data_4HIG # _entry.id 4HIG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4HIG pdb_00004hig 10.2210/pdb4hig/pdb NDB NA2072 ? ? RCSB RCSB075506 ? ? WWPDB D_1000075506 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3G2R . unspecified PDB 3FQ5 . unspecified PDB 1ICK . unspecified PDB 1D39 . unspecified PDB 3P4J . unspecified PDB 4HIF . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4HIG _pdbx_database_status.recvd_initial_deposition_date 2012-10-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Drozdzal, P.' 1 'Gilski, M.' 2 'Kierzek, R.' 3 'Lomozik, L.' 4 'Jaskolski, M.' 5 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.' 'Acta Crystallogr.,Sect.D' 69 1180 1190 2013 ABCRE6 DK 0907-4449 0766 ? 23695262 10.1107/S0907444913007798 1 'High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.' 'Nucleic Acids Res.' 39 6238 6248 2011 NARHAD UK 0305-1048 0389 ? ? ? 2 'Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.' 'Acta Crystallogr.,Sect.D' 57 990 995 2001 ABCRE6 DK 0907-4449 0766 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Drozdzal, P.' 1 ? primary 'Gilski, M.' 2 ? primary 'Kierzek, R.' 3 ? primary 'Lomozik, L.' 4 ? primary 'Jaskolski, M.' 5 ? 1 'Brzezinski, K.' 6 ? 1 'Brzuszkiewicz, A.' 7 ? 1 'Dauter, M.' 8 ? 1 'Kubicki, M.' 9 ? 1 'Jaskolski, M.' 10 ? 1 'Dauter, Z.' 11 ? 2 'Dauter, Z.' 12 ? 2 'Adamiak, D.A.' 13 ? # _cell.entry_id 4HIG _cell.length_a 17.732 _cell.length_b 31.436 _cell.length_c 43.935 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4HIG _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') ; 1810.205 2 ? ? ? ? 2 non-polymer syn 'SPERMINE (FULLY PROTONATED FORM)' 206.372 1 ? ? ? ? 3 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 4 water nat water 18.015 92 ? ? ? ? # _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)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _entity_poly.pdbx_strand_id A,B _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 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'Synthetic construct' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4HIG _struct_ref.pdbx_db_accession 4HIG _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4HIG A 1 ? 6 ? 4HIG 1 ? 6 ? 1 6 2 1 4HIG B 1 ? 6 ? 4HIG 7 ? 12 ? 7 12 # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 SPK non-polymer . 'SPERMINE (FULLY PROTONATED FORM)' ? 'C10 H30 N4 4' 206.372 # _exptl.entry_id 4HIG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.59 _exptl_crystal.density_percent_sol 22.70 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR MN2+ SOAKING, A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK. ; # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'MAR CCD 165 mm' 2009-12-04 ? 2 CCD 'RAYONIX MX-225' 2012-03-16 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'SI 111 CHANNEL' 'SINGLE WAVELENGTH' x-ray 2 1 M 'SI 111 CHANNEL' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.8010 1.0 2 0.9184 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'EMBL/DESY, HAMBURG BEAMLINE X12' 'EMBL/DESY, HAMBURG' X12 0.8010 ? 2 SYNCHROTRON 'BESSY BEAMLINE 14.2' BESSY 14.2 0.9184 ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4HIG _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.57 _reflns.d_resolution_high 0.75 _reflns.number_obs 47730 _reflns.number_all ? _reflns.percent_possible_obs 79.9 _reflns.pdbx_Rmerge_I_obs 0.05300 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.2800 _reflns.B_iso_Wilson_estimate 4.756 _reflns.pdbx_redundancy 3.280 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.75 _reflns_shell.d_res_low 0.77 _reflns_shell.percent_possible_all 10.6 _reflns_shell.Rmerge_I_obs 0.03800 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 11.390 _reflns_shell.pdbx_redundancy 1.15 _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4HIG _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 47730 _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 25.57 _refine.ls_d_res_high 0.75 _refine.ls_percent_reflns_obs 79.9 _refine.ls_R_factor_obs 0.071 _refine.ls_R_factor_all 0.071 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.081 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 2.11 _refine.ls_number_reflns_R_free 1009 _refine.ls_number_parameters 3409 _refine.ls_number_restraints 1139 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201.' