data_1JZV # _entry.id 1JZV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1JZV pdb_00001jzv 10.2210/pdb1jzv/pdb NDB AR0035 ? ? RCSB RCSB014383 ? ? WWPDB D_1000014383 ? ? # 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 2003-11-11 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.pdbx_dist_value' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JZV _pdbx_database_status.recvd_initial_deposition_date 2001-09-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Xiong, Y.' 1 'Sudarsanakumar, C.' 2 'Deng, J.' 3 'Pan, B.' 4 'Sundaralingam, M.' 5 # _citation.id primary _citation.title 'Crystal Structure of a Bulged RNA from the SL2 Stem-loop of the HIV-1 psi-RNA' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Xiong, Y.' 1 ? primary 'Sudarsanakumar, C.' 2 ? primary 'Deng, J.' 3 ? primary 'Pan, M.' 4 ? primary 'Sundaralingam, M.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'" 2660.497 2 ? ? ? 'SL2 STEM-LOOP OF THE HIV-1 PSI-RNA' 2 polymer syn "5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'" 2956.655 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 81 ? ? ? ? # 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 'GGCGAC(5BU)G' GGCGACUG A,C ? 2 polyribonucleotide no yes 'CAGUACG(5IC)C' CAGUACGCC B,D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 G n 1 5 A n 1 6 C n 1 7 5BU n 1 8 G n 2 1 C n 2 2 A n 2 3 G n 2 4 U n 2 5 A n 2 6 C n 2 7 G n 2 8 5IC n 2 9 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Solid phase phosphoramidite synthesis' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 5IC 'RNA linking' n "5-IODO-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 I N3 O8 P' 449.093 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 5BU 7 7 7 5BU 5BU A . n A 1 8 G 8 8 8 G G A . n B 2 1 C 1 9 9 C C B . n B 2 2 A 2 10 10 A A B . n B 2 3 G 3 11 11 G G B . n B 2 4 U 4 12 12 U U B . n B 2 5 A 5 13 13 A A B . n B 2 6 C 6 14 14 C C B . n B 2 7 G 7 15 15 G G B . n B 2 8 5IC 8 16 16 5IC 5IC B . n B 2 9 C 9 17 17 C C B . n C 1 1 G 1 21 21 G G C . n C 1 2 G 2 22 22 G G C . n C 1 3 C 3 23 23 C C C . n C 1 4 G 4 24 24 G G C . n C 1 5 A 5 25 25 A A C . n C 1 6 C 6 26 26 C C C . n C 1 7 5BU 7 27 27 5BU 5BU C . n C 1 8 G 8 28 28 G G C . n D 2 1 C 1 29 29 C C D . n D 2 2 A 2 30 30 A A D . n D 2 3 G 3 31 31 G G D . n D 2 4 U 4 32 32 U U D . n D 2 5 A 5 33 33 A A D . n D 2 6 C 6 34 34 C C D . n D 2 7 G 7 35 35 G G D . n D 2 8 5IC 8 36 36 5IC 5IC D . n D 2 9 C 9 37 37 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 3 MG 1 300 300 MG MG C . F 4 HOH 1 316 316 HOH HOH A . F 4 HOH 2 319 319 HOH HOH A . F 4 HOH 3 322 322 HOH HOH A . F 4 HOH 4 327 327 HOH HOH A . F 4 HOH 5 328 328 HOH HOH A . F 4 HOH 6 332 332 HOH HOH A . F 4 HOH 7 333 333 HOH HOH A . F 4 HOH 8 336 336 HOH HOH A . F 4 HOH 9 342 342 HOH HOH A . F 4 HOH 10 343 343 HOH HOH A . F 4 HOH 11 355 355 HOH HOH A . F 4 HOH 12 361 361 HOH HOH A . F 4 HOH 13 363 363 HOH HOH A . F 4 HOH 14 365 365 HOH HOH A . F 4 HOH 15 368 368 HOH HOH A . F 4 HOH 16 369 369 HOH HOH A . F 4 HOH 17 373 373 HOH HOH A . G 4 HOH 1 307 307 HOH HOH B . G 4 HOH 2 308 308 HOH HOH B . G 4 HOH 3 312 312 HOH HOH B . G 4 HOH 4 314 314 HOH HOH B . G 4 HOH 5 315 315 HOH HOH B . G 4 HOH 6 321 321 HOH HOH B . G 4 HOH 7 326 326 HOH HOH B . G 4 HOH 8 330 330 HOH HOH B . G 4 HOH 9 334 334 HOH HOH B . G 4 HOH 10 335 335 HOH HOH B . G 4 HOH 11 344 344 HOH HOH B . G 4 HOH 12 345 345 HOH HOH