data_4NYG # _entry.id 4NYG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4NYG pdb_00004nyg 10.2210/pdb4nyg/pdb NDB NA2830 ? ? RCSB RCSB083813 ? ? WWPDB D_1000083813 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NYA 'Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine' unspecified PDB 4NYB 'Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine' unspecified PDB 4NYC 'Crystal structure of the E. coli thiM riboswitch in complex with thieno[2,3-b]pyrazin-7-amine' unspecified PDB 4NYD 'Crystal structure of the E. coli thiM riboswitch in complex with hypoxanthine' unspecified # _pdbx_database_status.entry_id 4NYG _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-12-10 _pdbx_database_status.status_code REL _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_ _audit_author.name _audit_author.pdbx_ordinal 'Warner, K.D.' 1 'Homan, P.' 2 'Weeks, K.M.' 3 'Smith, A.G.' 4 'Abell, C.' 5 ;Ferre-D'Amare, A.R. ; 6 # _citation.id primary _citation.title 'Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 21 _citation.page_first 591 _citation.page_last 595 _citation.year 2014 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24768306 _citation.pdbx_database_id_DOI 10.1016/j.chembiol.2014.03.007 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Warner, K.D.' 1 ? primary 'Homan, P.' 2 ? primary 'Weeks, K.M.' 3 ? primary 'Smith, A.G.' 4 ? primary 'Abell, C.' 5 ? primary ;Ferre-D'Amare, A.R. ; 6 ? # _cell.length_a 61.503 _cell.length_b 61.503 _cell.length_c 103.935 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 4NYG _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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 32 1 2' _symmetry.entry_id 4NYG _symmetry.Int_Tables_number 153 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'thiM TPP riboswitch' 26860.900 1 ? ? ? ? 2 non-polymer syn '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' 265.355 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 6 ? ? ? ? 4 water nat water 18.015 4 ? ? ? ? # _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 ;GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GC(A23) ; _entity_poly.pdbx_seq_one_letter_code_can ;GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GCA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 A n 1 5 C n 1 6 U n 1 7 C n 1 8 G n 1 9 G n 1 10 G n 1 11 G n 1 12 U n 1 13 G n 1 14 C n 1 15 C n 1 16 C n 1 17 U n 1 18 U n 1 19 C n 1 20 U n 1 21 G n 1 22 C n 1 23 G n 1 24 U n 1 25 G n 1 26 A n 1 27 A n 1 28 G n 1 29 G n 1 30 C n 1 31 U n 1 32 G n 1 33 A n 1 34 G n 1 35 A n 1 36 A n 1 37 A n 1 38 U n 1 39 A n 1 40 C n 1 41 C n 1 42 C n 1 43 G n 1 44 U n 1 45 A n 1 46 U n 1 47 C n 1 48 A n 1 49 C n 1 50 C n 1 51 U n 1 52 G n 1 53 A n 1 54 U n 1 55 C n 1 56 U n 1 57 G n 1 58 G n 1 59 A n 1 60 U n 1 61 A n 1 62 A n 1 63 U n 1 64 G n 1 65 C n 1 66 C n 1 67 A n 1 68 G n 1 69 C n 1 70 G n 1 71 U n 1 72 A n 1 73 G n 1 74 G n 1 75 G n 1 76 A n 1 77 A n 1 78 G n 1 79 U n 1 80 C n 1 81 G n 1 82 C n 1 83 A23 n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4NYG _struct_ref.pdbx_db_accession 4NYG _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ;GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GC(A23) ; _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4NYG _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 83 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4NYG _struct_ref_seq.db_align_beg 9 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 91 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 9 _struct_ref_seq.pdbx_auth_seq_align_end 91 # 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 A23 'RNA linking' n ;ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ; ? 