data_1ZFM # _entry.id 1ZFM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1ZFM pdb_00001zfm 10.2210/pdb1zfm/pdb NDB BD0086 ? ? RCSB RCSB032663 ? ? WWPDB D_1000032663 ? ? # 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 2005-05-10 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' software 5 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # _database_PDB_caveat.id 1 _database_PDB_caveat.text 'chirality error at C1 (chain A)' # _pdbx_database_status.entry_id 1ZFM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2005-04-20 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1P4Y . unspecified PDB 1P4Z . unspecified PDB 1DCW . unspecified PDB 1DCV . unspecified PDB 1ZEW . unspecified PDB 1ZEX . unspecified PDB 1ZEY . unspecified PDB 1ZEZ . unspecified PDB 1ZF0 . unspecified PDB 1ZF1 . unspecified PDB 1ZF2 . unspecified PDB 1ZF3 . unspecified PDB 1ZF4 . unspecified PDB 1ZF5 . unspecified PDB 1ZF6 . unspecified PDB 1ZF7 . unspecified PDB 1ZF8 . unspecified PDB 1ZF9 . unspecified PDB 1ZFA . unspecified PDB 1ZFB . unspecified PDB 1ZFC . unspecified PDB 1ZFE . unspecified PDB 1ZFF . unspecified PDB 1ZFG . unspecified PDB 1ZFH . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hays, F.A.' 1 'Teegarden, A.T.' 2 'Jones, Z.J.R.' 3 'Harms, M.' 4 'Raup, D.' 5 'Watson, J.' 6 'Cavaliere, E.' 7 'Ho, P.S.' 8 # _citation.id primary _citation.title 'How sequence defines structure: a crystallographic map of DNA structure and conformation.' _citation.journal_abbrev Proc.Natl.Acad.Sci.Usa _citation.journal_volume 102 _citation.page_first 7157 _citation.page_last 7162 _citation.year 2005 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15870206 _citation.pdbx_database_id_DOI 10.1073/pnas.0409455102 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Teegarden, A.' 2 ? primary 'Jones, Z.J.' 3 ? primary 'Harms, M.' 4 ? primary 'Raup, D.' 5 ? primary 'Watson, J.' 6 ? primary 'Cavaliere, E.' 7 ? primary 'Ho, P.S.' 8 ? # 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(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3'" 3045.993 2 ? ? ? ? 2 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DG)(DC)(DT)(DA)(DG)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGCTAGCGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DG n 1 4 DC n 1 5 DT n 1 6 DA n 1 7 DG n 1 8 DC n 1 9 DG n 1 10 DG 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 ;DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. ; # 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 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 DT 5 15 15 DT T B . n B 1 6 DA 6 16 16 DA A B . n B 1 7 DG 7 17 17 DG G B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 21 21 HOH HOH A . C 2 HOH 2 22 22 HOH HOH A . C 2 HOH 3 23 23 HOH HOH A . C 2 HOH 4 25 25 HOH HOH A . C 2 HOH 5 26 26 HOH HOH A . C 2 HOH 6 27 27 HOH HOH A . C 2 HOH 7 29 29 HOH HOH A . C 2 HOH 8 32 32 HOH HOH A . C 2 HOH 9 34 34 HOH HOH A . C 2 HOH 10 35 35 HOH HOH A . C 2 HOH 11 36 36 HOH HOH A . C 2 HOH 12 37 37 HOH HOH A . C 2 HOH 13 46 46 HOH HOH A . C 2 HOH 14 49 49 HOH HOH A . C 2 HOH 15 52 52 HOH HOH A . C 2 HOH 16 53 53 HOH HOH A . C 2 HOH 17 55 55 HOH HOH A . C 2 HOH 18 61 61 HOH HOH A . C 2 HOH 19 62 62 HOH HOH A . C 2 HOH 20 64 64 HOH HOH A . D 2 HOH 1 30 30 HOH HOH B . D 2 HOH 2 31 31 HOH HOH B . D 2 HOH 3 38 38 HOH HOH B . D 2 HOH 4 39 39 HOH HOH B . D 2 HOH 5 41 41 HOH HOH B . D 2 