data_2JJA # _entry.id 2JJA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.359 _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 2JJA pdb_00002jja 10.2210/pdb2jja/pdb PDBE EBI-35740 ? ? WWPDB D_1290035740 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2JJA _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2008-03-28 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Schlegel, M.K.' 1 'Essen, L.-O.' 2 'Meggers, E.' 3 # _citation.id primary _citation.title 'Duplex Structure of a Minimal Nucleic Acid.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 130 _citation.page_first 8158 _citation.page_last ? _citation.year 2008 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18529005 _citation.pdbx_database_id_DOI 10.1021/JA802788G # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schlegel, M.K.' 1 ? primary 'Essen, L.-O.' 2 ? primary 'Meggers, E.' 3 ? # _cell.entry_id 2JJA _cell.length_a 18.160 _cell.length_b 48.590 _cell.length_c 59.870 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JJA _symmetry.space_group_name_H-M 'I 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 # 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 GNA 2079.336 1 ? ? ? ;3'-(S)-((ZCY)P(ZGU)P(ZHP)P(ZAD)P(ZTH)P(ZHP)P(ZCY)P (ZGU))-2' ; 2 non-polymer syn 'COPPER (II) ION' 63.546 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 5 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 6 water nat water 18.015 80 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(ZCY)(ZGU)(ZHP)(ZAD)(ZTH)(ZHP)(ZCY)(ZGU)' _entity_poly.pdbx_seq_one_letter_code_can CGNAXNCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ZCY n 1 2 ZGU n 1 3 ZHP n 1 4 ZAD n 1 5 ZTH n 1 6 ZHP n 1 7 ZCY n 1 8 ZGU 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 'SYNTHETIC CONSTRUCT' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2JJA _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 2JJA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2JJA _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2JJA _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # 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 CU non-polymer . 'COPPER (II) ION' ? 'Cu 2' 63.546 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 ZAD 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE" ? 'C8 H12 N5 O5 P' 289.185 ZCY 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" ? 'C7 H12 N3 O6 P' 265.160 ZGU 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" ? 'C8 H12 N5 O6 P' 305.185 ZHP 'RNA linking' . "(S)-1'-(2',3'-DIHYDROXYPROPYL)-HYDROXYPYRIDONE" ? 'C9 H14 N O7 P' 279.184 ZTH non-polymer . "(S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" ? 'C8 H13 N2 O7 P' 280.172 # _exptl.entry_id 2JJA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 38.50 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '10% MPD, 40 MM SODIUM CACODYLATE, PH=5.5, 20 MM COBALT HEXAMINE, 80 MM NACL, 20 MM MGCL2.' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date 2007-11-24 _diffrn_detector.details MIRRORS # _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 0.80000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-1' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-1 _diffrn_source.pdbx_wavelength 0.80000 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2JJA _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.00 _reflns.d_resolution_high 1.30 _reflns.number_obs 7095 _reflns.number_all ? _reflns.percent_possible_obs 99.1 _reflns.pdbx_Rmerge_I_obs 0.08 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 