data_2FZA # _entry.id 2FZA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 2FZA pdb_00002fza 10.2210/pdb2fza/pdb NDB UD0064 ? ? RCSB RCSB036490 ? ? WWPDB D_1000036490 ? ? # 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 2007-01-23 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 2FZA _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2006-02-09 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1UHX 'Original sequence crystallized under condition containing hexammine cobalt chloride.' unspecified PDB 1V3P 'Original sequence crystallized under lower potassium concentration.' unspecified PDB 1V3O 'Original sequence crystallized under higher potassium concentration.' unspecified PDB 1V3N 'Original sequence crystallized under higher potassium concentration.' unspecified PDB 1UE3 'Crystal structure used as a model in AMoRe.' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Ciengshin, T.' 2 'Juan, E.C.M.' 3 'Mitomi, K.' 4 'Takenaka, A.' 5 # _citation.id primary _citation.title ;Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation ; _citation.journal_abbrev 'Nucleosides Nucleotides Nucleic Acids' _citation.journal_volume 25 _citation.page_first 693 _citation.page_last 704 _citation.year 2006 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1525-7770 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16838856 _citation.pdbx_database_id_DOI 10.1080/15257770600686543 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Ciengshin, T.' 2 ? primary 'Juan, E.C.M.' 3 ? primary 'Sato, Y.' 4 ? primary 'Mitomi, K.' 5 ? primary 'Shimizu, S.' 6 ? primary 'Takenaka, A.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'" 2571.538 2 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 5 ? ? ? ? 4 water nat water 18.015 2 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(CBR)(DG)(DG)(DG)(DA)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGGGAGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 'SODIUM ION' NA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 CBR n 1 3 DG n 1 4 DG n 1 5 DG n 1 6 DA n 1 7 DG n 1 8 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'chemically synthesized' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # 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 DG 1 1 1 DG GUA A . n A 1 2 CBR 2 2 2 CBR CYT A . n A 1 3 DG 3 3 3 DG GUA A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 DG 5 5 5 DG GUA A . n A 1 6 DA 6 6 6 DA ADE A . n A 1 7 DG 7 7 7 DG GUA A . n A 1 8 DC 8 8 8 DC CYT A . n B 1 1 DG 1 1 1 DG GUA B . n B 1 2 CBR 2 2 2 CBR CYT B . n B 1 3 DG 3 3 3 DG GUA B . n B 1 4 DG 4 4 4 DG GUA B . n B 1 5 DG 5 5 5 DG GUA B . n B 1 6 DA 6 6 6 DA ADE B . n B 1 7 DG 7 7 7 DG GUA B . n B 1 8 DC 8 8 8 DC CYT B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 CA 1 11 11 CA CA A . D 3 NA 1 13 13 NA NA A . E 3 NA 1 15 15 NA NA A . F 3 NA 1 21 21 NA NA A . G 2 CA 1 12 12 CA CA B . H 3 NA 1 14 14 NA NA B . I 3 NA 1 22 22 NA NA B . J 4 HOH 1 32 32 HOH HOH A . K 4 HOH 1 31 31 HOH HOH B . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal SCALA . ? program 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran ? 1 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 2 PDB_EXTRACT 1.701 'Nov. 1, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 4 CCP4 '(SCALA)' ? ? ? ? 'data scaling' ? ? ? 5 AMoRE . ? ? ? ? phasing ? ? ? 