HOH 6 42 42 HOH HOH B . D 2 HOH 7 43 43 HOH HOH B . D 2 HOH 8 44 44 HOH HOH B . D 2 HOH 9 45 45 HOH HOH B . D 2 HOH 10 47 47 HOH HOH B . D 2 HOH 11 50 50 HOH HOH B . D 2 HOH 12 51 51 HOH HOH B . D 2 HOH 13 56 56 HOH HOH B . D 2 HOH 14 57 57 HOH HOH B . D 2 HOH 15 58 58 HOH HOH B . D 2 HOH 16 59 59 HOH HOH B . D 2 HOH 17 60 60 HOH HOH B . D 2 HOH 18 63 63 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 DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 REFMAC 5.2.0005 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran ? 3 EPMR . ? ? ? ? phasing ? ? ? 4 # _cell.entry_id 1ZFM _cell.length_a 63.891 _cell.length_b 24.303 _cell.length_c 40.388 _cell.angle_alpha 90.00 _cell.angle_beta 122.55 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZFM _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1ZFM _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.17 _exptl_crystal.density_percent_sol 43.30 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00' _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'Na Cacodylate' ? ? ? 1 2 1 CaCl2 ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'Na Cacodylate' ? ? ? 1 7 2 CaCl2 ? ? ? 1 8 2 MPD ? ? ? 1 9 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2002-12-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RUH3R' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1ZFM _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 99.000 _reflns.d_resolution_high 2.200 _reflns.number_obs 2577 _reflns.number_all ? _reflns.percent_possible_obs 92.3 _reflns.pdbx_Rmerge_I_obs 0.048 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.6000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.28 _reflns_shell.percent_possible_all 77.1 _reflns_shell.Rmerge_I_obs 0.224 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.000 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1ZFM _refine.ls_number_reflns_obs 2235 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 17.11 _refine.ls_d_res_high 2.20 _refine.ls_percent_reflns_obs 100.0 _refine.ls_R_factor_obs 0.275 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.266 _refine.ls_R_factor_R_free 0.364 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.400 _refine.ls_number_reflns_R_free 233 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.880 _refine.correlation_coeff_Fo_to_Fc_free 0.668 _refine.B_iso_mean 18.04 _refine.aniso_B[1][1] -0.33000 _refine.aniso_B[2][2] 1.19000 _refine.aniso_B[3][3] -0.87000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] -0.01000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'STRUCTURE IS NOT FULLY REFINED. REPEA BD0028 FROM SAME LAB. WILL BE UPDATED AS BETTER DATA IS OBTAINE TO CITATION.' _refine.pdbx_starting_model 'NDB ENTRY BD0028' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAWIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.589 _refine.pdbx_overall_ESU_R_Free 0.369 _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 404 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 442 _refine_hist.d_res_high 2.20 _refine_hist.d_res_low 17.11 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.032 0.021 ? 452 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 5.559 3.000 ? 694 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.217 0.200 ? 78 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.017 0.020 ? 208 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.432 0.200 ? 