20.40 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.2 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.30 _reflns_shell.d_res_low 1.33 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.30 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.00 _reflns_shell.pdbx_redundancy ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2JJA _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 6289 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.30 _refine.ls_percent_reflns_obs 99.0 _refine.ls_R_factor_obs 0.126 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.124 _refine.ls_R_factor_R_free 0.148 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.100 _refine.ls_number_reflns_R_free 479 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.978 _refine.correlation_coeff_Fo_to_Fc_free 0.978 _refine.B_iso_mean 13.68 _refine.aniso_B[1][1] -0.82000 _refine.aniso_B[2][2] 0.91000 _refine.aniso_B[3][3] -0.09000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _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 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.039 _refine.pdbx_overall_ESU_R_Free 0.038 _refine.overall_SU_ML 0.024 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.300 _refine.overall_SU_R_Cruickshank_DPI ? _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 136 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 80 _refine_hist.number_atoms_total 234 _refine_hist.d_res_high 1.30 _refine_hist.d_res_low 10.00 # 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 0.015 0.020 ? 160 'X-RAY DIFFRACTION' ? r_bond_other_d 0.007 0.020 ? 76 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.074 3.000 ? 219 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.955 3.000 ? 163 '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 0.061 0.200 ? 8 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.013 0.020 ? 87 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 32 'X-RAY DIFFRACTION' ? r_nbd_refined 0.092 0.200 ? 16 'X-RAY DIFFRACTION' ? r_nbd_other 0.188 0.200 ? 102 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.273 0.200 ? 54 'X-RAY DIFFRACTION' ? r_nbtor_other 0.085 0.200 ? 42 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.189 0.200 ? 46 '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 0.212 0.200 ? 16 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.545 0.200 ? 45 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.204 0.200 ? 25 '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_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.162 2.000 ? 195 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 3.755 3.000 ? 219 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? '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_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.30 _refine_ls_shell.d_res_low 1.33 _refine_ls_shell.number_reflns_R_work 432 _refine_ls_shell.R_factor_R_work 0.1910 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.2260 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 33 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2JJA _struct.title 'Crystal structure of GNA with synthetic copper base pair' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2JJA _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'NUCLEIC ACID, SYNTHETIC BASE PAIR, GLYCOL NUCLEIC ACID, GNA, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 5 ? H N N 6 ? # 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 one ? A ZCY 1 O2G ? ? ? 