data_3GOM
# 
_entry.id   3GOM 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.378 
_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   3GOM         pdb_00003gom 10.2210/pdb3gom/pdb 
NDB   UD0080       ?            ?                   
RCSB  RCSB052121   ?            ?                   
WWPDB D_1000052121 ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 1NVY 'Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4'            unspecified 
PDB 1P4Y 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified 
# 
_pdbx_database_status.entry_id                        3GOM 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.recvd_initial_deposition_date   2009-03-19 
_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.status_code_cs                  ? 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.status_code_nmr_data            ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Naseer, A.'   1 
'Cardin, C.J.' 2 
# 
_citation.id                        primary 
_citation.title                     
;Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
;
_citation.journal_abbrev            Proc.Natl.Acad.Sci.USA 
_citation.journal_volume            108 
_citation.page_first                17610 
_citation.page_last                 17614 
_citation.year                      2011 
_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   21969542 
_citation.pdbx_database_id_DOI      10.1073/pnas.1108685108 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Hall, J.P.'     1 ? 
primary 
;O'Sullivan, K.
;
2 ? 
primary 'Naseer, A.'     3 ? 
primary 'Smith, J.A.'    4 ? 
primary 'Kelly, J.M.'    5 ? 
primary 'Cardin, C.J.'   6 ? 
# 
_cell.length_a           65.2000 
_cell.length_b           23.8000 
_cell.length_c           37.4100 
_cell.angle_alpha        90.0000 
_cell.angle_beta         110.0100 
_cell.angle_gamma        90.0000 
_cell.entry_id           3GOM 
_cell.pdbx_unique_axis   ? 
_cell.Z_PDB              8 
_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.Int_Tables_number                5 
_symmetry.space_group_name_H-M             'C 1 2 1' 
_symmetry.entry_id                         3GOM 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_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 "5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'" 3045.992 2  ? ? ? 'Holliday junction structure' 
2 non-polymer syn 'BARIUM ION'                             137.327  5  ? ? ? ?                             
3 water       nat water                                    18.015   36 ? ? ? ?                             
# 
_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       '(DT)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA)' 
_entity_poly.pdbx_seq_one_letter_code_can   TCGGCGCCGA 
_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  DT n 
1 2  DC n 
1 3  DG n 
1 4  DG n 
1 5  DC n 
1 6  DG n 
1 7  DC n 
1 8  DC n 
1 9  DG n 
1 10 DA n 
# 
_struct_ref.id                         1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    3GOM 
_struct_ref.pdbx_db_accession          3GOM 
_struct_ref.entity_id                  1 
_struct_ref.pdbx_align_begin           1 
_struct_ref.pdbx_seq_one_letter_code   TCGGCGCCGA 
_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 3GOM A 1 ? 10 ? 3GOM 1  ? 10 ? 1  10 
2 1 3GOM B 1 ? 10 ? 3GOM 11 ? 20 ? 11 20 
# 
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 
BA  non-polymer   . 'BARIUM ION'                         ? 'Ba 2'            137.327 
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  
# 
_exptl.entry_id          3GOM 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_percent_sol   45.05 
_exptl_crystal.density_Matthews      2.24 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, SITTING DROP' 
_exptl_crystal_grow.pH              7 
_exptl_crystal_grow.temp            290 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pdbx_details    'BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K' 
_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 BaCl2           ? ? ? 
1 2 1 MPD             ? ? ? 
1 3 1 'Na Cacodylate' ? ? ? 
1 4 2 BaCl2           ? ? ? 
1 5 2 MPD             ? ? ? 
1 6 2 'Na Cacodylate' ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           100 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'OXFORD SAPPHIRE CCD' 
_diffrn_detector.pdbx_collection_date   ? 