245 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.429 0.200 ? 240 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.359 0.200 ? 50 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.308 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.000 3.000 ? 656 'X-RAY DIFFRACTION' ? r_scangle_it 4.429 4.500 ? 694 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.20 _refine_ls_shell.d_res_low 2.26 _refine_ls_shell.number_reflns_R_work 123 _refine_ls_shell.R_factor_R_work 0.354 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.361 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1ZFM _struct.title 'AGC Duplex B-DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'Crystallographic Screen, DNA Structure, Holliday Junction, Molecular Structure, DNA' _struct_keywords.entry_id 1ZFM _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1ZFM _struct_ref.pdbx_db_accession 1ZFM _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 1ZFM A 1 ? 10 ? 1ZFM 1 ? 10 ? 1 10 2 1 1ZFM B 1 ? 10 ? 1ZFM 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog9 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N4 A DC 4 ? ? O6 B DG 17 ? ? 1.94 2 1 "O3'" B DC 12 ? ? O B HOH 57 ? ? 2.09 3 1 O6 A DG 3 ? ? N4 B DC 18 ? ? 2.12 4 1 N2 A DG 9 ? ? N3 B DC 12 ? ? 2.13 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O3'" _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 10 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OP1 _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 DC _pdbx_validate_symm_contact.auth_seq_id_2 14 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 4_455 _pdbx_validate_symm_contact.dist 2.08 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 1.555 1.512 0.043 0.007 N 2 1 "C1'" A DC 1 ? ? N1 A DC 1 ? ? 1.355 1.468 -0.113 0.014 N 3 1 N1 A DC 2 ? ? C6 A DC 2 ? ? 1.324 1.367 -0.043 0.006 N 4 1 C2 A DG 3 ? ? N3 A DG 3 ? ? 1.269 1.323 -0.054 0.008 N 5 1 C5 A DG 3 ? ? N7 A DG 3 ? ? 1.455 1.388 0.067 0.006 N 6 1 N7 A DG 3 ? ? C8 A DG 3 ? ? 1.351 1.305 0.046 0.006 N 7 1 "O3'" A DC 4 ? ? "C3'" A DC 4 ? ? 1.533 1.435 0.098 0.013 N 8 1 "C1'" A DC 4 ? ? N1 A DC 4 ? ? 1.595 1.488 0.107 0.013 N 9 1 C4 A DC 4 ? ? C5 A DC 4 ? ? 1.359 1.425 -0.066 0.008 N 10 1 C6 A DA 6 ? ? N6 A DA 6 ? ? 1.395 1.335 0.060 0.008 N 11 1 "O3'" A DG 7 ? ? "C3'" A DG 7 ? ? 1.381 1.419 -0.038 0.006 N 12 1 C4 A DG 7 ? ? C5 A DG 7 ? ? 1.325 1.379 -0.054 0.007 N 13 1 C8 A DG 7 ? ? N9 A DG 7 ? ? 1.320 1.374 -0.054 0.007 N 14 1 "O3'" A DG 7 ? ? P A DC 8 ? ? 1.507 1.607 -0.100 0.012 Y 15 1 C5 A DG 10 ? ? C6 A DG 10 ? ? 1.339 1.419 -0.080 0.010 N 16 1 C5 A DG 10 ? ? N7 A DG 10 ? ? 1.343 1.388 -0.045 0.006 N 17 1 "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? 1.592 1.518 0.074 0.012 N 18 1 "O3'" B DG 13 ? ? "C3'" B DG 13 ? ? 1.554 1.435 0.119 0.013 N 19 1 "O3'" B DT 15 ? ? "C3'" B DT 15 ? ? 1.526 1.435 0.091 0.013 N 20 1 "C1'" B DT 15 ? ? N1 B DT 15 ? ? 1.620 1.488 0.132 0.013 N 21 1 C5 B DT 15 ? ? C6 B DT 15 ? ? 1.381 1.339 0.042 0.007 N 22 1 P B DA 16 ? ? "O5'" B DA 16 ? ? 1.530 1.593 -0.063 0.010 N 23 1 N3 B DA 16 ? ? C4 B DA 16 ? ? 1.304 1.344 -0.040 0.006 N 24 1 C5 B DA 16 ? ? C6 B DA 16 ? ? 1.350 1.406 -0.056 0.009 N 25 1 C6 B DA 16 ? ? N1 B DA 16 ? ? 1.259 1.351 -0.092 0.007 N 26 1 N9 B DA 16 ? ? C4 B DA 16 ? ? 1.338 1.374 -0.036 0.006 N 27 1 C6 B DA 16 ? ? N6 B DA 16 ? ? 1.260 1.335 -0.075 0.008 N 28 1 "O3'" B DG 17 ? ? "C3'" B DG 17 ? ? 