1_555 A ZGU 2 P ? ? A ZCY 1 A ZGU 2 1_555 ? ? ? ? ? ? ? 1.571 ? ? covale2 covale one ? A ZGU 2 O2G ? ? ? 1_555 A ZHP 3 P ? ? A ZGU 2 A ZHP 3 1_555 ? ? ? ? ? ? ? 1.561 ? ? covale3 covale one ? A ZHP 3 O2G ? ? ? 1_555 A ZAD 4 P ? ? A ZHP 3 A ZAD 4 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale4 covale one ? A ZAD 4 O2G ? ? ? 1_555 A ZTH 5 P ? ? A ZAD 4 A ZTH 5 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale5 covale one ? A ZTH 5 O2G ? ? ? 1_555 A ZHP 6 P ? ? A ZTH 5 A ZHP 6 1_555 ? ? ? ? ? ? ? 1.573 ? ? covale6 covale one ? A ZHP 6 O2G ? ? ? 1_555 A ZCY 7 P ? ? A ZHP 6 A ZCY 7 1_555 ? ? ? ? ? ? ? 1.575 ? ? covale7 covale one ? A ZCY 7 O2G ? ? ? 1_555 A ZGU 8 P ? ? A ZCY 7 A ZGU 8 1_555 ? ? ? ? ? ? ? 1.570 ? ? metalc1 metalc ? ? A ZHP 3 O3 ? ? ? 8_555 B CU . CU ? ? A ZHP 3 A CU 1001 1_555 ? ? ? ? ? ? ? 2.004 ? ? metalc2 metalc ? ? A ZHP 3 O4 ? ? ? 8_555 B CU . CU ? ? A ZHP 3 A CU 1001 1_555 ? ? ? ? ? ? ? 1.962 ? ? metalc3 metalc ? ? A ZHP 6 O3 ? ? ? 1_555 B CU . CU ? ? A ZHP 6 A CU 1001 1_555 ? ? ? ? ? ? ? 1.851 ? ? metalc4 metalc ? ? A ZHP 6 O4 ? ? ? 1_555 B CU . CU ? ? A ZHP 6 A CU 1001 1_555 ? ? ? ? ? ? ? 1.958 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2009 8_555 ? ? ? ? ? ? ? 1.941 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2023 8_655 ? ? ? ? ? ? ? 2.058 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2038 8_555 ? ? ? ? ? ? ? 2.011 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2039 8_655 ? ? ? ? ? ? ? 2.112 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2046 8_555 ? ? ? ? ? ? ? 2.140 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1002 A HOH 2060 1_555 ? ? ? ? ? ? ? 2.347 ? ? metalc11 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2036 7_556 ? ? ? ? ? ? ? 1.768 ? ? metalc12 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2036 1_555 ? ? ? ? ? ? ? 2.471 ? ? metalc13 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2072 7_556 ? ? ? ? ? ? ? 2.426 ? ? metalc14 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2072 1_555 ? ? ? ? ? ? ? 2.334 ? ? metalc15 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2073 7_556 ? ? ? ? ? ? ? 1.910 ? ? metalc16 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 1003 A HOH 2073 1_555 ? ? ? ? ? ? ? 2.381 ? ? metalc17 metalc ? ? G NA . NA ? ? ? 1_555 H HOH . O ? ? A NA 1006 A HOH 2008 1_555 ? ? ? ? ? ? ? 2.286 ? ? metalc18 metalc ? ? G NA . NA ? ? ? 1_555 H HOH . O ? ? A NA 1006 A HOH 2029 1_555 ? ? ? ? ? ? ? 2.037 ? ? metalc19 metalc ? ? G NA . NA ? ? ? 1_555 H HOH . O ? ? A NA 1006 A HOH 2037 1_555 ? ? ? ? ? ? ? 2.084 ? ? metalc20 metalc ? ? G NA . NA ? ? ? 1_555 H HOH . O ? ? A NA 1006 A HOH 2041 1_555 ? ? ? ? ? ? ? 2.568 ? ? hydrog1 hydrog ? ? A ZCY 1 N3 ? ? ? 1_555 A ZGU 8 N1 ? ? A ZCY 1 A ZGU 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A ZCY 1 N4 ? ? ? 1_555 A ZGU 8 O6 ? ? A ZCY 1 A ZGU 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A ZCY 1 O2 ? ? ? 1_555 A ZGU 8 N2 ? ? A ZCY 1 A ZGU 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A ZGU 2 N1 ? ? ? 1_555 A ZCY 7 N3 ? ? A ZGU 2 A ZCY 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A ZGU 2 N2 ? ? ? 1_555 A ZCY 7 O2 ? ? A ZGU 2 A ZCY 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A ZGU 2 O6 ? ? ? 1_555 A ZCY 7 N4 ? ? A ZGU 2 A ZCY 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A ZAD 4 N1 ? ? ? 1_555 A ZTH 5 N3 ? ? A ZAD 4 A ZTH 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A ZAD 4 N6 ? ? ? 1_555 A ZTH 5 O4 ? ? A ZAD 4 A ZTH 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A ZTH 5 N3 ? ? ? 