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ;THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE. ; _refine.pdbx_starting_model 1I0T _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _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.ls_redundancy_reflns_obs ? _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_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 4HIG _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 1 _refine_analyze.occupancy_sum_hydrogen 164.00 _refine_analyze.occupancy_sum_non_hydrogen 332.97 # _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 240 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 92 _refine_hist.number_atoms_total 347 _refine_hist.d_res_high 0.75 _refine_hist.d_res_low 25.57 # 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 s_bond_d 0.012 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.029 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.028 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.004 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.037 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.069 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4HIG _pdbx_refine.R_factor_all_no_cutoff 0.071 _pdbx_refine.R_factor_obs_no_cutoff 0.071 _pdbx_refine.free_R_factor_no_cutoff 0.081 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 2.11 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1009 _pdbx_refine.R_factor_all_4sig_cutoff 0.071 _pdbx_refine.R_factor_obs_4sig_cutoff 0.071 _pdbx_refine.free_R_factor_4sig_cutoff 0.079 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 2.11 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1005 _pdbx_refine.number_reflns_obs_4sig_cutoff 47641 # _struct.entry_id 4HIG _struct.title 'Ultrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4HIG _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'self-complementary DNA, Z-DNA, 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 3 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DG 6 N7 ? ? ? 1_555 D MN . MN ? ? A DG 6 A MN 102 1_555 ? ? ? ? ? ? ? 2.258 ? ? metalc2 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O A ? A MN 102 A HOH 203 1_555 ? ? ? ? ? ? ? 2.076 ? ? metalc3 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O B ? A MN 102 A HOH 203 1_555 ? ? ? ? ? ? ? 2.310 ? ? metalc4 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O A ? A MN 102 A HOH 216 1_555 ? ? ? ? ? ? ? 2.186 ? ? metalc5 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O B ? A MN 102 A HOH 216 1_555 ? ? ? ? ? ? ? 2.256 ? ? metalc6 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O B ? A MN 102 A HOH 250 1_555 ? ? ? ? ? ? ? 1.947 ? ? metalc7 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O A ? A MN 102 A HOH 250 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc8 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 102 A HOH 251 1_555 ? ? ? ? ? ? ? 2.159 ? ? metalc9 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 102 A HOH 252 1_555 ? ? ? ? ? ? ? 2.138 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SPK 101 ? 17 'BINDING SITE FOR RESIDUE SPK A 101' AC2 Software A MN 102 ? 6 'BINDING SITE FOR RESIDUE MN A 102' # 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 17 DG A 2 ? DG A 2 . ? 4_456 ? 2 AC1 17 DG A 4 ? DG A 4 . ? 1_555 ? 