1.317 1.419 -0.102 0.006 N 29 1 "O3'" B DG 17 ? ? P B DC 18 ? ? 1.529 1.607 -0.078 0.012 Y 30 1 "O3'" B DC 18 ? ? "C3'" B DC 18 ? ? 1.527 1.435 0.092 0.013 N 31 1 "C1'" B DC 18 ? ? N1 B DC 18 ? ? 1.606 1.488 0.118 0.013 N 32 1 "O3'" B DG 19 ? ? "C3'" B DG 19 ? ? 1.337 1.419 -0.082 0.006 N 33 1 N3 B DG 19 ? ? C4 B DG 19 ? ? 1.404 1.350 0.054 0.007 N 34 1 C6 B DG 20 ? ? N1 B DG 20 ? ? 1.344 1.391 -0.047 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C1'" A DC 1 ? ? "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? 99.92 110.10 -10.18 1.00 N 2 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 94.52 102.40 -7.88 0.80 N 3 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 95.38 105.90 -10.52 0.80 N 4 1 N1 A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 123.56 114.30 9.26 1.40 N 5 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 97.11 108.00 -10.89 0.70 N 6 1 C6 A DC 1 ? ? N1 A DC 1 ? ? C2 A DC 1 ? ? 124.19 120.30 3.89 0.40 N 7 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 124.81 118.90 5.91 0.60 N 8 1 "C3'" A DC 1 ? ? "O3'" A DC 1 ? ? P A DC 2 ? ? 136.39 119.70 16.69 1.20 Y 9 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP1 A DC 2 ? ? 121.61 110.50 11.11 1.10 Y 10 1 "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? 100.16 109.40 -9.24 0.80 N 11 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 97.98 104.50 -6.52 0.40 N 12 1 "C1'" A DC 2 ? ? "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 115.62 110.30 5.32 0.70 N 13 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 99.78 105.90 -6.12 0.80 N 14 1 C5 A DC 2 ? ? C6 A DC 2 ? ? N1 A DC 2 ? ? 124.14 121.00 3.14 0.50 N 15 1 N9 A DG 3 ? ? "C1'" A DG 3 ? ? "C2'" A DG 3 ? ? 126.72 114.30 12.42 1.40 N 16 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 100.53 108.00 -7.47 0.70 N 17 1 C4 A DG 3 ? ? C5 A DG 3 ? ? C6 A DG 3 ? ? 114.07 118.80 -4.73 0.60 N 18 1 C4 A DG 3 ? ? C5 A DG 3 ? ? N7 A DG 3 ? ? 107.00 110.80 -3.80 0.40 N 19 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 109.54 113.10 -3.56 0.50 N 20 1 N9 A DG 3 ? ? C4 A DG 3 ? ? C5 A DG 3 ? ? 109.17 105.40 3.77 0.40 N 21 1 N3 A DG 3 ? ? C4 A DG 3 ? ? N9 A DG 3 ? ? 119.60 126.00 -6.40 0.60 N 22 1 C6 A DG 3 ? ? C5 A DG 3 ? ? N7 A DG 3 ? ? 138.88 130.40 8.48 0.60 N 23 1 N1 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 113.51 119.90 -6.39 0.60 N 24 1 C5 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 134.72 128.60 6.12 0.60 N 25 1 C8 A DG 3 ? ? N9 A DG 3 ? ? "C1'" A DG 3 ? ? 141.10 127.00 14.10 1.30 N 26 1 C4 A DG 3 ? ? N9 A DG 3 ? ? "C1'" A DG 3 ? ? 111.62 126.50 -14.88 1.30 N 27 1 "C5'" A DC 4 ? ? "C4'" A DC 4 ? ? "O4'" A DC 4 ? ? 91.19 109.30 -18.11 1.90 N 28 1 "C1'" A DC 4 ? ? "O4'" A DC 4 ? ? "C4'" A DC 4 ? ? 115.15 110.30 4.85 0.70 N 29 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? "C2'" A DC 4 ? ? 94.97 105.90 -10.93 0.80 N 30 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.23 108.30 1.93 0.30 N 31 1 C6 A DC 4 ? ? N1 A DC 4 ? ? C2 A DC 4 ? ? 113.97 120.30 -6.33 0.40 N 32 1 C2 A DC 4 ? ? N3 A DC 4 ? ? C4 A DC 4 ? ? 126.29 119.90 6.39 0.50 N 33 1 N3 A DC 4 ? ? C4 A DC 4 ? ? C5 A DC 4 ? ? 117.44 121.90 -4.46 0.40 N 34 1 C5 A DC 4 ? ? C6 A DC 4 ? ? N1 A DC 4 ? ? 128.86 121.00 7.86 0.50 N 35 1 N3 A DC 4 ? ? C4 A DC 4 ? ? N4 A DC 4 ? ? 122.78 118.00 4.78 0.70 N 36 1 C2 A DC 4 ? ? N1 A DC 4 ? ? "C1'" A DC 4 ? ? 