B . G 4 HOH 13 346 346 HOH HOH B . G 4 HOH 14 350 350 HOH HOH B . G 4 HOH 15 351 351 HOH HOH B . G 4 HOH 16 352 352 HOH HOH B . G 4 HOH 17 353 353 HOH HOH B . G 4 HOH 18 358 358 HOH HOH B . G 4 HOH 19 359 359 HOH HOH B . G 4 HOH 20 364 364 HOH HOH B . G 4 HOH 21 366 366 HOH HOH B . G 4 HOH 22 367 367 HOH HOH B . G 4 HOH 23 377 377 HOH HOH B . G 4 HOH 24 378 378 HOH HOH B . H 4 HOH 1 301 301 HOH HOH C . H 4 HOH 2 302 302 HOH HOH C . H 4 HOH 3 303 303 HOH HOH C . H 4 HOH 4 304 304 HOH HOH C . H 4 HOH 5 306 306 HOH HOH C . H 4 HOH 6 309 309 HOH HOH C . H 4 HOH 7 313 313 HOH HOH C . H 4 HOH 8 317 317 HOH HOH C . H 4 HOH 9 323 323 HOH HOH C . H 4 HOH 10 324 324 HOH HOH C . H 4 HOH 11 329 329 HOH HOH C . H 4 HOH 12 337 337 HOH HOH C . H 4 HOH 13 338 338 HOH HOH C . H 4 HOH 14 339 339 HOH HOH C . H 4 HOH 15 347 347 HOH HOH C . H 4 HOH 16 357 357 HOH HOH C . H 4 HOH 17 362 362 HOH HOH C . H 4 HOH 18 371 371 HOH HOH C . I 4 HOH 1 305 305 HOH HOH D . I 4 HOH 2 310 310 HOH HOH D . I 4 HOH 3 311 311 HOH HOH D . I 4 HOH 4 318 318 HOH HOH D . I 4 HOH 5 320 320 HOH HOH D . I 4 HOH 6 325 325 HOH HOH D . I 4 HOH 7 331 331 HOH HOH D . I 4 HOH 8 340 340 HOH HOH D . I 4 HOH 9 341 341 HOH HOH D . I 4 HOH 10 348 348 HOH HOH D . I 4 HOH 11 349 349 HOH HOH D . I 4 HOH 12 354 354 HOH HOH D . I 4 HOH 13 356 356 HOH HOH D . I 4 HOH 14 360 360 HOH HOH D . I 4 HOH 15 370 370 HOH HOH D . I 4 HOH 16 372 372 HOH HOH D . I 4 HOH 17 374 374 HOH HOH D . I 4 HOH 18 375 375 HOH HOH D . I 4 HOH 19 376 376 HOH HOH D . I 4 HOH 20 379 379 HOH HOH D . I 4 HOH 21 380 380 HOH HOH D . I 4 HOH 22 381 381 HOH HOH D . # 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 B 5IC 16 ? "O2'" ? B 5IC 8 "O2'" 2 1 Y 1 D 5IC 36 ? "O2'" ? D 5IC 8 "O2'" # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement 1.0 ? 4 # _cell.entry_id 1JZV _cell.length_a 45.800 _cell.length_b 45.800 _cell.length_c 89.650 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JZV _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 # _exptl.entry_id 1JZV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.09 _exptl_crystal.density_percent_sol 41.22 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'MPD, magnesium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 2 MgCl2 ? ? ? 1 3 3 cacodylate ? ? ? # _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 4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9195 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-BM-D' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-BM-D _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9195 # _reflns.entry_id 1JZV _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.7 _reflns.number_obs 19682 _reflns.number_all ? _reflns.percent_possible_obs 98.0 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1JZV _refine.ls_number_reflns_obs 19558 _refine.ls_number_reflns_all 20028 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 20 _refine.ls_d_res_high 1.7 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.203 _refine.ls_R_factor_R_free 0.233 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.4 _refine.ls_number_reflns_R_free 1847 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _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.