'C10 H13 N5 O9 P2' 409.186 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VIB non-polymer . '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' 'THIAMIN; VITAMIN B1' 'C12 H17 N4 O S 1' 265.355 # _exptl.crystals_number 1 _exptl.entry_id 4NYG _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.11 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 41.78 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;30% PEG2000, 0.35 M ammonium chloride, 50 mM succinate/KOH, pH 7.0, 10 mM zinc chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K ; _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 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2012-09-12 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.99999 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 5.0.2' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.99999 _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 5.0.2 # _reflns.entry_id 4NYG _reflns.d_resolution_high 3.050 _reflns.d_resolution_low 30.0 _reflns.number_obs 4410 _reflns.pdbx_Rmerge_I_obs 0.164 _reflns.pdbx_netI_over_sigmaI 12.9 _reflns.pdbx_chi_squared 2.153 _reflns.pdbx_redundancy 11.3 _reflns.percent_possible_obs 99.9 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _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 # 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 3.050 3.100 ? ? ? 0.696 ? ? 1.014 8.40 ? 214 99.1 1 1 3.100 3.160 ? ? ? 0.652 ? ? 1.038 9.30 ? 212 100.0 2 1 3.160 3.220 ? ? ? 0.507 ? ? 1.050 10.10 ? 231 100.0 3 1 3.220 3.290 ? ? ? 0.435 ? ? 1.156 10.90 ? 196 100.0 4 1 3.290 3.360 ? ? ? 0.382 ? ? 1.174 11.40 ? 221 100.0 5 1 3.360 3.430 ? ? ? 0.368 ? ? 1.281 11.70 ? 227 100.0 6 1 3.430 3.520 ? ? ? 0.345 ? ? 1.311 12.10 ? 210 100.0 7 1 3.520 3.620 ? ? ? 0.340 ? ? 1.493 12.00 ? 214 100.0 8 1 3.620 3.720 ? ? ? 0.309 ? ? 1.650 12.00 ? 207 100.0 9 1 3.720 3.840 ? ? ? 0.277 ? ? 1.786 11.90 ? 240 100.0 10 1 3.840 3.980 ? ? ? 0.252 ? ? 2.005 12.20 ? 211 100.0 11 1 3.980 4.140 ? ? ? 0.232 ? ? 2.044 12.20 ? 219 100.0 12 1 4.140 4.330 ? ? ? 0.208 ? ? 2.483 11.80 ? 221 100.0 13 1 4.330 4.550 ? ? ? 0.204 ? ? 2.754 11.90 ? 211 100.0 14 1 4.550 4.840 ? ? ? 0.183 ? ? 2.816 12.00 ? 229 100.0 15 1 4.840 5.210 ? ? ? 0.169 ? ? 3.280 11.50 ? 229 100.0 16 1 5.210 5.730 ? ? ? 0.162 ? ? 3.472 11.50 ? 219 100.0 17 1 5.730 6.550 ? ? ? 0.160 ? ? 3.506 11.20 ? 221 100.0 18 1 6.550 8.220 ? ? ? 0.150 ? ? 3.656 10.80 ? 232 100.0 19 1 8.220 30.000 ? ? ? 0.130 ? ? 3.239 10.50 ? 246 98.4 20 1 # _refine.entry_id 4NYG _refine.ls_d_res_high 3.050 _refine.ls_d_res_low 30.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 94.2 _refine.ls_number_reflns_obs 4200 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2488 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.3229 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 435 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 109.6860 _refine.solvent_model_param_bsol 19.6923 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 11.7930 _refine.aniso_B[2][2] 11.7930 _refine.aniso_B[3][3] -23.5860 _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 ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'PDB ENTRY 2HOJ' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 187.280 _refine.B_iso_min 37.270 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _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.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 1582 _refine_hist.pdbx_number_atoms_ligand 24 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 1610 _refine_hist.d_res_high 3.050 _refine_hist.d_res_low 30.0 # 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 c_bond_d ? 0.006 ? ? ? 'X-RAY DIFFRACTION' c_angle_d ? 1.062 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 0.000 1.500 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 1.892 2.000 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 0.000 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 3.115 2.500 ? ? 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 CNS_TOPPAR:protein_rep.param CNS_TOPPAR:protein.top 'X-RAY DIFFRACTION' 2 cycp-dna-rna_rep-12.param cycp-dna-rna-12.top 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:ion.param CNS_TOPPAR:ion.top 'X-RAY DIFFRACTION' 5 thia.param thia.top 'X-RAY DIFFRACTION' # _struct.entry_id 4NYG _struct.title 'Crystal structure of the E. coli thiM riboswitch in complex with thiamine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NYG _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'fragment-based drug discovery, riboswitch, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 4 ? # _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 82 "O3'" ? ? ? 1_555 A A23 83 P ? ? A C 90 A A23 91 1_555 ? ? ? ? ? ? ? 1.598 ? ? metalc1 metalc ? ? A G 9 O6 ? ? ? 1_555 D MG . MG ? ? A G 17 A MG 103 1_555 ? ? ? ? ? ? ? 2.908 ? ? metalc2 metalc ? ? A A 27 OP2 ? ? ? 1_555 F MG . MG ? ? A A 35 A MG 105 1_555 ? ? ? ? ? ? ? 2.946 ? ? metalc3 metalc ? ? A G 32 OP1 ? ? ? 