130.34 118.80 11.54 1.10 N 37 1 "C1'" A DT 5 ? ? "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? 102.65 110.10 -7.45 1.00 N 38 1 "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? "C2'" A DT 5 ? ? 97.65 102.20 -4.55 0.70 N 39 1 "C3'" A DT 5 ? ? "C2'" A DT 5 ? ? "C1'" A DT 5 ? ? 94.91 102.40 -7.49 0.80 N 40 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 114.08 108.30 5.78 0.30 N 41 1 N3 A DT 5 ? ? C2 A DT 5 ? ? O2 A DT 5 ? ? 126.75 122.30 4.45 0.60 N 42 1 N3 A DT 5 ? ? C4 A DT 5 ? ? O4 A DT 5 ? ? 127.19 119.90 7.29 0.60 N 43 1 C5 A DT 5 ? ? C4 A DT 5 ? ? O4 A DT 5 ? ? 116.72 124.90 -8.18 0.70 N 44 1 "C3'" A DT 5 ? ? "O3'" A DT 5 ? ? P A DA 6 ? ? 108.31 119.70 -11.39 1.20 Y 45 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 123.18 118.60 4.58 0.60 N 46 1 C2 A DA 6 ? ? N3 A DA 6 ? ? C4 A DA 6 ? ? 107.16 110.60 -3.44 0.50 N 47 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N1 A DA 6 ? ? 113.04 117.70 -4.66 0.50 N 48 1 C4 A DA 6 ? ? C5 A DA 6 ? ? N7 A DA 6 ? ? 116.92 110.70 6.22 0.50 N 49 1 C5 A DA 6 ? ? N7 A DA 6 ? ? C8 A DA 6 ? ? 96.74 103.90 -7.16 0.50 N 50 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 120.56 113.80 6.76 0.50 N 51 1 C8 A DA 6 ? ? N9 A DA 6 ? ? C4 A DA 6 ? ? 103.15 105.80 -2.65 0.40 N 52 1 N9 A DA 6 ? ? C4 A DA 6 ? ? C5 A DA 6 ? ? 102.60 105.80 -3.20 0.40 N 53 1 C6 A DA 6 ? ? C5 A DA 6 ? ? N7 A DA 6 ? ? 123.54 132.30 -8.76 0.70 N 54 1 N1 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 128.64 118.60 10.04 0.60 N 55 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 118.32 123.70 -5.38 0.80 N 56 1 "C3'" A DA 6 ? ? "O3'" A DA 6 ? ? P A DG 7 ? ? 110.77 119.70 -8.93 1.20 Y 57 1 "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? 97.84 104.50 -6.66 0.40 N 58 1 "C5'" A DG 7 ? ? "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? 101.74 114.10 -12.36 1.80 N 59 1 N9 A DG 7 ? ? "C1'" A DG 7 ? ? "C2'" A DG 7 ? ? 125.84 114.30 11.54 1.40 N 60 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 98.78 108.00 -9.22 0.70 N 61 1 C2 A DG 7 ? ? N3 A DG 7 ? ? C4 A DG 7 ? ? 116.14 111.90 4.24 0.50 N 62 1 C4 A DG 7 ? ? C5 A DG 7 ? ? N7 A DG 7 ? ? 105.41 110.80 -5.39 0.40 N 63 1 N9 A DG 7 ? ? C4 A DG 7 ? ? C5 A DG 7 ? ? 110.54 105.40 5.14 0.40 N 64 1 N3 A DG 7 ? ? C4 A DG 7 ? ? N9 A DG 7 ? ? 121.54 126.00 -4.46 0.60 N 65 1 C6 A DG 7 ? ? C5 A DG 7 ? ? N7 A DG 7 ? ? 135.96 130.40 5.56 0.60 N 66 1 N1 A DG 7 ? ? C2 A DG 7 ? ? N2 A DG 7 ? ? 123.68 116.20 7.48 0.90 N 67 1 N3 A DG 7 ? ? C2 A DG 7 ? ? N2 A DG 7 ? ? 113.87 119.90 -6.03 0.70 N 68 1 "C3'" A DG 7 ? ? "O3'" A DG 7 ? ? P A DC 8 ? ? 103.56 119.70 -16.14 1.20 Y 69 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 115.62 108.30 7.32 0.30 N 70 1 N3 A DC 8 ? ? C4 A DC 8 ? ? N4 A DC 8 ? ? 122.30 118.00 4.30 0.70 N 71 1 "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 97.46 102.40 -4.94 0.80 N 72 1 N7 A DG 9 ? ? C8 A DG 9 ? ? N9 A DG 9 ? ? 109.66 113.10 -3.44 0.50 N 73 1 C8 A DG 9 ? ? N9 A DG 9 ? ? C4 A DG 9 ? ? 110.01 106.40 3.61 0.40 N 74 1 N9 A DG 9 ? ? C4 A DG 9 ? ? C5 A DG 9 ? ? 102.89 105.40 -2.51 0.40 N 75 1 "C1'" A DG 10 ? ? "O4'" A DG 10 ? ? "C4'" A DG 10 ? ? 102.76 110.10 -7.34 1.00 N 76 1 "C3'" A DG 10 ? ? "C2'" A DG 10 ? ? "C1'" A DG 10 ? ? 96.07 102.40 -6.33 0.80 N 77 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 116.33 108.30 8.03 0.30 N 78 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 128.79 125.10 3.69 0.60 N 79 1 C2 A DG 10 ? ? N3 A DG 10 ? ? C4 A DG 10 ? ? 