 -0.183 0.611 4.435 -11.357 6.631 7 A_A10:U5_B A 10 ? B 5 ? 20 1 1 A C 11 1_555 B G 3 1_555 0.419 0.068 0.262 3.763 -10.524 6.307 8 A_C11:G4_B A 11 ? B 4 ? 19 1 1 A C 12 1_555 B G 2 1_555 0.519 -0.097 0.437 1.375 -8.933 5.505 9 A_C12:G3_B A 12 ? B 3 ? 19 1 1 A G 13 1_555 B C 1 1_555 -0.318 0.090 0.137 -4.402 -8.229 6.190 10 A_G13:C2_B A 13 ? B 2 ? 19 1 1 C G 1 1_555 D C 19 1_555 -0.242 -0.016 1.318 16.374 -2.573 2.908 11 C_G15:C49_D C 15 ? D 49 ? 19 1 1 C G 2 1_555 D C 18 1_555 -0.516 0.144 0.574 14.551 -15.993 8.150 12 C_G16:C48_D C 16 ? D 48 ? ? 1 1 C C 3 1_555 D G 17 1_555 -0.297 0.103 0.438 2.744 -12.374 6.699 13 C_C17:G47_D C 17 ? D 47 ? 19 1 1 C A 4 1_555 D U 16 1_555 -0.281 -0.085 0.156 0.305 -7.861 6.213 14 C_A18:U46_D C 18 ? D 46 ? 20 1 1 C G 5 1_555 D C 15 1_555 -0.031 -0.177 -0.195 -4.531 -8.686 2.069 15 C_G19:C45_D C 19 ? D 45 ? 19 1 1 C A 6 1_555 D C 14 1_555 2.124 0.619 -0.254 -8.776 -5.835 20.224 16 C_A20:C44_D C 20 ? D 44 ? ? ? 1 C G 7 1_555 D A 13 1_555 7.173 -4.523 -0.193 -9.652 -1.111 -6.623 17 C_G21:A43_D C 21 ? D 43 ? ? 10 1 C A 8 1_555 D U 11 1_555 -4.048 -1.761 -0.169 -3.475 -4.344 -99.419 18 C_A22:U41_D C 22 ? D 41 ? 24 4 1 C A 9 1_555 D A 10 1_555 -4.457 0.852 -0.104 2.847 -12.730 -93.422 19 C_A23:A40_D C 23 ? D 40 ? ? ? 1 C A 10 1_555 D A 8 1_555 5.394 3.015 -0.408 -2.663 -10.945 -153.066 20 C_A24:A38_D C 24 ? D 38 ? ? ? 1 C C 11 1_555 A G 6 1_555 0.289 -0.022 0.323 12.744 -11.237 2.699 21 C_C25:G6_A C 25 ? A 6 ? 19 1 1 C A 12 1_555 D G 6 1_555 -0.036 1.346 -0.334 -9.147 -15.934 -16.366 22 C_A26:G36_D C 26 ? D 36 ? 8 1 1 C C 13 1_555 D G 5 1_555 0.018 -0.145 0.388 7.513 -18.633 4.904 23 C_C27:G35_D C 27 ? D 35 ? 19 1 1 C A 14 1_555 D U 4 1_555 0.172 -0.132 0.657 9.895 -15.603 -0.567 24 C_A28:U34_D C 28 ? D 34 ? 20 1 1 C C 15 1_555 D G 3 1_555 0.029 0.184 0.103 7.818 -12.828 5.706 25 C_C29:G33_D C 29 ? D 33 ? 19 1 1 C G 16 1_555 D C 2 1_555 -0.398 -0.004 0.454 -4.612 -14.585 -0.062 26 C_G30:C32_D C 30 ? D 32 ? 19 1 1 C A 17 1_555 D U 1 1_555 0.519 -0.008 0.585 2.802 -5.349 5.161 27 C_A31:U31_D C 31 ? D 31 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 2 1_555 B G 12 1_555 A C 3 1_555 B G 11 1_555 -0.462 -1.767 3.443 0.208 7.577 30.890 -4.599 0.882 2.934 13.964 -0.383 31.785 1 AA_C2C3:G12G13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A C 3 1_555 B G 11 1_555 A C 4 1_555 B G 10 1_555 0.955 -1.668 3.164 3.385 9.902 24.224 -6.016 -1.289 2.416 22.310 -7.626 26.356 2 AA_C3C4:G11G12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A C 4 1_555 B G 10 1_555 A 3DA 5 1_555 B A 8 1_555 0.216 -0.670 5.294 -0.711 26.301 77.448 -1.606 -0.195 4.909 20.479 0.554 81.126 3 AA_C43DA5:A9G11_BB A 4 ? B 11 ? A 5 ? B 9 ? 