1_555 E MG . MG ? ? A G 40 A MG 104 1_555 ? ? ? ? ? ? ? 2.785 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 102 A HOH 201 1_555 ? ? ? ? ? ? ? 2.409 ? ? metalc5 metalc ? ? H MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 107 A HOH 204 1_555 ? ? ? ? ? ? ? 1.967 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 82 N3 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 82 O2 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 82 N4 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 81 N1 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 81 O6 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 81 N2 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 80 N3 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 80 O2 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 80 N4 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 79 N3 ? ? A A 12 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 79 O4 ? ? A A 12 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 78 N2 ? ? A C 13 A G 86 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 N2 ? ? ? 1_555 A A 76 N3 ? ? A G 16 A A 84 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 A A 48 N3 ? ? A G 17 A A 56 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 40 O2 ? ? A G 18 A C 48 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog25 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 34 N3 ? ? A G 19 A G 42 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog26 hydrog ? ? A G 11 N3 ? ? ? 1_555 A G 34 N2 ? ? A G 19 A G 42 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog27 hydrog ? ? A G 11 N1 ? ? ? 1_555 A A 39 N1 ? ? A G 19 A A 47 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog28 hydrog ? ? A G 11 O6 ? ? ? 1_555 A A 39 N6 ? ? A G 19 A A 47 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog29 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 20 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 20 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 13 N2 ? ? ? 1_555 A U 63 O2 ? ? A G 21 A U 71 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog35 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 22 A G 37 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog36 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 31 N3 ? ? ? 1_555 A A 35 N7 ? ? A U 39 A A 43 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog40 hydrog ? ? A U 31 O2 ? ? ? 1_555 A A 35 N6 ? ? A U 39 A A 43 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog41 hydrog ? ? A A 45 N7 ? ? ? 1_555 A A 76 N6 ? ? A A 53 A A 84 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog42 hydrog ? ? A A 48 N6 ? ? ? 1_555 A G 75 N3 ? ? A A 56 A G 83 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog43 hydrog ? ? A A 48 N7 ? ? ? 1_555 A G 75 N2 ? ? A A 56 A G 83 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog44 hydrog ? ? A C 49 N3 ? ? ? 1_555 A G 74 N1 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 49 N4 ? ? ? 1_555 A G 74 O6 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 49 O2 ? ? ? 1_555 A G 74 N2 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 50 N3 ? ? ? 1_555 A G 73 N1 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 50 N4 ? ? ? 1_555 A G 73 O6 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 50 O2 ? ? ? 1_555 A G 73 N2 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A U 51 N3 ? ? ? 1_555 A A 72 N1 ? ? A U 59 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A U 51 O4 ? ? ? 1_555 A A 72 N6 ? ? A U 59 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 52 N1 ? ? ? 1_555 A C 69 N3 ? ? A G 60 A C 77 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog53 hydrog ? ? A G 58 N2 ? ? ? 1_555 A C 65 N3 ? ? A G 66 A C 73 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog54 hydrog ? ? A G 58 N1 ? ? ? 1_555 A C 66 N3 ? ? A G 66 A C 74 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A VIB 101 ? 5 'BINDING SITE FOR RESIDUE VIB A 101' AC2 Software A MG 102 ? 2 'BINDING SITE FOR RESIDUE MG A 102' AC3 Software A MG 103 ? 1 'BINDING SITE FOR RESIDUE MG A 103' AC4 Software A MG 104 ? 1 'BINDING SITE FOR RESIDUE MG A 104' AC5 Software A MG 105 ? 2 'BINDING SITE FOR RESIDUE MG A 105' AC6 Software A MG 106 ? 2 'BINDING SITE FOR RESIDUE MG A 106' AC7 Software A MG 107 ? 