105.65 111.90 -6.25 0.50 N 80 1 C4 A DG 10 ? ? C5 A DG 10 ? ? C6 A DG 10 ? ? 123.54 118.80 4.74 0.60 N 81 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 105.43 111.50 -6.07 0.50 N 82 1 C4 A DG 10 ? ? C5 A DG 10 ? ? N7 A DG 10 ? ? 113.59 110.80 2.79 0.40 N 83 1 C6 A DG 10 ? ? C5 A DG 10 ? ? N7 A DG 10 ? ? 122.85 130.40 -7.55 0.60 N 84 1 N1 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 127.72 119.90 7.82 0.60 N 85 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.50 108.30 6.20 0.30 N 86 1 "C3'" B DC 11 ? ? "O3'" B DC 11 ? ? P B DC 12 ? ? 127.71 119.70 8.01 1.20 Y 87 1 "C5'" B DC 12 ? ? "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 123.74 115.70 8.04 1.20 N 88 1 N3 B DC 12 ? ? C4 B DC 12 ? ? C5 B DC 12 ? ? 124.94 121.90 3.04 0.40 N 89 1 C4 B DC 12 ? ? C5 B DC 12 ? ? C6 B DC 12 ? ? 114.16 117.40 -3.24 0.50 N 90 1 "C3'" B DC 12 ? ? "O3'" B DC 12 ? ? P B DG 13 ? ? 127.58 119.70 7.88 1.20 Y 91 1 "O5'" B DG 13 ? ? P B DG 13 ? ? OP1 B DG 13 ? ? 97.76 105.70 -7.94 0.90 N 92 1 "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? 93.39 102.20 -8.81 0.70 N 93 1 "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? "C1'" B DG 13 ? ? 110.25 102.50 7.75 1.20 N 94 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? "C2'" B DG 13 ? ? 96.78 105.90 -9.12 0.80 N 95 1 N9 B DG 13 ? ? "C1'" B DG 13 ? ? "C2'" B DG 13 ? ? 127.29 114.30 12.99 1.40 N 96 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 113.02 108.30 4.72 0.30 N 97 1 C2 B DG 13 ? ? N3 B DG 13 ? ? C4 B DG 13 ? ? 115.45 111.90 3.55 0.50 N 98 1 C5 B DG 13 ? ? C6 B DG 13 ? ? N1 B DG 13 ? ? 116.30 111.50 4.80 0.50 N 99 1 N7 B DG 13 ? ? C8 B DG 13 ? ? N9 B DG 13 ? ? 117.59 113.10 4.49 0.50 N 100 1 C8 B DG 13 ? ? N9 B DG 13 ? ? C4 B DG 13 ? ? 100.22 106.40 -6.18 0.40 N 101 1 N9 B DG 13 ? ? C4 B DG 13 ? ? C5 B DG 13 ? ? 109.66 105.40 4.26 0.40 N 102 1 N1 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 112.39 119.90 -7.51 0.60 N 103 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DC 14 ? ? 128.37 119.70 8.67 1.20 Y 104 1 "O3'" B DG 13 ? ? P B DC 14 ? ? "O5'" B DC 14 ? ? 80.50 104.00 -23.50 1.90 Y 105 1 "O3'" B DG 13 ? ? P B DC 14 ? ? OP1 B DC 14 ? ? 121.77 110.50 11.27 1.10 Y 106 1 "O5'" B DC 14 ? ? "C5'" B DC 14 ? ? "C4'" B DC 14 ? ? 103.11 109.40 -6.29 0.80 N 107 1 "O4'" B DC 14 ? ? "C4'" B DC 14 ? ? "C3'" B DC 14 ? ? 98.62 104.50 -5.88 0.40 N 108 1 "C3'" B DC 14 ? ? "C2'" B DC 14 ? ? "C1'" B DC 14 ? ? 87.54 102.40 -14.86 0.80 N 109 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 112.51 108.30 4.21 0.30 N 110 1 C6 B DC 14 ? ? N1 B DC 14 ? ? C2 B DC 14 ? ? 126.08 120.30 5.78 0.40 N 111 1 N3 B DC 14 ? ? C4 B DC 14 ? ? C5 B DC 14 ? ? 124.38 121.90 2.48 0.40 N 112 1 C5 B DC 14 ? ? C6 B DC 14 ? ? N1 B DC 14 ? ? 116.39 121.00 -4.61 0.50 N 113 1 N1 B DT 15 ? ? "C1'" B DT 15 ? ? "C2'" B DT 15 ? ? 125.36 114.30 11.06 1.40 N 114 1 "O4'" B DT 15 ? ? "C1'" B DT 15 ? ? N1 B DT 15 ? ? 119.28 108.30 10.98 0.30 N 115 1 C6 B DT 15 ? ? N1 B DT 15 ? ? C2 B DT 15 ? ? 116.29 121.30 -5.01 0.50 N 116 1 N1 B DT 15 ? ? C2 B DT 15 ? ? N3 B DT 15 ? ? 119.53 114.60 4.93 0.60 N 117 1 N3 B DT 15 ? ? C2 B DT 15 ? ? O2 B DT 15 ? ? 117.06 122.30 -5.24 0.60 N 118 1 N3 B DT 15 ? ? C4 B DT 15 ? ? O4 B DT 15 ? ? 124.06 119.90 4.16 0.60 N 119 1 C4 B DT 15 ? ? C5 B DT 15 ? ? C7 B DT 15 ? ? 113.04 119.00 -5.96 0.60 N 120 1 "C3'" B DT 15 ? ? "O3'" B DT 15 ? ? P B DA 16 ? ? 