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 718 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 81 _refine_hist.number_atoms_total 800 _refine_hist.d_res_high 1.7 _refine_hist.d_res_low 20 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.38 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1JZV _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1JZV _struct.title 'Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1JZV _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-bulge, A-RNA, HIV-1 SL2, 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 1 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1JZV 1JZV ? ? ? 2 2 PDB 1JZV 1JZV ? ? ? # 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 1JZV A 1 ? 8 ? 1JZV 1 ? 8 ? 1 8 2 2 1JZV B 1 ? 9 ? 1JZV 9 ? 17 ? 9 17 3 1 1JZV C 1 ? 8 ? 1JZV 21 ? 28 ? 21 28 4 2 1JZV D 1 ? 9 ? 1JZV 29 ? 37 ? 29 37 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,F,G 2 1 C,D,E,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_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 6 "O3'" ? ? ? 1_555 A 5BU 7 P ? ? A C 6 A 5BU 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A 5BU 7 "O3'" ? ? ? 1_555 A G 8 P ? ? A 5BU 7 A G 8 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? B G 7 "O3'" ? ? ? 1_555 B 5IC 8 P ? ? B G 15 B 5IC 16 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? B 5IC 8 "O3'" ? ? ? 1_555 B C 9 P ? ? B 5IC 16 B C 17 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale5 covale both ? C C 6 "O3'" ? ? ? 1_555 C 5BU 7 P ? ? C C 26 C 5BU 27 1_555 ? ? ? ? ? ? ? 1.621 ? ? covale6 covale both ? C 5BU 7 "O3'" ? ? ? 1_555 C G 8 P ? ? C 5BU 27 C G 28 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale7 covale both ? D G 7 "O3'" ? ? ? 1_555 D 5IC 8 P ? ? D G 35 D 5IC 36 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale8 covale both ? D 5IC 8 "O3'" ? ? ? 1_555 D C 9 P ? ? D 5IC 36 D C 37 1_555 ? ? ? ? ? ? ? 1.602 ? ? metalc1 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? C MG 300 C HOH 301 1_555 ? ? ? ? ? ? ? 2.202 ? ? metalc2 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? C MG 300 C HOH 302 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc3 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? C MG 300 C HOH 303 1_555 ? ? ? ? ? ? ? 2.026 ? ? metalc4 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? C MG 300 C HOH 304 1_555 ? ? ? ? ? ? ? 2.263 ? ? metalc5 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? C MG 300 C HOH 306 1_555 ? ? ? ? ? ? ? 2.283 ? ? metalc6 metalc ? ? E MG . MG ? ? ? 1_555 I HOH . O ? ? C MG 300 D HOH 305 1_555 ? ? ? ? ? ? ? 2.192 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 1 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 1 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 1 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B 5IC 8 N3 ? ? A G 2 B 5IC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B 5IC 8 O2 ? ? A G 2 B 5IC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B 5IC 8 N4 ? ? A G 2 B 5IC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 4 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 4 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 4 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A 5BU 7 N3 ? ? ? 1_555 B A 2 N1 ? ? A 5BU 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A 5BU 7 O4 ? ? ? 1_555 B A 2 N6 ? ? A 5BU 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B G 3 N2 ? ? ? 1_555 D A 5 N3 ? ? B G 11 D A 33 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog24 hydrog ? ? B A 5 N3 ? ? ? 