1_555 A ZAD 4 N1 ? ? A ZTH 5 A ZAD 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A ZTH 5 O4 ? ? ? 1_555 A ZAD 4 N6 ? ? A ZTH 5 A ZAD 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A ZCY 7 N3 ? ? ? 1_555 A ZGU 2 N1 ? ? A ZCY 7 A ZGU 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A ZCY 7 N4 ? ? ? 1_555 A ZGU 2 O6 ? ? A ZCY 7 A ZGU 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A ZCY 7 O2 ? ? ? 1_555 A ZGU 2 N2 ? ? A ZCY 7 A ZGU 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A ZGU 8 N1 ? ? ? 1_555 A ZCY 1 N3 ? ? A ZGU 8 A ZCY 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A ZGU 8 N2 ? ? ? 1_555 A ZCY 1 O2 ? ? A ZGU 8 A ZCY 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A ZGU 8 O6 ? ? ? 1_555 A ZCY 1 N4 ? ? A ZGU 8 A ZCY 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE CU A1001' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MG A1002' AC3 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MG A1003' AC4 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE NCO A1004' AC5 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE NCO A1005' AC6 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE NA A1006' # 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 4 ZHP A 3 ? ZHP A 3 . ? 1_555 ? 2 AC1 4 ZAD A 4 ? ZAD A 4 . ? 1_555 ? 3 AC1 4 ZHP A 6 ? ZHP A 6 . ? 1_555 ? 4 AC1 4 ZCY A 7 ? ZCY A 7 . ? 1_555 ? 5 AC2 6 HOH H . ? HOH A 2009 . ? 1_555 ? 6 AC2 6 HOH H . ? HOH A 2023 . ? 1_555 ? 7 AC2 6 HOH H . ? HOH A 2038 . ? 1_555 ? 8 AC2 6 HOH H . ? HOH A 2039 . ? 1_555 ? 9 AC2 6 HOH H . ? HOH A 2046 . ? 1_555 ? 10 AC2 6 HOH H . ? HOH A 2060 . ? 1_555 ? 11 AC3 3 HOH H . ? HOH A 2036 . ? 1_555 ? 12 AC3 3 HOH H . ? HOH A 2072 . ? 1_555 ? 13 AC3 3 HOH H . ? HOH A 2073 . ? 1_555 ? 14 AC4 3 ZAD A 4 ? ZAD A 4 . ? 1_555 ? 15 AC4 3 ZTH A 5 ? ZTH A 5 . ? 1_555 ? 16 AC4 3 HOH H . ? HOH A 2075 . ? 1_555 ? 17 AC5 6 ZCY A 1 ? ZCY A 1 . ? 1_555 ? 18 AC5 6 ZGU A 2 ? ZGU A 2 . ? 1_555 ? 19 AC5 6 ZGU A 8 ? ZGU A 8 . ? 1_555 ? 20 AC5 6 HOH H . ? HOH A 2076 . ? 1_555 ? 21 AC5 6 HOH H . ? HOH A 2079 . ? 1_555 ? 22 AC5 6 HOH H . ? HOH A 2080 . ? 1_555 ? 23 AC6 4 HOH H . ? HOH A 2008 . ? 1_555 ? 24 AC6 4 HOH H . ? HOH A 2029 . ? 1_555 ? 25 AC6 4 HOH H . ? HOH A 2037 . ? 1_555 ? 26 AC6 4 HOH H . ? HOH A 2041 . ? 1_555 ? # _database_PDB_matrix.entry_id 2JJA _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2JJA _atom_sites.fract_transf_matrix[1][1] 0.055066 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.020580 _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] 0.016703 _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 CO CU MG N NA O P # 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 ZCY 1 1 1 ZCY ZCY A . n A 1 2 ZGU 2 2 2 ZGU ZGU A . n A 1 3 ZHP 3 3 3 ZHP ZHP A . n A 1 4 ZAD 4 4 4 ZAD ZAD A . n A 1 5 ZTH 5 5 5 ZTH ZTH A . n A 1 6 ZHP 6 6 6 ZHP ZHP A . n A 1 7 ZCY 7 7 7 ZCY ZCY A . n A 1 8 ZGU 8 8 8 ZGU ZGU A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CU 1 1001 1001 CU CU A . C 3 MG 1 1002 1002 MG MG A . D 3 MG 1 1003 1003 MG MG A . E 4 NCO 1 1004 1004 NCO NCO A . F 4 NCO 1 1005 1005 NCO NCO A . G 5 NA 1 1006 1006 NA NA A . H 6 HOH 1 2001 2001 HOH HOH A . H 6 HOH 2 2002 2002 HOH HOH A . H 6 HOH 3 2003 2003 HOH HOH A . H 6 HOH 4 2004 2004 HOH HOH A . H 6 HOH 5 2005 2005 HOH HOH A . H 6 HOH 6 2006 2006 HOH HOH A . H 6 HOH 7 2007 2007 HOH HOH A . H 6 HOH 8 2008 2008 HOH HOH A . H 6 HOH 9 2009 2009 HOH HOH A . H 6 HOH 10 2010 2010 HOH HOH A . H 6 HOH 11 2011 2011 HOH HOH A . H 6 HOH 