127.95 119.70 8.25 1.20 Y 121 1 "O3'" B DT 15 ? ? P B DA 16 ? ? OP1 B DA 16 ? ? 125.74 110.50 15.24 1.10 Y 122 1 "O5'" B DA 16 ? ? P B DA 16 ? ? OP1 B DA 16 ? ? 84.68 105.70 -21.02 0.90 N 123 1 "O5'" B DA 16 ? ? "C5'" B DA 16 ? ? "C4'" B DA 16 ? ? 104.00 109.40 -5.40 0.80 N 124 1 "C1'" B DA 16 ? ? "O4'" B DA 16 ? ? "C4'" B DA 16 ? ? 114.92 110.30 4.62 0.70 N 125 1 C6 B DA 16 ? ? N1 B DA 16 ? ? C2 B DA 16 ? ? 114.28 118.60 -4.32 0.60 N 126 1 N1 B DA 16 ? ? C2 B DA 16 ? ? N3 B DA 16 ? ? 134.51 129.30 5.21 0.50 N 127 1 C2 B DA 16 ? ? N3 B DA 16 ? ? C4 B DA 16 ? ? 105.11 110.60 -5.49 0.50 N 128 1 N1 B DA 16 ? ? C6 B DA 16 ? ? N6 B DA 16 ? ? 113.80 118.60 -4.80 0.60 N 129 1 "O3'" B DA 16 ? ? P B DG 17 ? ? OP2 B DG 17 ? ? 118.80 110.50 8.30 1.10 Y 130 1 "O5'" B DG 17 ? ? P B DG 17 ? ? OP1 B DG 17 ? ? 91.50 105.70 -14.20 0.90 N 131 1 "O5'" B DG 17 ? ? P B DG 17 ? ? OP2 B DG 17 ? ? 125.76 110.70 15.06 1.20 N 132 1 P B DG 17 ? ? "O5'" B DG 17 ? ? "C5'" B DG 17 ? ? 101.85 120.90 -19.05 1.60 N 133 1 "C2'" B DG 17 ? ? "C3'" B DG 17 ? ? "O3'" B DG 17 ? ? 93.63 109.40 -15.77 2.50 N 134 1 N1 B DG 17 ? ? C6 B DG 17 ? ? O6 B DG 17 ? ? 114.08 119.90 -5.82 0.60 N 135 1 C5 B DG 17 ? ? C6 B DG 17 ? ? O6 B DG 17 ? ? 133.48 128.60 4.88 0.60 N 136 1 "C3'" B DG 17 ? ? "O3'" B DG 17 ? ? P B DC 18 ? ? 110.44 119.70 -9.26 1.20 Y 137 1 "C4'" B DC 18 ? ? "C3'" B DC 18 ? ? "C2'" B DC 18 ? ? 95.37 102.20 -6.83 0.70 N 138 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? "C2'" B DC 18 ? ? 99.72 105.90 -6.18 0.80 N 139 1 N1 B DC 18 ? ? "C1'" B DC 18 ? ? "C2'" B DC 18 ? ? 126.96 114.30 12.66 1.40 N 140 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 114.32 108.30 6.02 0.30 N 141 1 C6 B DC 18 ? ? N1 B DC 18 ? ? C2 B DC 18 ? ? 114.34 120.30 -5.96 0.40 N 142 1 N3 B DC 18 ? ? C4 B DC 18 ? ? C5 B DC 18 ? ? 119.49 121.90 -2.41 0.40 N 143 1 C5 B DC 18 ? ? C6 B DC 18 ? ? N1 B DC 18 ? ? 125.78 121.00 4.78 0.50 N 144 1 "C3'" B DC 18 ? ? "O3'" B DC 18 ? ? P B DG 19 ? ? 128.23 119.70 8.53 1.20 Y 145 1 "O3'" B DC 18 ? ? P B DG 19 ? ? OP2 B DG 19 ? ? 118.44 110.50 7.94 1.10 Y 146 1 "O5'" B DG 19 ? ? P B DG 19 ? ? OP1 B DG 19 ? ? 99.42 105.70 -6.28 0.90 N 147 1 "O5'" B DG 19 ? ? "C5'" B DG 19 ? ? "C4'" B DG 19 ? ? 102.99 109.40 -6.41 0.80 N 148 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? 100.33 104.50 -4.17 0.40 N 149 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? "C2'" B DG 19 ? ? 96.89 105.90 -9.01 0.80 N 150 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 89.71 108.00 -18.29 0.70 N 151 1 C4 B DG 19 ? ? C5 B DG 19 ? ? N7 B DG 19 ? ? 114.70 110.80 3.90 0.40 N 152 1 C8 B DG 19 ? ? N9 B DG 19 ? ? C4 B DG 19 ? ? 110.48 106.40 4.08 0.40 N 153 1 N9 B DG 19 ? ? C4 B DG 19 ? ? C5 B DG 19 ? ? 99.87 105.40 -5.53 0.40 N 154 1 N3 B DG 19 ? ? C4 B DG 19 ? ? N9 B DG 19 ? ? 130.92 126.00 4.92 0.60 N 155 1 C6 B DG 19 ? ? C5 B DG 19 ? ? N7 B DG 19 ? ? 125.42 130.40 -4.98 0.60 N 156 1 N1 B DG 19 ? ? C6 B DG 19 ? ? O6 B DG 19 ? ? 127.70 119.90 7.80 0.60 N 157 1 C5 B DG 19 ? ? C6 B DG 19 ? ? O6 B DG 19 ? ? 121.09 128.60 -7.51 0.60 N 158 1 C8 B DG 19 ? ? N9 B DG 19 ? ? "C1'" B DG 19 ? ? 117.57 127.00 -9.43 1.30 N 159 1 "O4'" B DG 20 ? ? "C4'" B DG 20 ? ? "C3'" B DG 20 ? ? 102.00 104.50 -2.50 0.40 N 160 1 "C1'" B DG 20 ? ? "O4'" B DG 20 ? ? "C4'" B DG 20 ? ? 115.04 110.30 4.74 0.70 N 161 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? "C2'" B DG 20 ? ? 