1_555 D G 3 N2 ? ? B A 13 D G 31 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog25 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 9 N3 ? ? C G 21 D C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 9 O2 ? ? C G 21 D C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 9 N4 ? ? C G 21 D C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 2 N1 ? ? ? 1_555 D 5IC 8 N3 ? ? C G 22 D 5IC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 2 N2 ? ? ? 1_555 D 5IC 8 O2 ? ? C G 22 D 5IC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 2 O6 ? ? ? 1_555 D 5IC 8 N4 ? ? C G 22 D 5IC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 7 N1 ? ? C C 23 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 23 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 7 N2 ? ? C C 23 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 6 N3 ? ? C G 24 D C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 6 O2 ? ? C G 24 D C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 6 N4 ? ? C G 24 D C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C A 5 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 25 D U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C A 5 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 25 D U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C C 6 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 26 D G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C C 6 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 26 D G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C C 6 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 26 D G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C 5BU 7 N3 ? ? ? 1_555 D A 2 N1 ? ? C 5BU 27 D A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C 5BU 7 O4 ? ? ? 1_555 D A 2 N6 ? ? C 5BU 27 D A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C G 8 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 28 D C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C G 8 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 28 D C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 8 O6 ? ? ? 1_555 D C 1 N4 ? ? C G 28 D C 29 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 ? H HOH . ? C HOH 301 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 302 ? 1_555 90.4 ? 2 O ? H HOH . ? C HOH 301 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 303 ? 1_555 94.2 ? 3 O ? H HOH . ? C HOH 302 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 303 ? 1_555 90.5 ? 4 O ? H HOH . ? C HOH 301 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 304 ? 1_555 168.3 ? 5 O ? H HOH . ? C HOH 302 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 304 ? 1_555 78.8 ? 6 O ? H HOH . ? C HOH 303 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 304 ? 1_555 81.5 ? 7 O ? H HOH . ? C HOH 301 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 306 ? 1_555 100.9 ? 8 O ? H HOH . ? C HOH 302 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 306 ? 1_555 167.3 ? 9 O ? H HOH . ? C HOH 303 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 306 ? 1_555 83.0 ? 10 O ? H HOH . ? C HOH 304 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? H HOH . ? C HOH 306 ? 1_555 89.4 ? 11 O ? H HOH . ? C HOH 301 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? I HOH . ? D HOH 305 ? 1_555 93.4 ? 12 O ? H HOH . ? C HOH 302 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? I HOH . ? D HOH 305 ? 