12 2012 2012 HOH HOH A . H 6 HOH 13 2013 2013 HOH HOH A . H 6 HOH 14 2014 2014 HOH HOH A . H 6 HOH 15 2015 2015 HOH HOH A . H 6 HOH 16 2016 2016 HOH HOH A . H 6 HOH 17 2017 2017 HOH HOH A . H 6 HOH 18 2018 2018 HOH HOH A . H 6 HOH 19 2019 2019 HOH HOH A . H 6 HOH 20 2020 2020 HOH HOH A . H 6 HOH 21 2021 2021 HOH HOH A . H 6 HOH 22 2022 2022 HOH HOH A . H 6 HOH 23 2023 2023 HOH HOH A . H 6 HOH 24 2024 2024 HOH HOH A . H 6 HOH 25 2025 2025 HOH HOH A . H 6 HOH 26 2026 2026 HOH HOH A . H 6 HOH 27 2027 2027 HOH HOH A . H 6 HOH 28 2028 2028 HOH HOH A . H 6 HOH 29 2029 2029 HOH HOH A . H 6 HOH 30 2030 2030 HOH HOH A . H 6 HOH 31 2031 2031 HOH HOH A . H 6 HOH 32 2032 2032 HOH HOH A . H 6 HOH 33 2033 2033 HOH HOH A . H 6 HOH 34 2034 2034 HOH HOH A . H 6 HOH 35 2035 2035 HOH HOH A . H 6 HOH 36 2036 2036 HOH HOH A . H 6 HOH 37 2037 2037 HOH HOH A . H 6 HOH 38 2038 2038 HOH HOH A . H 6 HOH 39 2039 2039 HOH HOH A . H 6 HOH 40 2040 2040 HOH HOH A . H 6 HOH 41 2041 2041 HOH HOH A . H 6 HOH 42 2042 2042 HOH HOH A . H 6 HOH 43 2043 2043 HOH HOH A . H 6 HOH 44 2044 2044 HOH HOH A . H 6 HOH 45 2045 2045 HOH HOH A . H 6 HOH 46 2046 2046 HOH HOH A . H 6 HOH 47 2047 2047 HOH HOH A . H 6 HOH 48 2048 2048 HOH HOH A . H 6 HOH 49 2049 2049 HOH HOH A . H 6 HOH 50 2050 2050 HOH HOH A . H 6 HOH 51 2051 2051 HOH HOH A . H 6 HOH 52 2052 2052 HOH HOH A . H 6 HOH 53 2053 2053 HOH HOH A . H 6 HOH 54 2054 2054 HOH HOH A . H 6 HOH 55 2055 2055 HOH HOH A . H 6 HOH 56 2056 2056 HOH HOH A . H 6 HOH 57 2057 2057 HOH HOH A . H 6 HOH 58 2058 2058 HOH HOH A . H 6 HOH 59 2059 2059 HOH HOH A . H 6 HOH 60 2060 2060 HOH HOH A . H 6 HOH 61 2061 2061 HOH HOH A . H 6 HOH 62 2062 2062 HOH HOH A . H 6 HOH 63 2063 2063 HOH HOH A . H 6 HOH 64 2064 2064 HOH HOH A . H 6 HOH 65 2065 2065 HOH HOH A . H 6 HOH 66 2066 2066 HOH HOH A . H 6 HOH 67 2067 2067 HOH HOH A . H 6 HOH 68 2068 2068 HOH HOH A . H 6 HOH 69 2069 2069 HOH HOH A . H 6 HOH 70 2070 2070 HOH HOH A . H 6 HOH 71 2071 2071 HOH HOH A . H 6 HOH 72 2072 2072 HOH HOH A . H 6 HOH 73 2073 2073 HOH HOH A . H 6 HOH 74 2074 2074 HOH HOH A . H 6 HOH 75 2075 2075 HOH HOH A . H 6 HOH 76 2076 2076 HOH HOH A . H 6 HOH 77 2077 2077 HOH HOH A . H 6 HOH 78 2078 2078 HOH HOH A . H 6 HOH 79 2079 2079 HOH HOH A . H 6 HOH 80 2080 2080 HOH HOH A . # 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 ZCY 1 A ZCY 1 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" 2 A ZGU 2 A ZGU 2 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" 3 A ZAD 4 A ZAD 4 ? A "(S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE" 4 A ZTH 5 A ZTH 5 ? T "(S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" 5 A ZCY 7 A ZCY 7 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" 6 A ZGU 8 A ZGU 8 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id NCO _pdbx_struct_special_symmetry.auth_seq_id 1004 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id NCO _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O3 ? A ZHP 3 ? A ZHP 3 ? 8_555 CU ? B CU . ? A CU 1001 ? 1_555 O4 ? A ZHP 3 ? A ZHP 3 ? 8_555 83.9 ? 2 O3 ? A ZHP 3 ? A ZHP 3 ? 8_555 CU ? B CU . ? A CU 1001 ? 1_555 O3 ? A ZHP 6 ? A ZHP 6 ? 1_555 94.4 ? 3 O4 ? A ZHP 3 ? A ZHP 3 ? 8_555 CU ? B CU . ? A CU 1001 ? 1_555 O3 ? A ZHP 6 ? A ZHP 6 ? 1_555 174.9 ? 4 O3 ? A ZHP 3 ? A ZHP 3 ? 8_555 CU ? B CU . ? A CU 1001 ? 1_555 O4 ? A ZHP 6 ? A ZHP 6 ? 1_555 173.8 ? 5 O4 ? A ZHP 3 ? A ZHP 3 ? 8_555 CU ? B CU . ? A CU 1001 ? 1_555 O4 ? A ZHP 6 ? A ZHP 6 ? 1_555 98.0 ? 6 O3 ? A ZHP 6 ? A ZHP 6 ? 1_555 CU ? B CU . ? A CU 1001 ? 