3 AC1 17 DG A 4 ? DG A 4 . ? 3_746 ? 4 AC1 17 DC A 5 ? DC A 5 . ? 1_555 ? 5 AC1 17 DG A 6 ? DG A 6 . ? 1_555 ? 6 AC1 17 DG A 6 ? DG A 6 . ? 3_646 ? 7 AC1 17 HOH E . ? HOH A 207 . ? 1_555 ? 8 AC1 17 HOH E . ? HOH A 214 . ? 3_646 ? 9 AC1 17 HOH E . ? HOH A 233 . ? 3_746 ? 10 AC1 17 DC B 1 ? DC B 7 . ? 3_746 ? 11 AC1 17 DG B 2 ? DG B 8 . ? 3_746 ? 12 AC1 17 DC B 3 ? DC B 9 . ? 3_646 ? 13 AC1 17 HOH F . ? HOH B 111 . ? 3_646 ? 14 AC1 17 HOH F . ? HOH B 112 . ? 3_646 ? 15 AC1 17 HOH F . ? HOH B 113 . ? 3_746 ? 16 AC1 17 HOH F . ? HOH B 123 . ? 3_646 ? 17 AC1 17 HOH F . ? HOH B 126 . ? 3_646 ? 18 AC2 6 DG A 6 ? DG A 6 . ? 1_555 ? 19 AC2 6 HOH E . ? HOH A 203 . ? 1_555 ? 20 AC2 6 HOH E . ? HOH A 216 . ? 1_555 ? 21 AC2 6 HOH E . ? HOH A 250 . ? 1_555 ? 22 AC2 6 HOH E . ? HOH A 251 . ? 1_555 ? 23 AC2 6 HOH E . ? HOH A 252 . ? 1_555 ? # _database_PDB_matrix.entry_id 4HIG _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 4HIG _atom_sites.fract_transf_matrix[1][1] 0.056395 _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] 0.031811 _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] 0.022761 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MN N 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 DG 2 8 8 DG DG B . n B 1 3 DC 3 9 9 DC DC B . n B 1 4 DG 4 10 10 DG DG B . n B 1 5 DC 5 11 11 DC DC B . n B 1 6 DG 6 12 12 DG DG 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 SPK 1 101 13 SPK SPK A . D 3 MN 1 102 14 MN MN A . E 4 HOH 1 201 16 HOH HOH A . E 4 HOH 2 202 17 HOH HOH A . E 4 HOH 3 203 19 HOH HOH A . E 4 HOH 4 204 20 HOH HOH A . E 4 HOH 5 205 23 HOH HOH A . E 4 HOH 6 206 27 HOH HOH A . E 4 HOH 7 207 28 HOH HOH A . E 4 HOH 8 208 29 HOH HOH A . E 4 HOH 9 209 31 HOH HOH A . E 4 HOH 10 210 33 HOH HOH A . E 4 HOH 11 211 36 HOH HOH A . E 4 HOH 12 212 39 HOH HOH A . E 4 HOH 13 213 40 HOH HOH A . E 4 HOH 14 214 41 HOH HOH A . E 4 HOH 15 215 45 HOH HOH A . E 4 HOH 16 216 47 HOH HOH A . E 4 HOH 17 217 49 HOH HOH A . E 4 HOH 18 218 50 HOH HOH A . E 4 HOH 19 219 52 HOH HOH A . E 4 HOH 20 220 53 HOH HOH A . E 4 HOH 21 221 54 HOH HOH A . E 4 HOH 22 222 55 HOH HOH A . E 4 HOH 23 223 56 HOH HOH A . E 4 HOH 24 224 62 HOH HOH A . E 4 HOH 25 225 64 HOH HOH A . E 4 HOH 26 226 65 HOH HOH A . E 4 HOH 27 227 66 HOH HOH A . E 4 HOH 28 228 68 HOH HOH A . E 4 HOH 29 229 69 HOH HOH A . E 4 HOH 30 230 70 HOH HOH A . E 4 HOH 31 231 73 HOH HOH A . E 4 HOH 32 232 74 HOH HOH A . E 4 HOH 33 233 75 HOH HOH A . E 4 HOH 34 234 76 HOH HOH A . E 4 HOH 35 235 79 HOH HOH A . E 4 HOH 36 236 80 HOH HOH A . E 4 HOH 37 237 84 HOH HOH A . E 4 HOH 38 238 86 HOH HOH A . E 4 HOH 39 239 87 HOH HOH A . E 4 HOH 40 240 89 HOH HOH A . E 4 HOH 41 241 90 HOH HOH A . E 4 HOH 42 242 91 HOH HOH A . E 4 HOH 43 243 93 HOH HOH A . E 4 HOH 44 244 94 HOH HOH A . E 4 HOH 45 245 99 HOH HOH A . E 4 HOH 46 246 102 HOH HOH A . E 4 HOH 47 247 103 HOH HOH A . E 4 HOH 48 248 104 HOH HOH A . E 4 HOH 49 249 105 HOH HOH A . E 4 HOH 50 250 106 HOH HOH A . E 4 HOH 51 251 107 HOH HOH A . E 4 HOH 52 252 108 HOH HOH A . E 4 HOH 53 253 109 HOH HOH A . F 4 HOH 1 101 15 HOH HOH B . F 4 HOH 2 102 18 HOH HOH B . F 4 HOH 3 103 21 HOH HOH B . F 4 HOH 4 104 22 HOH HOH B . F 4 HOH 5 105 24 HOH HOH B . F 4 HOH 6 106 26 HOH HOH B . F 4 HOH 7 107 32 HOH HOH B . F 4 HOH 8 108 34 HOH HOH B . F 4 HOH 9 109 35 HOH HOH B . F 4 HOH 10 110 37 HOH HOH B . F 4 HOH 11 111 38 HOH HOH B . F 4 HOH 12 112 42 HOH HOH B . F 4 HOH 13 113 43 HOH HOH B . F 4 HOH 14 114 46 HOH HOH B . F 4 HOH 15 115 48 HOH HOH B . F 4 HOH 16 116 51 HOH HOH B . F 4 HOH 17 117 57 HOH HOH B . F 4 HOH 18 118 58 HOH HOH B . F 4 HOH 19 119 59 HOH HOH B . F 4 HOH 20 120 60 HOH HOH B . F 4 HOH 21 121 61 HOH HOH B . F 4 HOH 22 122 63 HOH HOH B . F 4 HOH 23 123 67 HOH HOH B . F 4 HOH 24 124 71 HOH HOH B . F 4 HOH 25 125 72 HOH HOH B . F 4 HOH 26 126 77 HOH HOH B . F 4 HOH 27 127 78 HOH HOH B . F 4 HOH 28 128 81 HOH HOH B . F 4 HOH 29 129 82 HOH HOH B . F 4 HOH 30 130 83 HOH HOH B . F 4 HOH 31 131 85 HOH HOH B . F 4 HOH 32 132 88 HOH HOH B . F 4 HOH 33 133 92 HOH HOH B . F 4 HOH 34 134 95 HOH HOH B . F 4 HOH 35 135 96 HOH HOH B . F 4 HOH 36 136 97 HOH HOH B . F 4 HOH 37 137 98 HOH HOH B . F 4 HOH 38 138 100 HOH HOH B . F 4 HOH 39 139 101 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 940 ? 