98.61 105.90 -7.29 0.80 N 162 1 N1 B DG 20 ? ? C6 B DG 20 ? ? O6 B DG 20 ? ? 115.62 119.90 -4.28 0.60 N 163 1 C5 B DG 20 ? ? C6 B DG 20 ? ? O6 B DG 20 ? ? 133.11 128.60 4.51 0.60 N # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 1ZFM _ndb_struct_conf_na.feature 'b-form double helix' # 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 DC 1 1_555 B DG 10 1_555 -1.047 -0.559 -0.040 -1.134 -14.305 -3.549 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 1.001 -0.878 -0.184 -0.383 -7.146 3.013 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 0.102 -0.285 -0.119 -2.065 -13.733 -9.784 3 A_DG3:DC18_B A 3 ? B 18 ? ? 1 1 A DC 4 1_555 B DG 7 1_555 -0.700 -0.670 0.636 -21.724 -1.593 -9.112 4 A_DC4:DG17_B A 4 ? B 17 ? ? 1 1 A DT 5 1_555 B DA 6 1_555 -0.600 -0.483 -0.643 -2.687 -27.471 -8.807 5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 -1.004 -0.124 0.029 -10.529 -23.602 -6.952 6 A_DA6:DT15_B A 6 ? B 15 ? 20 1 1 A DG 7 1_555 B DC 4 1_555 2.029 0.073 0.178 2.932 -10.722 -15.242 7 A_DG7:DC14_B A 7 ? B 14 ? ? 1 1 A DC 8 1_555 B DG 3 1_555 0.868 -0.631 0.492 -3.577 -18.490 -11.138 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 1.578 -0.721 0.439 2.885 -7.496 -5.800 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 -0.014 -0.152 0.405 8.713 -18.896 -15.681 10 A_DG10:DC11_B A 10 ? B 11 ? ? ? # 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 DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.089 2.082 3.885 2.916 0.231 46.576 2.605 0.177 3.893 0.292 -3.683 46.662 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 -0.557 2.552 3.444 -0.865 -2.612 34.681 4.677 0.796 3.262 -4.373 1.449 34.787 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DC 4 1_555 B DG 7 1_555 -0.463 -0.645 3.557 -7.939 7.746 37.905 -1.949 -0.331 3.392 11.623 11.914 39.437 3 AA_DG3DC4:DG17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DC 4 1_555 B DG 7 1_555 A DT 5 1_555 B DA 6 1_555 -0.461 -0.026 2.728 10.353 -3.001 30.504 0.386 2.321 2.437 -5.493 -18.950 32.310 4 AA_DC4DT5:DA16DG17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 0.626 1.916 3.411 -4.702 -0.944 48.720 2.386 -1.122 3.306 -1.141 5.684 48.941 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DA 6 1_555 B DT 5 1_555 A DG 7 1_555 B DC 4 1_555 -0.242 0.130 3.287 0.281 1.367 37.645 0.023 0.412 3.287 2.117 -0.436 37.670 6 AA_DA6DG7:DC14DT15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DG 7 1_555 B DC 4 1_555 A DC 8 1_555 B DG 3 1_555 0.255 0.506 3.093 3.439 -7.070 33.941 1.852 0.063 2.943 -11.913 -5.794 34.813 7 AA_DG7DC8:DG13DC14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 0.521 0.755 3.295 5.634 0.380 38.391 1.090 -0.082 3.342 0.575 -8.511 38.789 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DG 10 1_555 B DC 1 1_555 0.153 0.464 3.703 -2.946 17.113 31.214 -2.162 -0.752 3.463 29.150 5.018 35.614 9 AA_DG9DG10:DC11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_initial_refinement_model.accession_code 1DCV _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.details 'NDB ENTRY BD0028' # _atom_sites.entry_id 1ZFM _atom_sites.fract_transf_matrix[1][1] 0.015652 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009990 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041147 _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] 0.029374 _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 N O P # loop_