1 A 3DA 5 1_555 B A 8 1_555 A C 8 1_555 B A 6 1_555 -1.100 -0.639 6.112 7.111 9.238 56.591 -1.576 1.843 5.788 9.631 -7.413 57.682 4 AA_3DA5C8:A7A9_BB A 5 ? B 9 ? A 8 ? B 7 ? 1 A C 8 1_555 B A 6 1_555 A C 9 1_555 B G 5 1_555 -0.140 -1.504 3.991 -11.745 12.115 41.722 -3.258 -1.065 3.371 16.236 15.739 44.864 5 AA_C8C9:G6A7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A C 9 1_555 B G 5 1_555 A A 10 1_555 B U 4 1_555 -0.243 -1.938 2.943 -4.780 8.489 30.990 -4.704 -0.261 2.355 15.417 8.682 32.449 6 AA_C9A10:U5G6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A A 10 1_555 B U 4 1_555 A C 11 1_555 B G 3 1_555 -0.630 -1.378 3.286 1.088 1.063 32.275 -2.664 1.323 3.218 1.910 -1.955 32.310 7 AA_A10C11:G4U5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A C 11 1_555 B G 3 1_555 A C 12 1_555 B G 2 1_555 0.031 -1.910 3.102 -0.736 6.102 31.027 -4.515 -0.178 2.686 11.268 1.359 31.615 8 AA_C11C12:G3G4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A C 12 1_555 B G 2 1_555 A G 13 1_555 B C 1 1_555 0.021 -2.088 3.146 4.343 10.220 27.752 -5.869 0.731 2.232 20.308 -8.630 29.851 9 AA_C12G13:C2G3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 C G 1 1_555 D C 19 1_555 C G 2 1_555 D C 18 1_555 -0.517 -1.114 3.130 3.294 7.654 32.425 -3.088 1.394 2.739 13.431 -5.780 33.451 10 CC_G15G16:C48C49_DD C 15 ? D 49 ? C 16 ? D 48 ? 1 C G 2 1_555 D C 18 1_555 C C 3 1_555 D G 17 1_555 0.222 -1.394 3.402 -1.481 9.879 35.153 -3.570 -0.556 2.906 15.963 2.393 36.502 11 CC_G16C17:G47C48_DD C 16 ? D 48 ? C 17 ? D 47 ? 1 C C 3 1_555 D G 17 1_555 C A 4 1_555 D U 16 1_555 -0.015 -1.740 3.063 -1.212 8.967 29.761 -4.728 -0.171 2.446 16.971 2.294 31.077 12 CC_C17A18:U46G47_DD C 17 ? D 47 ? C 18 ? D 46 ? 1 C A 4 1_555 D U 16 1_555 C G 5 1_555 D C 15 1_555 0.180 -1.968 3.460 1.379 3.824 31.585 -4.301 -0.071 3.210 6.989 -2.520 31.839 13 CC_A18G19:C45U46_DD C 18 ? D 46 ? C 19 ? D 45 ? 1 C G 5 1_555 D C 15 1_555 C A 6 1_555 D C 14 1_555 1.091 -1.420 3.390 2.273 6.049 38.060 -2.907 -1.367 3.193 9.195 -3.454 38.585 14 CC_G19A20:C44C45_DD C 19 ? D 45 ? C 20 ? D 44 ? 