1 MORE -13 ? 1 'SSA (A^2)' 2620 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_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 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 203 ? 1_555 91.6 ? 2 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 203 ? 1_555 86.8 ? 3 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 203 ? 1_555 8.4 ? 4 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 216 ? 1_555 92.1 ? 5 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 216 ? 1_555 96.9 ? 6 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 216 ? 1_555 103.9 ? 7 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 216 ? 1_555 87.0 ? 8 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 216 ? 1_555 69.7 ? 9 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 216 ? 1_555 76.3 ? 10 O A E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 216 ? 1_555 27.9 ? 11 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 250 ? 1_555 92.5 ? 12 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 250 ? 1_555 148.2 ? 13 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 250 ? 1_555 155.4 ? 14 O A E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 250 ? 1_555 51.5 ? 15 O B E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O B E HOH . ? A HOH 250 ? 1_555 79.1 ? 16 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 84.6 ? 17 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 174.3 ? 18 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 171.0 ? 19 O A E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 79.1 ? 20 O B E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 105.8 ? 21 O B E HOH . ? A HOH 250 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O A E HOH . ? A HOH 250 ? 1_555 28.4 ? 22 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 175.9 ? 23 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 92.4 ? 24 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 97.0 ? 25 O A E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 88.4 ? 26 O B E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 95.4 ? 27 O B E HOH . ? A HOH 250 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 84.6 ? 28 O A E HOH . ? A HOH 250 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 91.5 ? 29 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 93.8 ? 30 O A E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 92.2 ? 31 O B E HOH . ? A HOH 203 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 85.6 ? 32 O A E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 169.0 ? 33 O B E HOH . ? A HOH 216 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 161.9 ? 34 O B E HOH . ? A HOH 250 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 118.9 ? 35 O A E HOH . ? A HOH 250 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 92.3 ? 36 O ? E HOH . ? A HOH 251 ? 1_555 MN ? D MN . ? A MN 102 ? 1_555 O ? E HOH . ? A HOH 252 ? 1_555 85.0 ? # 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 2013-06-05 2 'Structure model' 1 1 2023-09-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' diffrn_source 5 2 'Structure model' pdbx_initial_refinement_model 6 2 'Structure model' pdbx_struct_conn_angle 7 2 'Structure model' struct_conn 8 2 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 7 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 14 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 2 'Structure model' '_pdbx_struct_conn_angle.value' 19 2 'Structure model' '_struct_conn.pdbx_dist_value' 20 2 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 21 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 2 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 2 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 PHASER phasing . ? 