2 'BINDING SITE FOR RESIDUE MG A 107' # 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 5 G A 11 ? G A 19 . ? 1_555 ? 2 AC1 5 G A 34 ? G A 42 . ? 1_555 ? 3 AC1 5 A A 35 ? A A 43 . ? 1_555 ? 4 AC1 5 C A 49 ? C A 57 . ? 1_555 ? 5 AC1 5 G A 64 ? G A 72 . ? 1_555 ? 6 AC2 2 A A 33 ? A A 41 . ? 1_555 ? 7 AC2 2 HOH I . ? HOH A 201 . ? 1_555 ? 8 AC3 1 G A 9 ? G A 17 . ? 1_555 ? 9 AC4 1 G A 32 ? G A 40 . ? 1_555 ? 10 AC5 2 A A 27 ? A A 35 . ? 1_555 ? 11 AC5 2 G A 28 ? G A 36 . ? 1_555 ? 12 AC6 2 A A 72 ? A A 80 . ? 1_555 ? 13 AC6 2 G A 73 ? G A 81 . ? 1_555 ? 14 AC7 2 G A 32 ? G A 40 . ? 1_555 ? 15 AC7 2 HOH I . ? HOH A 204 . ? 1_555 ? # _atom_sites.entry_id 4NYG _atom_sites.fract_transf_matrix[1][1] 0.016259 _atom_sites.fract_transf_matrix[1][2] 0.009387 _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] 0.018775 _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] 0.009621 _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 MG N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 9 9 G G A . n A 1 2 C 2 10 10 C C A . n A 1 3 G 3 11 11 G G A . n A 1 4 A 4 12 12 A A A . n A 1 5 C 5 13 13 C C A . n A 1 6 U 6 14 14 U U A . n A 1 7 C 7 15 15 C C A . n A 1 8 G 8 16 16 G G A . n A 1 9 G 9 17 17 G G A . n A 1 10 G 10 18 18 G G A . n A 1 11 G 11 19 19 G G A . n A 1 12 U 12 20 20 U U A . n A 1 13 G 13 21 21 G G A . n A 1 14 C 14 22 22 C C A . n A 1 15 C 15 23 23 C C A . n A 1 16 C 16 24 24 C C A . n A 1 17 U 17 25 25 U U A . n A 1 18 U 18 26 ? ? ? A . n A 1 19 C 19 27 ? ? ? A . n A 1 20 U 20 28 ? ? ? A . n A 1 21 G 21 29 ? ? ? A . n A 1 22 C 22 30 30 C C A . n A 1 23 G 23 31 31 G G A . n A 1 24 U 24 32 32 U U A . n A 1 25 G 25 33 33 G G A . n A 1 26 A 26 34 34 A A A . n A 1 27 A 27 35 35 A A A . n A 1 28 G 28 36 36 G G A . n A 1 29 G 29 37 37 G G A . n A 1 30 C 30 38 38 C C A . n A 1 31 U 31 39 39 U U A . n A 1 32 G 32 40 40 G G A . n A 1 33 A 33 41 41 A A A . n A 1 34 G 34 42 42 G G A . n A 1 35 A 35 43 43 A A A . n A 1 36 A 36 44 44 A A A . n A 1 37 A 37 45 45 A A A . n A 1 38 U 38 46 46 U U A . n A 1 39 A 39 47 47 A A A . n A 1 40 C 40 48 48 C C A . n A 1 41 C 41 49 49 C C A . n A 1 42 C 42 50 50 C C A . n A 1 43 G 43 51 51 G G A . n A 1 44 U 44 52 52 U U A . n A 1 45 A 45 53 53 A A A . n A 1 46 U 46 54 54 U U A . n A 1 47 C 47 55 55 C C A . n A 1 48 A 48 56 56 A A A . n A 1 49 C 49 57 57 C C A . n A 1 50 C 50 58 58 C C A . n A 1 51 U 51 59 59 U U A . n A 1 52 G 52 60 60 G G A . n A 1 53 A 53 61 61 A A A . n A 1 54 U 54 62 62 U U A . n A 1 55 C 55 63 63 C C A . n A 1 56 U 56 64 64 U U A . n A 1 57 G 57 65 65 G G A . n A 1 58 G 58 66 66 G G A . n A 1 59 A 59 67 67 A A A . n A 1 60 U 60 68 68 U U A . n A 1 61 A 61 69 69 A A A . n A 1 62 A 62 70 70 A A A . n A 1 63 U 63 71 71 U U A . n A 1 64 G 64 72 72 G G A . n A 1 65 C 65 73 73 C C A . n A 1 66 C 66 74 74 C C A . n A 1 67 A 67 75 75 A A A . n A 1 68 G 68 76 76 G G A . n A 1 69 C 69 77 77 C C A . n A 1 70 G 70 78 78 G G A . n A 1 71 U 71 79 79 U U A . n A 1 72 A 72 80 80 A A A . n A 1 73 G 73 81 81 G G A . n A 1 74 G 74 82 82 G G A . n A 1 75 G 75 83 83 G G A . n A 1 76 A 76 84 84 A A A . n A 1 77 A 77 85 85 A A A . n A 1 78 G 78 86 86 G G A . n A 1 79 U 79 87 87 U U A . n A 1 80 C 80 88 88 C C A . n A 1 81 G 81 89 89 G G A . n A 1 82 C 82 90 90 C C A . n A 1 83 A23 83 91 91 A23 A23 A . 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 B 2 VIB 1 101 200 VIB VIB A . C 3 MG 1 102 102 MG MG A . D 3 MG 1 103 103 MG MG A . E 3 MG 1 104 104 MG MG A . F 3 MG 1 105 105 MG MG A . G 3 MG 1 106 108 MG MG A . H 3 MG 1 107 109 MG MG A . I 4 HOH 1 201 110 HOH HOH A . I 4 HOH 2 202 107 HOH HOH A . I 4 HOH 3 203 111 HOH HOH A . I 4 HOH 4 204 101 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id A23 _pdbx_struct_mod_residue.label_seq_id 83 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id A23 _pdbx_struct_mod_residue.auth_seq_id 91 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id A _pdbx_struct_mod_residue.details ? # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # _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 # 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 2014-06-04 2 'Structure model' 1 1 2023-09-20 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' 'Refinement description' 5 2 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp 2 2 'Structure model' chem_comp_atom 3 2 'Structure model' chem_comp_bond 