6 # _cell.length_a 36.368 _cell.length_b 36.368 _cell.length_c 62.826 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.entry_id 2FZA _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 63' _symmetry.entry_id 2FZA _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 173 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.entry_id 2FZA _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.96 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;50mM sodium cacodylate, 10mM spermine tetrahydrochloride, 20mM calcium chloride, 100mM sodium chloride, 10%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 'sodium cacodylate' ? ? ? 1 2 1 'spermine tetrahydrochloride' ? ? ? 1 3 1 'calcium chloride' ? ? ? 1 4 1 'sodium chloride' ? ? ? 1 5 1 2-methyl-2,4-pentanediol ? ? ? 1 6 1 HOH ? ? ? 1 7 2 'sodium cacodylate' ? ? ? 1 8 2 'calcium chloride' ? ? ? 1 9 2 'sodium chloride' ? ? ? 1 10 2 HOH ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAC Science DIP-2040' _diffrn_detector.pdbx_collection_date 2003-06-03 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'ROTATED-INCLINED SI(111) DOUBLE CRYSTAL 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 0.900 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.900 _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44XU # _reflns.entry_id 2FZA _reflns.d_resolution_high 3.605 _reflns.d_resolution_low 31.496 _reflns.number_obs 525 _reflns.pdbx_Rmerge_I_obs 0.112 _reflns.pdbx_netI_over_sigmaI 3.100 _reflns.pdbx_Rsym_value 0.112 _reflns.pdbx_redundancy 14.500 _reflns.percent_possible_obs 93.600 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 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_diffrn_id _reflns_shell.pdbx_ordinal 3.60 3.79 ? 689 45 0.293 2.5 0.293 ? 15.30 95.30 ? ? ? 1 3.79 4.02 ? 753 46 0.349 2.2 0.349 ? 16.40 92.40 ? ? ? 2 4.02 4.30 ? 548 35 0.19 3.8 0.19 ? 15.70 91.40 ? ? ? 3 4.30 4.65 ? 661 44 0.142 4.6 0.142 ? 15.00 94.10 ? ? ? 4 4.65 5.09 ? 523 33 0.127 5.0 0.127 ? 15.80 92.70 ? ? ? 5 5.09 5.69 ? 508 36 0.097 6.7 0.097 ? 14.10 94.40 ? ? ? 6 5.69 6.57 ? 436 33 0.107 6.4 0.107 ? 13.20 95.20 ? ? ? 7 6.57 8.05 ? 338 27 0.104 5.5 0.104 ? 12.50 94.00 ? ? ? 8 8.05 11.38 ? 295 23 0.1 5.5 0.1 ? 12.80 92.60 ? ? ? 9 11.38 31.50 ? 148 17 0.082 5.7 0.082 ? 8.70 94.70 ? ? ? 10 # _refine.ls_d_res_high 3.600 _refine.ls_d_res_low 10.000 _refine.pdbx_ls_sigma_F 3.0 _refine.ls_percent_reflns_obs 85.600 _refine.ls_number_reflns_obs 458 _refine.ls_R_factor_R_work 0.294 _refine.ls_R_factor_R_free 0.329 _refine.ls_percent_reflns_R_free 12.300 _refine.ls_number_reflns_R_free 66 _refine.B_iso_mean ? _refine.solvent_model_param_bsol 300.000 _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.overall_FOM_work_R_set 0.831 _refine.entry_id 2FZA _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ;G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D52, 57-64 (1996). ; _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 334 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 343 _refine_hist.d_res_high 3.600 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.0 ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 3.600 3.760 8 . 37 . 0.361 0.469 . 7 . . 44 . 'X-RAY DIFFRACTION' 3.760 3.940 8 . 50 . 0.331 0.798 . 7 . . 57 . 'X-RAY DIFFRACTION' 3.940 4.170 8 . 50 . 0.223 0.314 . 11 . . 61 . 'X-RAY DIFFRACTION' 4.170 4.470 8 . 41 . 0.304 0.237 . 8 . . 49 . 'X-RAY DIFFRACTION' 4.470 4.870 8 . 55 . 0.204 0.423 . 8 . . 63 . 'X-RAY DIFFRACTION' 4.870 5.470 8 . 52 . 0.243 0.523 . 8 . . 60 . 'X-RAY DIFFRACTION' 5.470 6.550 8 . 