1_555 O4 ? A ZHP 6 ? A ZHP 6 ? 1_555 84.3 ? 7 O ? H HOH . ? A HOH 2009 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2023 ? 8_655 91.6 ? 8 O ? H HOH . ? A HOH 2009 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2038 ? 8_555 110.5 ? 9 O ? H HOH . ? A HOH 2023 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2038 ? 8_555 99.4 ? 10 O ? H HOH . ? A HOH 2009 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2039 ? 8_655 88.2 ? 11 O ? H HOH . ? A HOH 2023 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2039 ? 8_655 87.7 ? 12 O ? H HOH . ? A HOH 2038 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2039 ? 8_655 159.6 ? 13 O ? H HOH . ? A HOH 2009 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2046 ? 8_555 87.9 ? 14 O ? H HOH . ? A HOH 2023 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2046 ? 8_555 165.1 ? 15 O ? H HOH . ? A HOH 2038 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2046 ? 8_555 94.7 ? 16 O ? H HOH . ? A HOH 2039 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2046 ? 8_555 77.3 ? 17 O ? H HOH . ? A HOH 2009 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2060 ? 1_555 162.4 ? 18 O ? H HOH . ? A HOH 2023 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2060 ? 1_555 96.2 ? 19 O ? H HOH . ? A HOH 2038 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2060 ? 1_555 83.9 ? 20 O ? H HOH . ? A HOH 2039 ? 8_655 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2060 ? 1_555 76.4 ? 21 O ? H HOH . ? A HOH 2046 ? 8_555 MG ? C MG . ? A MG 1002 ? 1_555 O ? H HOH . ? A HOH 2060 ? 1_555 80.5 ? 22 O ? H HOH . ? A HOH 2036 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2036 ? 1_555 113.0 ? 23 O ? H HOH . ? A HOH 2036 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2072 ? 7_556 92.9 ? 24 O ? H HOH . ? A HOH 2036 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2072 ? 7_556 88.3 ? 25 O ? H HOH . ? A HOH 2036 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2072 ? 1_555 111.8 ? 26 O ? H HOH . ? A HOH 2036 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2072 ? 1_555 79.4 ? 27 O ? H HOH . ? A HOH 2072 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2072 ? 1_555 155.2 ? 28 O ? H HOH . ? A HOH 2036 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 7_556 109.0 ? 29 O ? H HOH . ? A HOH 2036 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 7_556 137.6 ? 30 O ? H HOH . ? A HOH 2072 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 7_556 95.4 ? 31 O ? H HOH . ? A HOH 2072 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 7_556 80.0 ? 32 O ? H HOH . ? A HOH 2036 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 1_555 160.5 ? 33 O ? H HOH . ? A HOH 2036 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 1_555 76.2 ? 34 O ? H HOH . ? A HOH 2072 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 1_555 69.7 ? 35 O ? H HOH . ? A HOH 2072 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 1_555 86.3 ? 36 O ? H HOH . ? A HOH 2073 ? 7_556 MG ? D MG . ? A MG 1003 ? 1_555 O ? H HOH . ? A HOH 2073 ? 1_555 65.8 ? 37 O ? H HOH . ? A HOH 2008 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2029 ? 1_555 81.3 ? 38 O ? H HOH . ? A HOH 2008 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2037 ? 1_555 163.8 ? 39 O ? H HOH . ? A HOH 2029 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2037 ? 1_555 84.1 ? 40 O ? H HOH . ? A HOH 2008 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2041 ? 1_555 94.9 ? 41 O ? H HOH . ? A HOH 2029 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2041 ? 