1 C A 6 1_555 D C 14 1_555 C G 7 1_555 D A 13 1_555 -0.539 -0.948 3.337 8.175 5.581 58.970 -1.230 0.950 3.151 5.626 -8.241 59.721 15 CC_A20G21:A43C44_DD C 20 ? D 44 ? C 21 ? D 43 ? 1 C G 7 1_555 D A 13 1_555 C A 8 1_555 D U 11 1_555 -2.402 -0.617 3.296 4.570 2.404 13.474 -4.342 13.148 2.220 9.787 -18.610 14.425 16 CC_G21A22:U41A43_DD C 21 ? D 43 ? C 22 ? D 41 ? 1 C A 8 1_555 D U 11 1_555 C A 9 1_555 D A 10 1_555 0.112 -2.192 3.375 -9.966 3.877 43.184 -3.258 -1.072 3.079 5.173 13.298 44.426 17 CC_A22A23:A40U41_DD C 22 ? D 41 ? C 23 ? D 40 ? 1 C A 9 1_555 D A 10 1_555 C A 10 1_555 D A 8 1_555 -3.299 -3.129 3.632 -3.628 0.749 76.811 -2.541 2.535 3.735 0.602 2.918 76.886 18 CC_A23A24:A38A40_DD C 23 ? D 40 ? C 24 ? D 38 ? 1 C A 10 1_555 D A 8 1_555 C C 11 1_555 A G 6 1_555 2.352 0.033 3.083 -1.225 6.102 -33.532 -0.982 3.826 3.111 -10.464 -2.100 -34.088 19 CC_A24C25:G6A38_AD C 24 ? D 38 ? C 25 ? A 6 ? 1 C C 11 1_555 A G 6 1_555 C A 12 1_555 D G 6 1_555 0.140 -2.114 3.584 5.850 3.649 45.926 -3.014 0.354 3.408 4.645 -7.447 46.413 20 CC_C25A26:G36G6_DA C 25 ? A 6 ? C 26 ? D 36 ? 1 C A 12 1_555 D G 6 1_555 C C 13 1_555 D G 5 1_555 1.319 -0.624 2.887 -6.433 4.125 29.913 -1.838 -3.518 2.451 7.831 12.213 30.852 21 CC_A26C27:G35G36_DD C 26 ? D 36 ? C 27 ? D 35 ? 1 C C 13 1_555 D G 5 1_555 C A 14 1_555 D U 4 1_555 -0.190 -1.144 3.035 -1.502 3.173 35.891 -2.259 0.113 2.931 5.133 2.430 36.056 22 CC_C27A28:U34G35_DD C 27 ? D 35 ? C 28 ? D 34 ? 1 C A 14 1_555 D U 4 1_555 C C 15 1_555 D G 3 1_555 0.730 -1.299 3.221 6.790 2.991 31.356 -2.871 -0.117 3.171 5.440 -12.348 32.200 23 CC_A28C29:G33U34_DD C 28 ? D 34 ? C 29 ? D 33 ? 1 C C 15 1_555 D G 3 1_555 C G 16 1_555 D C 2 1_555 0.408 -1.700 3.339 1.128 8.036 33.278 -4.110 -0.522 2.874 13.779 -1.933 34.226 24 CC_C29G30:C32G33_DD C 29 ? D 33 ? C 30 ? D 32 ? 1 C G 16 1_555 D C 2 1_555 C A 17 1_555 D U 1 1_555 0.918 -1.535 2.876 4.458 2.118 34.805 -2.821 -0.932 2.873 3.519 -7.406 35.143 25 CC_G30A31:U31C32_DD C 30 ? D 32 ? C 31 ? D 31 ? # _atom_sites.entry_id 4G6R _atom_sites.fract_transf_matrix[1][1] 0.010738 _atom_sites.fract_transf_matrix[1][2] 0.006200 _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] 0.012399 _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] 0.007760 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P S # loop_