53 . 0.261 0.158 . 7 . . 60 . 'X-RAY DIFFRACTION' 6.550 10.000 8 . 54 . 0.38 0.298 . 10 . . 64 . '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 dna_free.param dna_free.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 brc_rep.param brc.top 'X-RAY DIFFRACTION' 4 ion.param ion.top 'X-RAY DIFFRACTION' # _struct.entry_id 2FZA _struct.title 'Crystal structure of d(GCGGGAGC): the base-intercalated duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2FZA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'base-intercalated duplex, base-intercalated motif, sheared G:A pair, DNA, DNA hexaplex, deoxyribonucleic acid' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 2 ? H N N 3 ? I N N 3 ? J N N 4 ? K N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2FZA _struct_ref.pdbx_db_accession 2FZA _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2FZA A 1 ? 8 ? 2FZA 1 ? 8 ? 1 8 2 1 2FZA B 1 ? 8 ? 2FZA 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 18.1840000000 0.8660254038 -0.5000000000 0.0000000000 31.4956118848 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5000000000 0.8660254038 0.0000000000 -18.1840000000 -0.8660254038 -0.5000000000 0.0000000000 31.4956118848 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a DNA hexaplex generate from the three DNA duplex (X,Y,Z),(-Y,X-Y,Z) and (-X+Y,-X,Z).' _struct_biol.pdbx_parent_biol_id ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A CBR 2 P ? ? A DG 1 A CBR 2 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? A CBR 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A CBR 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B DG 1 "O3'" ? ? ? 1_555 B CBR 2 P ? ? B DG 1 B CBR 2 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale4 covale both ? B CBR 2 "O3'" ? ? ? 1_555 B DG 3 P ? ? B CBR 2 B DG 3 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? A DG 5 O6 ? ? ? 1_555 E NA . NA ? ? A DG 5 A NA 15 1_555 ? ? ? ? ? ? ? 2.826 ? ? metalc2 metalc ? ? A DG 7 N7 ? ? ? 1_555 F NA . NA ? ? A DG 7 A NA 21 1_555 ? ? ? ? ? ? ? 2.879 ? ? metalc3 metalc ? ? E NA . NA ? ? ? 1_555 B DG 5 O6 ? ? A NA 15 B DG 5 1_555 ? ? ? ? ? ? ? 2.795 ? ? metalc4 metalc ? ? B DG 7 N7 ? ? ? 1_555 I NA . NA ? ? B DG 7 B NA 22 1_555 ? ? ? ? ? ? ? 2.877 ? ? hydrog1 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DG 7 N1 ? ? A DG 1 B DG 7 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog2 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A CBR 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A CBR 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A CBR 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A CBR 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A CBR 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A CBR 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DA 6 N7 ? ? A DG 3 B DA 6 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog9 hydrog ? ? A DG 3 N3 ? ? ? 1_555 B DA 6 N6 ? ? A DG 3 B DA 6 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DG 3 N3 ? ? A DA 6 B DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DA 6 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DA 6 B DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog12 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DG 1 O6 ? ? A DG 7 B DG 1 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog13 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B CBR 2 N3 ? ? A DG 7 B CBR 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B