1_555 90.5 ? 13 O ? H HOH . ? C HOH 303 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? I HOH . ? D HOH 305 ? 1_555 172.3 ? 14 O ? H HOH . ? C HOH 304 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? I HOH . ? D HOH 305 ? 1_555 91.2 ? 15 O ? H HOH . ? C HOH 306 ? 1_555 MG ? E MG . ? C MG 300 ? 1_555 O ? I HOH . ? D HOH 305 ? 1_555 94.5 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id C _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 300 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG C 300' # 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 6 HOH H . ? HOH C 301 . ? 1_555 ? 2 AC1 6 HOH H . ? HOH C 302 . ? 1_555 ? 3 AC1 6 HOH H . ? HOH C 303 . ? 1_555 ? 4 AC1 6 HOH H . ? HOH C 304 . ? 1_555 ? 5 AC1 6 HOH H . ? HOH C 306 . ? 1_555 ? 6 AC1 6 HOH I . ? HOH D 305 . ? 1_555 ? # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G C 24 ? ? 0.057 'SIDE CHAIN' 2 1 C D 29 ? ? 0.072 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5BU 7 A 5BU 7 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 B 5IC 8 B 5IC 16 ? C "5-IODO-CYTIDINE-5'-MONOPHOSPHATE" 3 C 5BU 7 C 5BU 27 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 4 D 5IC 8 D 5IC 36 ? C "5-IODO-CYTIDINE-5'-MONOPHOSPHATE" # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 5IC "O2'" O N N 35 5IC "C2'" C N S 36 5IC "C3'" C N S 37 5IC "O3'" O N N 38 5IC "C4'" C N R 39 5IC "O4'" O N N 40 5IC "C1'" C N R 41 5IC N1 N N N 42 5IC C6 C N N 43 5IC C5 C N N 44 5IC I I N N 45 5IC C4 C N N 46 5IC N3 N N N 47 5IC C2 C N N 48 5IC O2 O N N 49 5IC N4 N N N 50 5IC "C5'" C N N 51 5IC "O5'" O N N 52 5IC P P N N 53 5IC OP1 O N N 54 5IC OP3 O N N 55 5IC OP2 O N N 56 5IC "HO2'" H N N 57 5IC "H2'" H N N 58 5IC "H3'" H N N 59 5IC "HO3'" H N N 60 5IC "H4'" H N N 61 5IC "H1'" H N N 62 5IC H6 H N N 63 5IC H41 H N N 64 5IC H42 H N N 65 5IC "H5'" H N N 66 5IC "H5''" H N N 67 5IC HOP3 H N N 68 5IC HOP2 H N N 69 A OP3 O N N 70 A P P N N 71 A OP1 O N N 72 A OP2 O N N 73 A "O5'" O N N 74 A "C5'" C N N 75 A "C4'" C N R 76 A "O4'" O N N 77 A "C3'" C N S 78 A "O3'" O N N 79 A "C2'" C N R 80 A "O2'" O N N 81 A "C1'" C N R 82 A N9 N Y N 83 A C8 C Y N 84 A N7 N Y N 85 A C5 C Y N 86 A C6 C Y N 87 A N6 N N N 88 A N1 N Y N 89 A C2 C Y N 90 A N3 N Y N 91 A C4 C Y N 92 A HOP3 H N N 93 A HOP2 H N N 94 A "H5'" H N N 95 A "H5''" H N N 96 A "H4'" H N N 97 A "H3'" H N N 98 A "HO3'" H N N 99 A "H2'" H N N 100 A "HO2'" H N N 101 A "H1'" H N N 102 A H8 H N N 103 A H61 H N N 104 A H62 H N N 105 A H2 H N N 106 C OP3 O N N 107 C P P N N 108 C OP1 O N N 109 C OP2 O N N 110 C "O5'" O N N 111 C "C5'" C N N 112 C "C4'" C N R 113 C "O4'" O N N 114 C "C3'" C N S 115 C "O3'" O N N 116 C "C2'" C N R 117 C "O2'" O N N 118 C "C1'" C N R 119 C N1 N N N 120 C C2 C N N 121 C O2 O N N 122 C N3 N N N 123 C C4 C N N 124 C N4 N N N 125 C C5 C N N 126 C C6 C N N 127 C HOP3 H N N 128 C HOP2 H N N 129 C "H5'" H N N 130 C "H5''" H N N 131 C "H4'" H N N 132 C "H3'" H N N 133 C "HO3'" H N N 134 C "H2'" H N N 135 C "HO2'" H N N 136 C "H1'" H N N 137 C H41 H N N 138 C H42 H N N 139 C H5 H N N 140 C H6 H N N 141 G OP3 O N N 142 G P P N N 143 G OP1 O N N 144 G OP2 O N N 145 G "O5'" O N N 146 G "C5'" C N N 147 G "C4'" C N R 148 G "O4'" O N N 149 G "C3'" C N S 150 G "O3'" O N N 151 G "C2'" C N R 152 G "O2'" O N N 153 G "C1'" C N R 154 G N9 N Y N 155 G C8 C Y N 156 G N7 N Y N 157 G C5 C Y N 158 G C6 C