4 2 'Structure model' database_2 5 2 'Structure model' pdbx_initial_refinement_model 6 2 'Structure model' struct_conn 7 2 '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 2 'Structure model' '_chem_comp.pdbx_synonyms' 2 2 'Structure model' '_database_2.pdbx_DOI' 3 2 'Structure model' '_database_2.pdbx_database_accession' 4 2 'Structure model' '_struct_conn.pdbx_dist_value' 5 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 2 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 13 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 2 'Structure model' '_struct_conn.ptnr2_label_atom_id' 16 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 17 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 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 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 5 DENZO . ? ? ? ? 'data reduction' ? ? ? 6 PHASER . ? ? ? ? phasing ? ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N7 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 A _pdbx_validate_close_contact.auth_seq_id_1 41 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 MG _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 MG _pdbx_validate_close_contact.auth_seq_id_2 102 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.69 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 24 ? N1 ? A C 16 N1 2 1 Y 1 A C 24 ? C2 ? A C 16 C2 3 1 Y 1 A C 24 ? O2 ? A C 16 O2 4 1 Y 1 A C 24 ? N3 ? A C 16 N3 5 1 Y 1 A C 24 ? C4 ? A C 16 C4 6 1 Y 1 A C 24 ? N4 ? A C 16 N4 7 1 Y 1 A C 24 ? C5 ? A C 16 C5 8 1 Y 1 A C 24 ? C6 ? A C 16 C6 9 1 Y 1 A G 33 ? N9 ? A G 25 N9 10 1 Y 1 A G 33 ? C8 ? A G 25 C8 11 1 Y 1 A G 33 ? N7 ? A G 25 N7 12 1 Y 1 A G 33 ? C5 ? A G 25 C5 13 1 Y 1 A G 33 ? C6 ? A G 25 C6 14 1 Y 1 A G 33 ? O6 ? A G 25 O6 15 1 Y 1 A G 33 ? N1 ? A G 25 N1 16 1 Y 1 A G 33 ? C2 ? A G 25 C2 17 1 Y 1 A G 33 ? N2 ? A G 25 N2 18 1 Y 1 A G 33 ? N3 ? A G 25 N3 19 1 Y 1 A G 33 ? C4 ? A G 25 C4 20 1 Y 1 A A 44 ? N9 ? A A 36 N9 21 1 Y 1 A A 44 ? C8 ? A A 36 C8 22 1 Y 1 A A 44 ? N7 ? A A 36 N7 23 1 Y 1 A A 44 ? C5 ? A A 36 C5 24 1 Y 1 A A 44 ? C6 ? A A 36 C6 25 1 Y 1 A A 44 ? N6 ? A A 36 N6 26 1 Y 1 A A 44 ? N1 ? A A 36 N1 27 1 Y 1 A A 44 ? C2 ? A A 36 C2 28 1 Y 1 A A 44 ? N3 ? A A 36 N3 29 1 Y 1 A A 44 ? C4 ? A A 36 C4 30 1 Y 1 A U 46 ? "O5'" ? A U 38 "O5'" 31 1 Y 1 A U 46 ? "C5'" ? A U 38 "C5'" 32 1 Y 1 A U 46 ? "C4'" ? A U 38 "C4'" 33 1 Y 1 A U 46 ? "O4'" ? A U 38 "O4'" 34 1 Y 1 A U 46 ? "C3'" ? A U 38 "C3'" 35 1 Y 1 A U 46 ? "O3'" ? A U 38 "O3'" 36 1 Y 1 A U 46 ? "C2'" ? A U 38 "C2'" 37 1 Y 1 A U 46 ? "O2'" ? A U 38 "O2'" 38 1 Y 1 A U 46 ? "C1'" ? A U 38 "C1'" 39 1 Y 1 A U 46 ? N1 ? A U 38 N1 40 1 Y 1 A U 46 ? C2 ? A U 38 C2 41 1 Y 1 A U 46 ? O2 ? A U 38 O2 42 1 Y 1 A U 46 ? N3 ? A U 38 N3 43 1 Y 1 A U 46 ? C4 ? A U 38 C4 44 1 Y 1 A U 46 ? O4 ? A U 38 O4 45 1 Y 1 A U 46 ? C5 ? A U 38 C5 46 1 Y 1 A U 46 ? C6 ? A U 38 C6 47 1 Y 1 A A 61 ? N9 ? A A 53 N9 48 1 Y 1 A A 61 ? C8 ? A A 53 C8 49 1 Y 1 A A 61 ? N7 ? A A 53 N7 50 1 Y 1 A A 61 ? C5 ? A A 53 C5 51 1 Y 1 A A 61 ? C6 ? A A 53 C6 52 1 Y 1 A A 61 ? N6 ? A A 53 N6 53 1 Y 1 A A 61 ? N1 ? A A 53 N1 54 1 Y 1 A A 61 ? C2 ? A A 53 C2 55 1 Y 1 A A 61 ? N3 ? A A 53 N3 56 1 Y 1 A A 61 ? C4 ? A A 53 C4 57 1 Y 1 A U 62 ? N1 ? A U 54 N1 58 1 Y 1 A U 62 ? C2 ? A U 54 C2 59 1 Y 1 A U 62 ? O2 ? A U 54 O2 60 1 Y 1 A U 62 ? N3 ? A U 54 N3 61 1 Y 1 A U 62 ? C4 ? A U 54 C4 62 1 Y 1 A U 62 ? O4 ? A U 54 O4 63 1 Y 1 A U 62 ? C5 ? A U 54 C5 64 1 Y 1 A U 62 ? C6 ? A U 54 C6 65 1 Y 1 A C 63 ? N1 ? A C 55 N1 66 1 Y 1 A C 63 ? C2 ? A C 55 C2 67 1 Y 1 A C 63 ? O2 ? A C 55 O2 68 1 Y 1 A C 63 ? N3 ? A C 55 N3 69 1 Y 1 A C 63 ? C4 ? A C 55 C4 70 1 Y 1 A C 63 ? N4 ? A C 55 N4 71 1 Y 1 A C 63 ? C5 ? A C 55 C5 72 1 Y 1 A C 63 ? C6 ? A C 55 C6 73 1 Y 1 A U 64 ? "O5'" ? A U 56 "O5'" 74 1 Y 1 A U 64 ? "C5'" ? A U 56 "C5'" 75 1 Y 1 A U 64 ? "C4'" ? A U 56 "C4'" 76 1 Y 1 A U 64 ? "O4'" ? A U 56 "O4'" 77 1 Y 1 A U 64 ? "C3'" ? A U 56 "C3'" 78 1 Y 1 A U 64 ? "O3'" ? A U 56 "O3'" 79 1 Y 1 A U 64 ? "C2'" ? A U 56 "C2'" 80 1 Y 1 A U 64 ? "O2'" ? A U 56 "O2'" 81 1 Y 1 A U 64 ? "C1'" ? A U 56 "C1'" 82 1 Y 1 A U 64 ? N1 ? A U 56 N1 83 1 Y 1 A U 64 ? C2 ? A U 56 C2 84 1 Y 1 A U 64 ? O2 ? A U 56 O2 85 1 Y 1 A U 64 ? N3 ? A U 56 N3 86 1 Y 1 A U 64 ? C4 ? A U 56 C4 87 1 Y 1 A U 64 ? O4 ? A U 56 O4 88 1 Y 1 A U 64 ? C5 ? A U 56 C5 89 1 Y 1 A U 