CBR 2 O2 ? ? A DG 7 B CBR 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B CBR 2 N4 ? ? A DG 7 B CBR 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id O6 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id DG _pdbx_struct_conn_angle.ptnr1_label_seq_id 5 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id DG _pdbx_struct_conn_angle.ptnr1_auth_seq_id 5 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id E _pdbx_struct_conn_angle.ptnr2_label_comp_id NA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id NA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 15 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id O6 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id B _pdbx_struct_conn_angle.ptnr3_label_comp_id DG _pdbx_struct_conn_angle.ptnr3_label_seq_id 5 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id B _pdbx_struct_conn_angle.ptnr3_auth_comp_id DG _pdbx_struct_conn_angle.ptnr3_auth_seq_id 5 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 72.9 _pdbx_struct_conn_angle.value_esd ? # 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 B CA 12 ? 2 'BINDING SITE FOR RESIDUE CA B 12' AC2 Software A NA 13 ? 3 'BINDING SITE FOR RESIDUE NA A 13' AC3 Software B NA 14 ? 3 'BINDING SITE FOR RESIDUE NA B 14' AC4 Software A NA 15 ? 6 'BINDING SITE FOR RESIDUE NA A 15' AC5 Software A NA 21 ? 1 'BINDING SITE FOR RESIDUE NA A 21' AC6 Software B NA 22 ? 1 'BINDING SITE FOR RESIDUE NA B 22' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 DG B 3 ? DG B 3 . ? 2_665 ? 2 AC1 2 DG B 3 ? DG B 3 . ? 3_565 ? 3 AC2 3 DG A 4 ? DG A 4 . ? 2_665 ? 4 AC2 3 DG A 4 ? DG A 4 . ? 1_555 ? 5 AC2 3 DG A 4 ? DG A 4 . ? 3_565 ? 6 AC3 3 DG B 4 ? DG B 4 . ? 2_665 ? 7 AC3 3 DG B 4 ? DG B 4 . ? 1_555 ? 8 AC3 3 DG B 4 ? DG B 4 . ? 3_565 ? 9 AC4 6 DG A 5 ? DG A 5 . ? 2_665 ? 10 AC4 6 DG A 5 ? DG A 5 . ? 1_555 ? 11 AC4 6 DG A 5 ? DG A 5 . ? 3_565 ? 12 AC4 6 DG B 5 ? DG B 5 . ? 1_555 ? 13 AC4 6 DG B 5 ? DG B 5 . ? 3_565 ? 14 AC4 6 DG B 5 ? DG B 5 . ? 2_665 ? 15 AC5 1 DG A 7 ? DG A 7 . ? 1_555 ? 16 AC6 1 DG B 7 ? DG B 7 . ? 1_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CBR 2 A CBR 2 ? DC ? 2 B CBR 2 B CBR 2 ? DC ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CA 11 ? C CA . 2 1 A NA 13 ? D NA . 3 1 A NA 15 ? E NA . 4 1 B CA 12 ? G CA . 5 1 B NA 14 ? H NA . # 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 CA CA CA N N 1 CBR BR BR N N 2 CBR P P N N 3 CBR OP1 O N N 4 CBR OP2 O N N 5 CBR "O5'" O N N 6 CBR N1 N N N 7 CBR C6 C N N 8 CBR C2 C N N 9 CBR O2 O N N 10 CBR N3 N N N 11 CBR C4 C N N 12 CBR N4 N N N 13 CBR C5 C N N 14 CBR "C2'" C N N 15 CBR "C5'" C N N 16 CBR "C4'" C N R 17 CBR "O4'" O N N 18 CBR "C1'" C N R 19 CBR "C3'" C N S 20 CBR "O3'" O N N 21 CBR OP3 O N N 22 CBR HOP2 H N N 23 CBR H6 H N N 24 CBR H41 H N N 25 CBR H42 H N N 26 CBR "H2'" H N N 27 CBR "H2''" H N N 28 CBR "H5'" H N N 29 CBR "H5''" H N N 30 CBR "H4'" H N N 31 CBR "H1'" H N N 32 CBR "H3'" H N N 33 CBR "HO3'" H N N 34 CBR HOP3 H N N 35 DA OP3 O N N 36 DA P P N N 37 DA OP1 O N N 38 DA OP2 O N N 39 DA "O5'" O N N 40 DA "C5'" C N N 41 DA "C4'" C N R 42 DA "O4'" O N N 43 DA "C3'" C N S 44 DA "O3'" O N N 45 DA "C2'" C N N 46 DA "C1'" C N R 47 DA N9 N Y N 48 DA C8 C Y N 49 DA N7 N Y N 50 DA C5 C Y N 51 DA C6 C Y N 52 DA N6 N N N 53 DA N1 N Y N 54 DA C2 C Y N 55 DA N3 N Y N 56 DA C4 C Y N 57 DA HOP3 H N N 58 DA HOP2 H N N 59 DA "H5'" H N N 60 DA "H5''" H N N 61 DA "H4'" H