N N 159 G O6 O N N 160 G N1 N N N 161 G C2 C N N 162 G N2 N N N 163 G N3 N N N 164 G C4 C Y N 165 G HOP3 H N N 166 G HOP2 H N N 167 G "H5'" H N N 168 G "H5''" H N N 169 G "H4'" H N N 170 G "H3'" H N N 171 G "HO3'" H N N 172 G "H2'" H N N 173 G "HO2'" H N N 174 G "H1'" H N N 175 G H8 H N N 176 G H1 H N N 177 G H21 H N N 178 G H22 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 MG MG MG N N 183 U OP3 O N N 184 U P P N N 185 U OP1 O N N 186 U OP2 O N N 187 U "O5'" O N N 188 U "C5'" C N N 189 U "C4'" C N R 190 U "O4'" O N N 191 U "C3'" C N S 192 U "O3'" O N N 193 U "C2'" C N R 194 U "O2'" O N N 195 U "C1'" C N R 196 U N1 N N N 197 U C2 C N N 198 U O2 O N N 199 U N3 N N N 200 U C4 C N N 201 U O4 O N N 202 U C5 C N N 203 U C6 C N N 204 U HOP3 H N N 205 U HOP2 H N N 206 U "H5'" H N N 207 U "H5''" H N N 208 U "H4'" H N N 209 U "H3'" H N N 210 U "HO3'" H N N 211 U "H2'" H N N 212 U "HO2'" H N N 213 U "H1'" H N N 214 U H3 H N N 215 U H5 H N N 216 U H6 H N N 217 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 5IC "O2'" "C2'" sing N N 36 5IC "O2'" "HO2'" sing N N 37 5IC "C2'" "C3'" sing N N 38 5IC "C2'" "C1'" sing N N 39 5IC "C2'" "H2'" sing N N 40 5IC "C3'" "O3'" sing N N 41 5IC "C3'" "C4'" sing N N 42 5IC "C3'" "H3'" sing N N 43 5IC "O3'" "HO3'" sing N N 44 5IC "C4'" "O4'" sing N N 45 5IC "C4'" "C5'" sing N N 46 5IC "C4'" "H4'" sing N N 47 5IC "O4'" "C1'" sing N N 48 5IC "C1'" N1 sing N N 49 5IC "C1'" "H1'" sing N N 50 5IC N1 C6 sing N N 51 5IC N1 C2 sing N N 52 5IC C6 C5 doub N N 53 5IC C6 H6 sing N N 54 5IC C5 I sing N N 55 5IC C5 C4 sing N N 56 5IC C4 N3 doub N N 57 5IC C4 N4 sing N N 58 5IC N3 C2 sing N N 59 5IC C2 O2 doub N N 60 5IC N4 H41 sing N N 61 5IC N4 H42 sing N N 62 5IC "C5'" "O5'" sing N N 63 5IC "C5'" "H5'" sing N N 64 5IC "C5'" "H5''" sing N N 65 5IC "O5'" P sing N N 66 5IC P OP1 doub N N 67 5IC P OP3 sing N N 68 5IC P OP2 sing N N 69 5IC OP3 HOP3 sing N N 70 5IC OP2 HOP2 sing N N 71 A OP3 P sing N N 72 A OP3 HOP3 sing N N 73 A P OP1 doub N N 74 A P OP2 sing N N 75 A P "O5'" sing N N 76 A OP2 HOP2 sing N N 77 A "O5'" "C5'" sing N N 78 A "C5'" "C4'" sing N N 79 A "C5'" "H5'" sing N N 80 A "C5'" "H5''" sing N N 81 A "C4'" "O4'" sing N N 82 A "C4'" "C3'" sing N N 83 A "C4'" "H4'" sing N N 84 A "O4'" "C1'" sing N N 85 A "C3'" "O3'" sing N N 86 A "C3'" "C2'" sing N N 87 A "C3'" "H3'" sing N N 88 A "O3'" "HO3'" sing N N 89 A "C2'" "O2'" sing N N 90 A "C2'" "C1'" sing N N 91 A "C2'" "H2'" sing N N 92 A "O2'" "HO2'" sing N N 93 A "C1'" N9 sing N N 94 A "C1'" "H1'" sing N N 95 A N9 C8 sing Y N 96 A N9 C4 sing Y N 97 A C8 N7 doub Y N 98 A C8 H8 sing N N 99 A N7 C5 sing Y N 100 A C5 C6 sing Y N 101 A C5 C4 doub Y N 102 A C6 N6 sing N N 103 A C6 N1 doub Y N 104 A N6 H61 sing N N 105 A N6 H62 sing N N 106 A N1 C2 sing Y N 107 A C2 N3 doub Y N 108 A C2 H2 sing N N 109 A N3 C4 sing Y N 110 C OP3 P sing N N 111 C OP3 HOP3 sing N N 112 C P OP1 doub N N 113 C P OP2 sing N N 114 C P "O5'" sing N N 115 C OP2 HOP2 sing N N 116 C "O5'" "C5'" sing N N 117 C "C5'" "C4'" sing N N 118 C "C5'" "H5'" sing N N 119 C "C5'" "H5''" sing N N 120 C "C4'" "O4'" sing N N 121 C "C4'" "C3'" sing N N 122 C "C4'" "H4'" sing N N 123 C "O4'" "C1'" sing N N 124 C "C3'" "O3'" sing N N 125 C "C3'" "C2'" sing N N 126 C "C3'" "H3'" sing N N 127 C "O3'" "HO3'" sing N N 128 C "C2'" "O2'" sing N N 129 C "C2'" "C1'" sing N N 130 C "C2'" "H2'" sing N N 131 C "O2'" "HO2'" sing