1_555 166.4 ? 42 O ? H HOH . ? A HOH 2037 ? 1_555 NA ? G NA . ? A NA 1006 ? 1_555 O ? H HOH . ? A HOH 2041 ? 1_555 100.9 ? # 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 2008-07-22 2 'Structure model' 1 1 2011-05-07 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2022-06-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 4 'Structure model' 'Polymer sequence' # 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 2 4 'Structure model' database_2 3 4 'Structure model' entity_poly 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn # 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' '_chem_comp.mon_nstd_flag' 2 4 'Structure model' '_chem_comp.type' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 6 4 'Structure model' '_pdbx_database_status.status_code_sf' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 11 4 'Structure model' '_pdbx_struct_conn_angle.value' 12 4 'Structure model' '_struct_conn.pdbx_dist_value' 13 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 14 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 15 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 16 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 20 4 'Structure model' '_struct_conn.ptnr1_symmetry' 21 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_symmetry' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.2.0019 ? 1 ? ? ? ? XDS 'data reduction' . ? 2 ? ? ? ? XSCALE 'data scaling' . ? 3 ? ? ? ? # _pdbx_entry_details.entry_id 2JJA _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;(S)-1-(2,3-DIHYDROXYPROPYL)-HYDROXYPYRIDONE (ZHP): COPPER-CHELATING ARTIFICIAL BASE ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 2016 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2047 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C2 ? A ZHP 3 ? PLANAR . 2 1 C2 ? A ZHP 6 ? PLANAR . # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 2020 ? 6.23 . 2 1 O ? A HOH 2021 ? 6.43 . # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2JJA 'double helix' 2JJA 'mismatched base pair' # 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 ZCY 1 1_555 A ZGU 8 8_555 -0.225 -0.112 -0.017 9.250 7.281 1.845 1 A_ZCY1:ZGU8_A A 1 ? A 8 ? 19 1 1 A ZGU 2 1_555 A ZCY 7 8_555 0.135 -0.112 0.069 1.245 7.662 1.195 2 A_ZGU2:ZCY7_A A 2 ? A 7 ? 19 1 1 A ZCY 1 8_555 A ZGU 8 1_555 -0.225 -0.112 -0.017 9.250 7.281 1.845 3 A_ZCY1:ZGU8_A A 1 ? A 8 ? 19 1 1 A ZGU 2 8_555 A ZCY 7 1_555 0.135 -0.112 0.069 1.245 7.662 1.195 4 A_ZGU2:ZCY7_A A 2 ? A 7 ? 19 1 1 A ZAD 4 1_555 A ZTH 5 8_555 0.044 -0.130 0.000 -4.116 -2.345 -1.569 5 A_ZAD4:ZTH5_A A 4 ? A 5 ? 20 1 1 A ZTH 5 1_555 A ZAD 4 8_555 -0.044 -0.130 0.000 4.116 -2.345 -1.569 6 A_ZTH5:ZAD4_A A 5 ? A 4 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A ZCY 1 1_555 A ZGU 8 8_555 A ZGU 2 1_555 A ZCY 7 8_555 -0.280 -4.171 3.513 -2.375 -5.282 22.302 -8.174 -0.320 4.376 -13.367 6.012 23.033 1 AA_ZCY1ZGU2:ZCY7ZGU8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A ZCY 1 8_555 A ZGU 8 1_555 A ZGU 2 8_555 A ZCY 7 1_555 -0.280 -4.171 3.513 -2.375 -5.282 22.302 -8.174 -0.320 4.376 -13.367 6.012 23.033 2 AA_ZCY1ZGU2:ZCY7ZGU8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A ZAD 4 1_555 A ZTH 5 8_555 A ZTH 5 1_555 A ZAD 4 8_555 0.000 -3.861 3.048 0.000 0.851 28.654 -7.973 0.000 2.934 1.720 0.000 28.666 3 AA_ZAD4ZTH5:ZAD4ZTH5_AA A 4 ? A 5 ? A 5 ? A 4 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COPPER (II) ION' CU 3 'MAGNESIUM ION' MG 4 'COBALT HEXAMMINE(III)' NCO 5 'SODIUM ION' NA 6 water HOH #