N N 62 DA "H3'" H N N 63 DA "HO3'" H N N 64 DA "H2'" H N N 65 DA "H2''" H N N 66 DA "H1'" H N N 67 DA H8 H N N 68 DA H61 H N N 69 DA H62 H N N 70 DA H2 H N N 71 DC OP3 O N N 72 DC P P N N 73 DC OP1 O N N 74 DC OP2 O N N 75 DC "O5'" O N N 76 DC "C5'" C N N 77 DC "C4'" C N R 78 DC "O4'" O N N 79 DC "C3'" C N S 80 DC "O3'" O N N 81 DC "C2'" C N N 82 DC "C1'" C N R 83 DC N1 N N N 84 DC C2 C N N 85 DC O2 O N N 86 DC N3 N N N 87 DC C4 C N N 88 DC N4 N N N 89 DC C5 C N N 90 DC C6 C N N 91 DC HOP3 H N N 92 DC HOP2 H N N 93 DC "H5'" H N N 94 DC "H5''" H N N 95 DC "H4'" H N N 96 DC "H3'" H N N 97 DC "HO3'" H N N 98 DC "H2'" H N N 99 DC "H2''" H N N 100 DC "H1'" H N N 101 DC H41 H N N 102 DC H42 H N N 103 DC H5 H N N 104 DC H6 H N N 105 DG OP3 O N N 106 DG P P N N 107 DG OP1 O N N 108 DG OP2 O N N 109 DG "O5'" O N N 110 DG "C5'" C N N 111 DG "C4'" C N R 112 DG "O4'" O N N 113 DG "C3'" C N S 114 DG "O3'" O N N 115 DG "C2'" C N N 116 DG "C1'" C N R 117 DG N9 N Y N 118 DG C8 C Y N 119 DG N7 N Y N 120 DG C5 C Y N 121 DG C6 C N N 122 DG O6 O N N 123 DG N1 N N N 124 DG C2 C N N 125 DG N2 N N N 126 DG N3 N N N 127 DG C4 C Y N 128 DG HOP3 H N N 129 DG HOP2 H N N 130 DG "H5'" H N N 131 DG "H5''" H N N 132 DG "H4'" H N N 133 DG "H3'" H N N 134 DG "HO3'" H N N 135 DG "H2'" H N N 136 DG "H2''" H N N 137 DG "H1'" H N N 138 DG H8 H N N 139 DG H1 H N N 140 DG H21 H N N 141 DG H22 H N N 142 HOH O O N N 143 HOH H1 H N N 144 HOH H2 H N N 145 NA NA NA N N 146 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 HOH O H1 sing N N 148 HOH O H2 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2FZA 'double helix' 2FZA 'mismatched base pair' 2FZA 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 8 1_555 -0.342 -0.279 1.506 14.438 9.135 0.571 1 A_DG1:DC8_B A 1 ? B 8 ? 19 1 1 A CBR 2 1_555 B DG 7 1_555 -0.408 -0.149 0.224 24.176 4.342 -5.508 2 A_CBR2:DG7_B A 2 ? B 7 ? 19 1 1 A DG 3 1_555 B DA 6 1_555 6.060 -4.268 2.299 16.964 -22.677 13.829 3 A_DG3:DA6_B A 3 ? B 6 ? 11 9 1 A DA 6 1_555 B DG 3 1_555 -6.095 -4.259 2.320 -17.021 -22.456 13.850 4 A_DA6:DG3_B A 6 ? B 3 ? 11 9 1 A DG 7 1_555 B CBR 2 1_555 0.406 -0.104 0.209 -24.035 4.423 -5.389 5 A_DG7:CBR2_B A 7 ? B 2 ? 19 1 1 A DC 8 1_555 B DG 1 1_555 0.357 -0.237 1.513 -14.548 9.336 0.527 6 A_DC8:DG1_B A 8 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B DC 8 1_555 A CBR 2 1_555 B DG 7 1_555 0.080 -0.250 2.982 11.168 5.949 26.882 -1.632 1.990 2.688 11.990 -22.507 29.662 1 AA_DG1CBR2:DG7DC8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A CBR 2 1_555 B DG 7 1_555 A DG 3 1_555 B DA 6 1_555 0.499 1.131 3.550 -1.233 12.482 60.302 0.450 -0.553 3.687 12.282 1.214 61.473 2 AA_CBR2DG3:DA6DG7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A DA 6 1_555 B DG 3 1_555 A DG 7 1_555 B CBR 2 1_555 -0.497 1.136 3.543 1.376 12.721 60.325 0.443 0.558 3.682 12.507 -1.353 61.542 3 AA_DA6DG7:CBR2DG3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A DG 7 1_555 B CBR 2 1_555 A DC 8 1_555 B DG 1 1_555 -0.094 -0.237 2.988 -11.339 5.994 26.898 -1.609 -1.990 2.695 12.054 22.802 29.749 4 AA_DG7DC8:DG1CBR2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _atom_sites.entry_id 2FZA _atom_sites.fract_transf_matrix[1][1] 0.027497 _atom_sites.fract_transf_matrix[1][2] 0.015875 _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] 0.031750 _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] 0.015917 _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 CA N NA O P # loop_