N N 132 C "C1'" N1 sing N N 133 C "C1'" "H1'" sing N N 134 C N1 C2 sing N N 135 C N1 C6 sing N N 136 C C2 O2 doub N N 137 C C2 N3 sing N N 138 C N3 C4 doub N N 139 C C4 N4 sing N N 140 C C4 C5 sing N N 141 C N4 H41 sing N N 142 C N4 H42 sing N N 143 C C5 C6 doub N N 144 C C5 H5 sing N N 145 C C6 H6 sing N N 146 G OP3 P sing N N 147 G OP3 HOP3 sing N N 148 G P OP1 doub N N 149 G P OP2 sing N N 150 G P "O5'" sing N N 151 G OP2 HOP2 sing N N 152 G "O5'" "C5'" sing N N 153 G "C5'" "C4'" sing N N 154 G "C5'" "H5'" sing N N 155 G "C5'" "H5''" sing N N 156 G "C4'" "O4'" sing N N 157 G "C4'" "C3'" sing N N 158 G "C4'" "H4'" sing N N 159 G "O4'" "C1'" sing N N 160 G "C3'" "O3'" sing N N 161 G "C3'" "C2'" sing N N 162 G "C3'" "H3'" sing N N 163 G "O3'" "HO3'" sing N N 164 G "C2'" "O2'" sing N N 165 G "C2'" "C1'" sing N N 166 G "C2'" "H2'" sing N N 167 G "O2'" "HO2'" sing N N 168 G "C1'" N9 sing N N 169 G "C1'" "H1'" sing N N 170 G N9 C8 sing Y N 171 G N9 C4 sing Y N 172 G C8 N7 doub Y N 173 G C8 H8 sing N N 174 G N7 C5 sing Y N 175 G C5 C6 sing N N 176 G C5 C4 doub Y N 177 G C6 O6 doub N N 178 G C6 N1 sing N N 179 G N1 C2 sing N N 180 G N1 H1 sing N N 181 G C2 N2 sing N N 182 G C2 N3 doub N N 183 G N2 H21 sing N N 184 G N2 H22 sing N N 185 G N3 C4 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 U OP3 P sing N N 189 U OP3 HOP3 sing N N 190 U P OP1 doub N N 191 U P OP2 sing N N 192 U P "O5'" sing N N 193 U OP2 HOP2 sing N N 194 U "O5'" "C5'" sing N N 195 U "C5'" "C4'" sing N N 196 U "C5'" "H5'" sing N N 197 U "C5'" "H5''" sing N N 198 U "C4'" "O4'" sing N N 199 U "C4'" "C3'" sing N N 200 U "C4'" "H4'" sing N N 201 U "O4'" "C1'" sing N N 202 U "C3'" "O3'" sing N N 203 U "C3'" "C2'" sing N N 204 U "C3'" "H3'" sing N N 205 U "O3'" "HO3'" sing N N 206 U "C2'" "O2'" sing N N 207 U "C2'" "C1'" sing N N 208 U "C2'" "H2'" sing N N 209 U "O2'" "HO2'" sing N N 210 U "C1'" N1 sing N N 211 U "C1'" "H1'" sing N N 212 U N1 C2 sing N N 213 U N1 C6 sing N N 214 U C2 O2 doub N N 215 U C2 N3 sing N N 216 U N3 C4 sing N N 217 U N3 H3 sing N N 218 U C4 O4 doub N N 219 U C4 C5 sing N N 220 U C5 C6 doub N N 221 U C5 H5 sing N N 222 U C6 H6 sing N N 223 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1JZV 'double helix' 1JZV 'a-form double helix' 1JZV 'bulge 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 G 1 1_555 B C 9 1_555 -0.221 -0.223 0.035 -4.792 -8.832 -3.201 1 A_G1:C17_B A 1 ? B 17 ? 19 1 1 A G 2 1_555 B 5IC 8 1_555 -0.522 -0.104 0.076 -4.921 -12.594 1.326 2 A_G2:5IC16_B A 2 ? B 16 ? 19 1 1 A C 3 1_555 B G 7 1_555 0.194 -0.185 0.204 -0.620 -6.523 1.263 3 A_C3:G15_B A 3 ? B 15 ? 19 1 1 A G 4 1_555 B C 6 1_555 -0.197 -0.162 0.305 8.927 0.354 2.316 4 A_G4:C14_B A 4 ? B 14 ? 19 1 1 A A 5 1_555 B U 4 1_555 0.090 0.027 0.077 10.080 -14.818 -7.134 5 A_A5:U12_B A 5 ? B 12 ? 20 1 1 A C 6 1_555 B G 3 1_555 0.335 -0.093 0.023 8.752 -18.467 4.043 6 A_C6:G11_B A 6 ? B 11 ? 19 1 1 A 5BU 7 1_555 B A 2 1_555 -0.124 -0.116 -0.138 5.821 -12.291 2.835 7 A_5BU7:A10_B A 7 ? B 10 ? 20 1 1 A G 8 1_555 B C 1 1_555 -0.114 -0.144 0.141 5.538 -7.456 -0.291 8 A_G8:C9_B A 8 ? B 9 ? 19 1 1 C G 1 1_555 D C 9 1_555 -0.343 -0.234 -0.017 -3.107 -14.951 0.654 9 C_G21:C37_D C 21 ? D 37 ? 19 1 1 C G 2 1_555 D 5IC 8 1_555 -0.620 0.003 -0.180 -10.612 -12.778 3.748 10 C_G22:5IC36_D C 22 ? D 36 ? 19 1 1 C C 3 1_555 D G 7 1_555 0.121 -0.074 -0.078 -4.713 -9.240 -0.584 11 C_C23:G35_D C 23 ? D 35 ? 