2 SHELXL-97 refinement . ? 3 XDS 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 MN MN MN N N 75 SPK N1 N N N 76 SPK C2 C N N 77 SPK C3 C N N 78 SPK C4 C N N 79 SPK N5 N N N 80 SPK C6 C N N 81 SPK C7 C N N 82 SPK C8 C N N 83 SPK C9 C N N 84 SPK N10 N N N 85 SPK C11 C N N 86 SPK C12 C N N 87 SPK C13 C N N 88 SPK N14 N N N 89 SPK H1A H N N 90 SPK H1B H N N 91 SPK H1C H N N 92 SPK H2A H N N 93 SPK H2B H N N 94 SPK H3A H N N 95 SPK H3B H N N 96 SPK H4A H N N 97 SPK H4B H N N 98 SPK H5A H N N 99 SPK H5B H N N 100 SPK H6A H N N 101 SPK H6B H N N 102 SPK H7A H N N 103 SPK H7B H N N 104 SPK H8A H N N 105 SPK H8B H N N 106 SPK H9A H N N 107 SPK H9B H N N 108 SPK H101 H N N 109 SPK H102 H N N 110 SPK H111 H N N 111 SPK H112 H N N 112 SPK H121 H N N 113 SPK H122 H N N 114 SPK H131 H N N 115 SPK H132 H N N 116 SPK H141 H N N 117 SPK H142 H N N 118 SPK H143 H N N 119 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 SPK N1 C2 sing N N 77 SPK N1 H1A sing N N 78 SPK N1 H1B sing N N 79 SPK N1 H1C sing N N 80 SPK C2 C3 sing N N 81 SPK C2 H2A sing N N 82 SPK C2 H2B sing N N 83 SPK C3 C4 sing N N 84 SPK C3 H3A sing N N 85 SPK C3 H3B sing N N 86 SPK C4 N5 sing N N 87 SPK C4 H4A sing N N 88 SPK C4 H4B sing N N 89 SPK N5 C6 sing N N 90 SPK N5 H5A sing N N 91 SPK N5 H5B sing N N 92 SPK C6 C7 sing N N 93 SPK C6 H6A sing N N 94 SPK C6 H6B sing N N 95 SPK C7 C8 sing N N 96 SPK C7 H7A sing N N 97 SPK C7 H7B sing N N 98 SPK C8 C9 sing N N 99 SPK C8 H8A sing N N 100 SPK C8 H8B sing N N 101 SPK C9 N10 sing N N 102 SPK C9 H9A sing N N 103 SPK C9 H9B sing N N 104 SPK N10 C11 sing N N 105 SPK N10 H101 sing N N 106 SPK N10 H102 sing N N 107 SPK C11 C12 sing N N 108 SPK C11 H111 sing N N 109 SPK C11 H112 sing N N 110 SPK C12 C13 sing N N 111 SPK C12 H121 sing N N 112 SPK C12 H122 sing N N 113 SPK C13 N14 sing N N 114 SPK C13 H131 sing N N 115 SPK C13 H132 sing N N 116 SPK N14 H141 sing N N 117 SPK N14 H142 sing N N 118 SPK N14 H143 sing N N 119 # _ndb_struct_conf_na.entry_id 4HIG _ndb_struct_conf_na.feature 'z-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 6 1_555 -0.251 -0.165 0.253 0.652 -2.477 1.004 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 0.241 -0.168 -0.103 -7.376 -5.475 1.952 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.252 -0.151 -0.040 5.260 -4.092 1.825 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.199 -0.136 0.058 -8.235 0.677 2.372 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.119 -0.128 -0.027 0.716 0.159 3.118 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.321 -0.185 0.230 3.877 6.111 2.825 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B DC 5 1_555 -0.026 5.226 3.669 1.533 -3.730 -4.646 -17.767 12.471 5.945 37.900 15.580 -6.152 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 -0.022 -1.004 3.191 0.082 -5.373 -53.052 1.447 -0.020 3.083 5.998 0.092 -53.304 2 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 -0.082 5.473 3.774 0.217 -3.119 -5.484 -26.287 0.879 5.984 29.638 2.058 -6.312 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 -0.252 -0.831 3.219 0.825 -1.893 -53.736 1.035 -0.228 3.193 2.093 0.912 -53.773 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 0.037 5.065 3.406 0.888 -1.376 -6.660 -35.777 4.545 4.318 11.616 7.495 -6.858 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SPERMINE (FULLY PROTONATED FORM)' SPK 3 'MANGANESE (II) ION' MN 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1I0T _pdbx_initial_refinement_model.details ? #