64 ? C6 ? A U 56 C6 90 1 Y 1 A G 65 ? P ? A G 57 P 91 1 Y 1 A G 65 ? OP1 ? A G 57 OP1 92 1 Y 1 A G 65 ? OP2 ? A G 57 OP2 93 1 Y 1 A G 78 ? N9 ? A G 70 N9 94 1 Y 1 A G 78 ? C8 ? A G 70 C8 95 1 Y 1 A G 78 ? N7 ? A G 70 N7 96 1 Y 1 A G 78 ? C5 ? A G 70 C5 97 1 Y 1 A G 78 ? C6 ? A G 70 C6 98 1 Y 1 A G 78 ? O6 ? A G 70 O6 99 1 Y 1 A G 78 ? N1 ? A G 70 N1 100 1 Y 1 A G 78 ? C2 ? A G 70 C2 101 1 Y 1 A G 78 ? N2 ? A G 70 N2 102 1 Y 1 A G 78 ? N3 ? A G 70 N3 103 1 Y 1 A G 78 ? C4 ? A G 70 C4 104 1 Y 1 A U 79 ? N1 ? A U 71 N1 105 1 Y 1 A U 79 ? C2 ? A U 71 C2 106 1 Y 1 A U 79 ? O2 ? A U 71 O2 107 1 Y 1 A U 79 ? N3 ? A U 71 N3 108 1 Y 1 A U 79 ? C4 ? A U 71 C4 109 1 Y 1 A U 79 ? O4 ? A U 71 O4 110 1 Y 1 A U 79 ? C5 ? A U 71 C5 111 1 Y 1 A U 79 ? C6 ? A U 71 C6 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 26 ? A U 18 2 1 Y 1 A C 27 ? A C 19 3 1 Y 1 A U 28 ? A U 20 4 1 Y 1 A G 29 ? A G 21 # 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 A23 PC P N S 38 A23 O1C O N N 39 A23 O2C O N N 40 A23 P P N N 41 A23 OP1 O N N 42 A23 OP2 O N N 43 A23 OP3 O N N 44 A23 "O5'" O N N 45 A23 "C5'" C N N 46 A23 "C4'" C N R 47 A23 "O4'" O N N 48 A23 "C3'" C N R 49 A23 "O3'" O N N 50 A23 "C2'" C N R 51 A23 "O2'" O N N 52 A23 "C1'" C N R 53 A23 N9 N Y N 54 A23 C8 C Y N 55 A23 N7 N Y N 56 A23 C5 C Y N 57 A23 C6 C Y N 58 A23 N6 N N N 59 A23 N1 N Y N 60 A23 C2 C Y N 61 A23 N3 N Y N 62 A23 C4 C Y N 63 A23 HOC2 H N N 64 A23 HOP2 H N N 65 A23 HOP3 H N N 66 A23 "H5'" H N N 67 A23 "H5''" H N N 68 A23 "H4'" H N N 69 A23 "H3'" H N N 70 A23 "H2'" H N N 71 A23 "H1'" H N N 72 A23 H8 H N N 73 A23 HN61 H N N 74 A23 HN62 H N N 75 A23 H2 H N N 76 C OP3 O N N 77 C P P N N 78 C OP1 O N N 79 C OP2 O N N 80 C "O5'" O N N 81 C "C5'" C N N 82 C "C4'" C N R 83 C "O4'" O N N 84 C "C3'" C N S 85 C "O3'" O N N 86 C "C2'" C N R 87 C "O2'" O N N 88 C "C1'" C N R 89 C N1 N N N 90 C C2 C N N 91 C O2 O N N 92 C N3 N N N 93 C C4 C N N 94 C N4 N N N 95 C C5 C N N 96 C C6 C N N 97 C HOP3 H N N 98 C HOP2 H N N 99 C "H5'" H N N 100 C "H5''" H N N 101 C "H4'" H N N 102 C "H3'" H N N 103 C "HO3'" H N N 104 C "H2'" H N N 105 C "HO2'" H N N 106 C "H1'" H N N 107 C H41 H N N 108 C H42 H N N 109 C H5 H N N 110 C H6 H N N 111 G OP3 O N N 112 G P P N N 113 G OP1 O N N 114 G OP2 O N N 115 G "O5'" O N N 116 G "C5'" C N N 117 G "C4'" C N R 118 G "O4'" O N N 119 G "C3'" C N S 120 G "O3'" O N N 121 G "C2'" C N R 122 G "O2'" O N N 123 G "C1'" C N R 124 G N9 N Y N 125 G C8 C Y N 126 G N7 N Y N 127 G C5 C Y N 128 G C6 C N N 129 G O6 O N N 130 G N1 N N N 131 G C2 C N N 132 G N2 N N N 133 G N3 N N N 134 G C4 C Y N 135 G HOP3 H N N 136 G HOP2 H N N 137 G "H5'" H N N 138 G "H5''" H N N 139 G "H4'" H N N 140 G "H3'" H N N 141 G "HO3'" H N N 142 G "H2'" H N N 143 G "HO2'" H N N 144 G "H1'" H N N 145 G H8 H N N 146 G H1 H N N 147 G H21 H N N 148 G H22 H N N 149 HOH O O N N 150 HOH H1 H N N 151 HOH H2 H N N 152 MG MG MG N N 153 U OP3 O N N 154 U P P N N 155 U OP1 O N N 156 U OP2 O N N 157 U "O5'" O N N 158 U "C5'" C N N 159 U "C4'" C N R 160 U "O4'" O N N 161 U "C3'" C N S 162 U "O3'" O N N 163 U "C2'" C N R 164 U "O2'" O N N 165 U "C1'" C N R 166 U N1 N N N 167 U C2 C N N 168 U O2 O N N 169 U N3 N N N 170 U C4 C N N 171 U O4 O N N 172 U C5 C N N 173 U C6 C N N 174 U HOP3 H N N 175 U HOP2 H N N 176 U "H5'" H N N 177 U "H5''" H N N 178 U "H4'" H N N 179 U "H3'" H N N 180 U "HO3'" H N N 181 U "H2'" H N N 182 U "HO2'" H N N 183 U "H1'" H N N 184 U H3 H N N 185 U H5 H N N 186 U H6 H N N 187 VIB CM2 C N N 188 VIB N4A N N N 189 VIB CM4 C N N 190 VIB O1 O N N 191 VIB C7 C N N 192 VIB C6 C N N 193 VIB C2 C Y N 194 VIB S1 S Y N 195 VIB C5 C Y N 196 VIB C4 C Y N 197 VIB N3 N Y N 198 VIB C7A C N N 199 VIB C4A C Y N 200 VIB N3A N Y N 201 VIB C2A C Y N 202 VIB N1A N Y N 203 VIB C6A C Y N 204 VIB C5A C Y N 205 VIB HM21 H N N 206 VIB HM22 H N N 207 VIB HM23 H N N 208 VIB H4A1 H N N 209 VIB H4A2 H N N 210 VIB HM41 H N N 211 VIB HM42 H N N 212 VIB HM43 H N N 213 VIB HO1 H N N 214 VIB HC71 H N N 215 VIB HC72 H N N 216 VIB HC61 H N N 217 VIB HC62 H N N 218 VIB HC2 H N N 219 VIB H7A1 H N N 220 VIB H7A2 H N N 221 VIB H6AC H N N 222 # 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 A23 PC O1C doub N N 40 A23 PC O2C sing N N 41 A23 PC "O3'" sing N N 42 A23 PC "O2'" sing N N 43 A23 O2C HOC2 sing N N 44 A23 P OP1 doub N N 45 A23 P OP2 sing N N 46 A23 P OP3 