19 1 1 C G 4 1_555 D C 6 1_555 -0.152 -0.081 0.294 8.079 0.694 2.467 12 C_G24:C34_D C 24 ? D 34 ? 19 1 1 C A 5 1_555 D U 4 1_555 0.099 -0.073 0.057 9.865 -15.159 -3.846 13 C_A25:U32_D C 25 ? D 32 ? 20 1 1 C C 6 1_555 D G 3 1_555 0.405 -0.201 0.142 7.505 -18.315 2.380 14 C_C26:G31_D C 26 ? D 31 ? 19 1 1 C 5BU 7 1_555 D A 2 1_555 -0.258 -0.125 -0.112 -3.322 -14.393 1.938 15 C_5BU27:A30_D C 27 ? D 30 ? 20 1 1 C G 8 1_555 D C 1 1_555 -0.231 -0.120 0.196 -0.903 -2.730 1.274 16 C_G28:C29_D C 28 ? D 29 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 9 1_555 A G 2 1_555 B 5IC 8 1_555 0.160 -1.647 3.166 0.297 6.355 32.060 -3.941 -0.237 2.798 11.367 -0.531 32.669 1 AA_G1G2:5IC16C17_BB A 1 ? B 17 ? A 2 ? B 16 ? 1 A G 2 1_555 B 5IC 8 1_555 A C 3 1_555 B G 7 1_555 0.619 -1.687 3.180 0.870 0.538 33.440 -3.017 -0.936 3.168 0.934 -1.512 33.455 2 AA_G2C3:G155IC16_BB A 2 ? B 16 ? A 3 ? B 15 ? 1 A C 3 1_555 B G 7 1_555 A G 4 1_555 B C 6 1_555 0.528 -2.104 2.922 -2.181 0.987 24.718 -5.153 -1.803 2.781 2.298 5.079 24.831 3 AA_C3G4:C14G15_BB A 3 ? B 15 ? A 4 ? B 14 ? 1 A G 4 1_555 B C 6 1_555 A A 5 1_555 B U 4 1_555 0.832 -2.398 3.181 -2.292 6.329 45.461 -3.575 -1.248 2.798 8.136 2.947 45.931 4 AA_G4A5:U12C14_BB A 4 ? B 14 ? A 5 ? B 12 ? 1 A A 5 1_555 B U 4 1_555 A C 6 1_555 B G 3 1_555 0.940 -1.715 3.168 -0.685 4.519 36.335 -3.311 -1.584 2.923 7.212 1.093 36.611 5 AA_A5C6:G11U12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A C 6 1_555 B G 3 1_555 A 5BU 7 1_555 B A 2 1_555 -0.740 -2.313 3.318 -0.457 8.792 28.155 -6.257 1.365 2.508 17.538 0.911 29.473 6 AA_C65BU7:A10G11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A 5BU 7 1_555 B A 2 1_555 A G 8 1_555 B C 1 1_555 -0.040 -1.608 3.190 -2.419 12.605 30.376 -4.738 -0.294 2.351 22.818 4.379 32.918 7 AA_5BU7G8:C9A10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 C G 1 1_555 D C 9 1_555 C G 2 1_555 D 5IC 8 1_555 0.081 -2.200 3.342 -1.167 10.307 30.181 -5.722 -0.342 2.471 19.098 2.162 31.874 8 CC_G21G22:5IC36C37_DD C 21 ? D 37 ? C 22 ? D 36 ? 1 C G 2 1_555 D 5IC 8 1_555 C C 3 1_555 D G 7 1_555 -0.824 -1.053 3.101 -1.667 6.519 33.542 -2.742 1.158 2.887 11.157 2.852 34.191 9 CC_G22C23:G355IC36_DD C 22 ? D 36 ? C 23 ? D 35 ? 1 C C 3 1_555 D G 7 1_555 C G 4 1_555 D C 6 1_555 1.089 -2.064 2.882 -3.554 6.811 24.964 -6.012 -3.164 2.082 15.301 7.983 26.102 10 CC_C23G24:C34G35_DD C 23 ? D 35 ? C 24 ? D 34 ? 1 C G 4 1_555 D C 6 1_555 C A 5 1_555 D U 4 1_555 0.998 -2.511 3.130 -1.400 11.662 41.164 -4.442 -1.489 2.333 16.193 1.944 42.737 11 CC_G24A25:U32C34_DD C 24 ? D 34 ? C 25 ? D 32 ? 1 C A 5 1_555 D U 4 1_555 C C 6 1_555 D G 3 1_555 0.697 -1.655 3.183 -0.804 4.567 36.538 -3.204 -1.206 2.946 7.248 1.276 36.821 12 CC_A25C26:G31U32_DD C 25 ? D 32 ? C 26 ? D 31 ? 1 C C 6 1_555 D G 3 1_555 C 5BU 7 1_555 D A 2 1_555 -0.962 -2.285 3.497 1.916 10.124 27.541 -6.551 2.284 2.449 20.384 -3.858 29.370 13 CC_C265BU27:A30G31_DD C 26 ? D 31 ? C 27 ? D 30 ? 1 C 5BU 7 1_555 D A 2 1_555 C G 8 1_555 D C 1 1_555 0.657 -1.377 3.077 -1.321 10.331 31.946 -3.867 -1.328 2.495 18.176 2.324 33.559 14 CC_5BU27G28:C29A30_DD C 27 ? D 30 ? C 28 ? D 29 ? # _atom_sites.entry_id 1JZV _atom_sites.fract_transf_matrix[1][1] 0.021834 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.021834 _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] 0.011154 _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 BR C I MG N O P # loop_