sing N N 47 A23 P "O5'" sing N N 48 A23 OP2 HOP2 sing N N 49 A23 OP3 HOP3 sing N N 50 A23 "O5'" "C5'" sing N N 51 A23 "C5'" "C4'" sing N N 52 A23 "C5'" "H5'" sing N N 53 A23 "C5'" "H5''" sing N N 54 A23 "C4'" "O4'" sing N N 55 A23 "C4'" "C3'" sing N N 56 A23 "C4'" "H4'" sing N N 57 A23 "O4'" "C1'" sing N N 58 A23 "C3'" "O3'" sing N N 59 A23 "C3'" "C2'" sing N N 60 A23 "C3'" "H3'" sing N N 61 A23 "C2'" "O2'" sing N N 62 A23 "C2'" "C1'" sing N N 63 A23 "C2'" "H2'" sing N N 64 A23 "C1'" N9 sing N N 65 A23 "C1'" "H1'" sing N N 66 A23 N9 C8 sing Y N 67 A23 N9 C4 sing Y N 68 A23 C8 N7 doub Y N 69 A23 C8 H8 sing N N 70 A23 N7 C5 sing Y N 71 A23 C5 C6 sing Y N 72 A23 C5 C4 doub Y N 73 A23 C6 N6 sing N N 74 A23 C6 N1 doub Y N 75 A23 N6 HN61 sing N N 76 A23 N6 HN62 sing N N 77 A23 N1 C2 sing Y N 78 A23 C2 N3 doub Y N 79 A23 C2 H2 sing N N 80 A23 N3 C4 sing Y N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 HOH O H1 sing N N 158 HOH O H2 sing N N 159 U OP3 P sing N N 160 U OP3 HOP3 sing N N 161 U P OP1 doub N N 162 U P OP2 sing N N 163 U P "O5'" sing N N 164 U OP2 HOP2 sing N N 165 U "O5'" "C5'" sing N N 166 U "C5'" "C4'" sing N N 167 U "C5'" "H5'" sing N N 168 U "C5'" "H5''" sing N N 169 U "C4'" "O4'" sing N N 170 U "C4'" "C3'" sing N N 171 U "C4'" "H4'" sing N N 172 U "O4'" "C1'" sing N N 173 U "C3'" "O3'" sing N N 174 U "C3'" "C2'" sing N N 175 U "C3'" "H3'" sing N N 176 U "O3'" "HO3'" sing N N 177 U "C2'" "O2'" sing N N 178 U "C2'" "C1'" sing N N 179 U "C2'" "H2'" sing N N 180 U "O2'" "HO2'" sing N N 181 U "C1'" N1 sing N N 182 U "C1'" "H1'" sing N N 183 U N1 C2 sing N N 184 U N1 C6 sing N N 185 U C2 O2 doub N N 186 U C2 N3 sing N N 187 U N3 C4 sing N N 188 U N3 H3 sing N N 189 U C4 O4 doub N N 190 U C4 C5 sing N N 191 U C5 C6 doub N N 192 U C5 H5 sing N N 193 U C6 H6 sing N N 194 VIB CM2 C2A sing N N 195 VIB CM2 HM21 sing N N 196 VIB CM2 HM22 sing N N 197 VIB CM2 HM23 sing N N 198 VIB N4A C4A sing N N 199 VIB N4A H4A1 sing N N 200 VIB N4A H4A2 sing N N 201 VIB CM4 C4 sing N N 202 VIB CM4 HM41 sing N N 203 VIB CM4 HM42 sing N N 204 VIB CM4 HM43 sing N N 205 VIB O1 C7 sing N N 206 VIB O1 HO1 sing N N 207 VIB C7 C6 sing N N 208 VIB C7 HC71 sing N N 209 VIB C7 HC72 sing N N 210 VIB C6 C5 sing N N 211 VIB C6 HC61 sing N N 212 VIB C6 HC62 sing N N 213 VIB C2 S1 sing Y N 214 VIB C2 N3 doub Y N 215 VIB C2 HC2 sing N N 216 VIB S1 C5 sing Y N 217 VIB C5 C4 doub Y N 218 VIB C4 N3 sing Y N 219 VIB N3 C7A sing N N 220 VIB C7A C5A sing N N 221 VIB C7A H7A1 sing N N 222 VIB C7A H7A2 sing N N 223 VIB C4A N3A sing Y N 224 VIB C4A C5A doub Y N 225 VIB N3A C2A doub Y N 226 VIB C2A N1A sing Y N 227 VIB N1A C6A doub Y N 228 VIB C6A C5A sing Y N 229 VIB C6A H6AC sing N N 230 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4NYG 'double helix' 4NYG 'a-form double helix' 4NYG 'hairpin loop' 4NYG 'mismatched base pair' 4NYG 'internal loop' 4NYG 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 82 1_555 -0.778 -0.121 -0.034 -0.075 -6.614 2.746 1 A_G9:C90_A A 9 ? A 90 ? 19 1 1 A C 2 1_555 A G 81 1_555 -0.405 -0.348 0.671 -10.170 -11.145 -1.971 2 A_C10:G89_A A 10 ? A 89 ? 19 1 1 A G 3 1_555 A C 80 1_555 -0.500 0.013 0.848 7.895 -1.814 6.143 3 A_G11:C88_A A 11 ? A 88 ? 19 1 1 A A 4 1_555 A U 79 1_555 -0.185 0.092 0.114 6.388 -18.119 -0.502 4 A_A12:U87_A A 12 ? A 87 ? 20 1 1 A C 5 1_555 A G 78 1_555 0.208 0.283 1.089 -11.808 -10.825 -0.681 5 A_C13:G86_A A 13 ? A 86 ? ? 1 1 A C 7 1_555 A G 43 1_555 -0.811 -0.395 0.444 -4.826 -7.780 -9.655 6 A_C15:G51_A A 15 ? A 51 ? 19 1 1 A G 8 1_555 A C 42 1_555 -0.958 -0.110 -0.245 -5.636 -15.737 7.585 7 A_G16:C50_A A 16 ? A 50 ? 19 1 1 A G 9 1_555 A C 41 1_555 -0.009 -0.113 0.353 -12.988 -13.141 1.646 8 A_G17:C49_A A 17 ? A 49 ? 19 1 1 A G 10 1_555 A C 40 1_555 -1.314 -0.448 -0.056 -4.272 -17.512 -10.653 9 A_G18:C48_A A 18 ? A 48 ? ? 1 1 A G 11 1_555 A A 39 1_555 -0.099 1.412 -0.086 1.198 -18.494 -26.083 10 A_G19:A47_A A 19 ? A 47 ? 8 1 1 A U 12 1_555 A A 37 1_555 -0.570 -0.176 -0.410 11.771 9.840 2.516 11 A_U20:A45_A A 20 ? A 45 ? 20 1 1 A G 28 1_555 A C 15 1_555 -0.654 -0.450 0.011 1.429 -18.590 -4.258 12 A_G36:C23_A A 36 ? A 23 ? 19 1 1 A G 29 1_555 A C 14 1_555 -0.324 0.251 0.232 -2.505 -9.770 9.415 13 A_G37:C22_A A 37 ? A 22 ? ? 1 1 A C 30 1_555 A G 13 1_555 0.909 0.169 0.655 -16.284 0.764 -5.123 14 A_C38:G21_A A 38 ? A 21 ? 19 1 1 A U 31 1_555 A A 35 1_555 4.323 -2.160 0.327 3.927 5.830 -95.361 15 A_U39:A43_A A 39 ? A 43 ? 24 4 1 A A 45 1_555 A A 76 1_555 6.689 -5.190 -0.184 -17.078 18.868 158.127 16 A_A53:A84_A A 53 ? A 84 ? ? ? 1 A A 48 1_555 A G 75 1_555 -6.633 -4.360 0.588 14.496 -24.602 -20.098 17 A_A56:G83_A A 56 ? A 83 ? 11 10 1 A C 49 1_555 A G 74 1_555 0.750 0.137 0.260 15.417 -13.890 -2.770 18 A_C57:G82_A A 57 ? A 82 ? 19 1 1 A C 50 1_555 A G 73 1_555 0.315 -0.313 0.503 -5.449 -3.703 -4.193 19 A_C58:G81_A A 58 ? A 81 ? 19 1 1 A U 51 1_555 A A 72 1_555 1.456 -0.630 1.128 -9.878 -8.302 0.336 20 A_U59:A80_A A 59 ? A 80 ? 20 1 1 A G 52 1_555 A C 69 1_555 -0.064 -0.642 -2.311 27.008 -7.084 41.533 21 A_G60:C77_A A 60 ? A 77 ? ? 1 1 A G 58 1_555 A C 66 1_555 0.959 -0.089 1.085 -13.676 28.136 53.809 22 A_G66:C74_A A 66 ? A 74 ? ? 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 82 1_555 A C 2 1_555 A G 81 1_555 0.046 -1.313 3.427 -4.148 2.925 34.096 -2.686 -0.741 3.279 4.954 7.025 34.460 1 AA_G9C10:G89C90_AA A 9 ? A 90 ? A 10 ? A 89 ? 1 A C 2 1_555 A G 81 1_555 A G 3 1_555 A C 80 1_555 0.389 -1.547 2.481 0.494 -1.210 34.111 -2.489 -0.603 2.538 -2.061 -0.841 34.136 2 AA_C10G11:C88G89_AA A 10 ? A 89 ? A 11 ? A 88 ? 1 A G 3 1_555 A C 80 1_555 A A 4 1_555 A U 79 1_555 -0.315 -1.459 3.100 7.272 7.406 34.311 -3.326 1.447 2.620 12.211 -11.991 35.801 3 AA_G11A12:U87C88_AA A 11 ? A 88 ? A 12 ? A 87 ? 1 A A 4 1_555 A U 79 1_555 A C 5 1_555 A G 78 1_555 -0.153 -1.477 3.488 -7.746 12.079 38.735 -3.415 -0.627 2.898 17.497 11.220 41.212 4 AA_A12C13:G86U87_AA A 12 ? A 87 ? A 13 ? A 86 ? 1 A C 5 1_555 A G 78 1_555 A C 7 1_555 A G 43 1_555 0.229 -2.643 6.205 3.167 -1.149 65.298 -2.357 0.036 6.250 -1.064 -2.933 65.376 5 AA_C13C15:G51G86_AA A 13 ? A 86 ? A 15 ? A 51 ? 1 A C 7 1_555 A G 43 1_555 A G 8 1_555 A C 42 1_555 1.740 -1.610 3.267 4.894 4.690 31.210 -3.784 -2.272 3.226 8.590 -8.964 31.920 6 AA_C15G16:C50G51_AA A 15 ? A 51 ? A 16 ? A 50 ? 1 A G 8 1_555 A C 42 1_555 A G 9 1_555 A C 41 1_555 -0.777 -1.377 3.265 -5.165 6.916 41.945 -2.565 0.560 3.081 9.540 7.124 42.785 7 AA_G16G17:C49C50_AA A 16 ? A 50 ? A 17 ? A 49 ? 1 A G 9 1_555 A C 41 1_555 A G 10 1_555 A C 40 1_555 -0.440 -2.067 2.970 3.918 8.619 22.743 -6.928 1.977 1.964 20.739 -9.427 24.611 8 AA_G17G18:C48C49_AA A 17 ? A 49 ? A 18 ? A 48 ? 1 A G 10 1_555 A C 40 1_555 A G 11 1_555 A A 39 1_555 -0.560 -0.640 3.182 1.760 3.867 42.369 -1.256 0.942 3.090 5.334 -2.428 42.572 9 AA_G18G19:A47C48_AA A 18 ? A 48 ? A 19 ? A 47 ? 1 A G 11 1_555 A A 39 1_555 A U 12 1_555 A A 37 1_555 -0.197 -0.347 3.260 6.167 10.594 -4.461 -11.123 6.496 1.492 -60.566 35.253 -13.042 10 AA_G19U20:A45A47_AA A 19 ? A 47 ? A 20 ? A 45 ? 1 A G 28 1_555 A C 15 1_555 A G 29 1_555 A C 14 1_555 -0.169 -1.890 3.351 -6.822 3.499 32.971 -3.813 -0.812 3.112 6.063 11.822 33.827 11 AA_G36G37:C22C23_AA A 36 ? A 23 ? A 37 ? A 22 ? 1 A G 29 1_555 A C 14 1_555 A C 30 1_555 A G 13 1_555 -0.975 -1.829 3.609 -0.790 8.682 44.013 -3.231 1.203 3.226 11.452 1.042 44.826 12 AA_G37C38:G21C22_AA A 37 ? A 22 ? A 38 ? A 21 ? 1 A C 30 1_555 A G 13 1_555 A U 31 1_555 A A 35 1_555 -2.915 -1.186 2.723 12.721 5.291 68.051 -1.188 2.913 2.131 4.679 -11.249 69.267 13 AA_C38U39:A43G21_AA A 38 ? A 21 ? A 39 ? A 43 ? 1 A A 45 1_555 A A 76 1_555 A A 48 1_555 A G 75 1_555 -1.809 -2.351 2.026 148.275 -87.588 -165.266 1.242 -0.792 2.056 43.810 74.165 -179.002 14 AA_A53A56:G83A84_AA A 53 ? A 84 ? A 56 ? A 83 ? 1 A A 48 1_555 A G 75 1_555 A C 49 1_555 A G 74 1_555 1.579 -1.563 3.376 -3.947 10.920 63.813 -1.912 -1.638 3.010 10.241 3.702 64.751 15 AA_A56C57:G82G83_AA A 56 ? A 83 ? A 57 ? A 82 ? 1 A C 49 1_555 A G 74 1_555 A C 50 1_555 A G 73 1_555 -0.759 -1.610 3.840 -2.205 4.361 32.783 -3.667 0.904 3.643 7.674 3.879 33.135 16 AA_C57C58:G81G82_AA A 57 ? A 82 ? A 58 ? A 81 ? 1 A C 50 1_555 A G 73 1_555 A U 51 1_555 A A 72 1_555 0.642 -1.613 3.259 1.790 4.867 41.980 -2.721 -0.711 3.085 6.763 -2.487 42.284 17 AA_C58U59:A80G81_AA A 58 ? A 81 ? A 59 ? A 80 ? 1 A U 51 1_555 A A 72 1_555 A G 52 1_555 A C 69 1_555 2.236 -0.252 4.132 3.949 9.488 15.568 -7.527 -4.097 3.799 31.004 -12.903 18.636 18 AA_U59G60:C77A80_AA A 59 ? A 80 ? A 60 ? A 77 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' VIB 3 'MAGNESIUM ION' MG 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2HOJ _pdbx_initial_refinement_model.details 'PDB ENTRY 2HOJ' #