_diffrn_detector.details                'multigraded optics' 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.monochromator                    ? 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.5418 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'SEALED TUBE' 
_diffrn_source.type                        'OXFORD DIFFRACTION ENHANCE ULTRA' 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.5418 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
# 
_reflns.d_resolution_high            2.300 
_reflns.d_resolution_low             19.956 
_reflns.limit_h_max                  26 
_reflns.limit_h_min                  -28 
_reflns.limit_k_max                  10 
_reflns.limit_k_min                  0 
_reflns.limit_l_max                  16 
_reflns.limit_l_min                  0 
_reflns.number_all                   2518 
_reflns.number_obs                   2351 
_reflns.entry_id                     3GOM 
_reflns.observed_criterion_sigma_F   1.00 
_reflns.observed_criterion_sigma_I   1.00 
_reflns.percent_possible_obs         93.220 
_reflns.pdbx_Rmerge_I_obs            0.052 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        31.247 
_reflns.pdbx_redundancy              2.7 
_reflns.R_free_details               ? 
_reflns.observed_criterion_F_max     ? 
_reflns.observed_criterion_F_min     ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_ordinal                 1 
_reflns.pdbx_diffrn_id               1 
# 
_reflns_shell.d_res_high             2.300 
_reflns_shell.d_res_low              2.360 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.percent_possible_all   93.220 
_reflns_shell.Rmerge_I_obs           0.21 
_reflns_shell.meanI_over_sigI_obs    3.21 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.pdbx_redundancy        2.6 
_reflns_shell.number_unique_all      461 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_ordinal           1 
_reflns_shell.pdbx_diffrn_id         1 
# 
_refine.ls_d_res_high                            2.300 
_refine.ls_d_res_low                             19.956 
_refine.pdbx_ls_sigma_F                          . 
_refine.ls_percent_reflns_obs                    93.220 
_refine.ls_number_reflns_obs                     2351 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.pdbx_R_Free_selection_details            RANDOM 
_refine.ls_R_factor_all                          0.264 
_refine.ls_R_factor_R_work                       0.260 
_refine.ls_R_factor_R_free                       0.349 
_refine.ls_percent_reflns_R_free                 4.300 
_refine.ls_number_reflns_R_free                  101 
_refine.B_iso_mean                               31.247 
_refine.aniso_B[1][1]                            -2.250 
_refine.aniso_B[2][2]                            3.160 
_refine.aniso_B[3][3]                            -1.570 
_refine.aniso_B[1][2]                            0.000 
_refine.aniso_B[1][3]                            -0.970 
_refine.aniso_B[2][3]                            0.000 
_refine.correlation_coeff_Fo_to_Fc               0.918 
_refine.correlation_coeff_Fo_to_Fc_free          0.860 
_refine.overall_SU_R_Cruickshank_DPI             0.604 
_refine.pdbx_overall_ESU_R_Free                  0.371 
_refine.overall_SU_ML                            0.291 
_refine.overall_SU_B                             13.500 
_refine.solvent_model_details                    MASK 
_refine.pdbx_solvent_vdw_probe_radii             1.200 
_refine.pdbx_solvent_ion_probe_radii             0.800 
_refine.pdbx_solvent_shrinkage_radii             0.800 
_refine.entry_id                                 3GOM 
_refine.pdbx_ls_sigma_I                          ? 
_refine.ls_number_reflns_all                     2351 
_refine.ls_R_factor_obs                          0.264 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_starting_model                      'PDB entry 1NVY' 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.solvent_model_param_bsol                 ? 
_refine.solvent_model_param_ksol                 ? 
_refine.occupancy_max                            ? 
_refine.occupancy_min                            ? 
_refine.pdbx_isotropic_thermal_model             ? 
_refine.details                                  ? 
_refine.B_iso_min                                ? 
_refine.B_iso_max                                ? 
_refine.overall_SU_R_free                        ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_wR_factor_R_work                      ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.pdbx_overall_phase_error                 ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_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         5 
_refine_hist.number_atoms_solvent             36 
_refine_hist.number_atoms_total               445 
_refine_hist.d_res_high                       2.300 
_refine_hist.d_res_low                        19.956 
# 
loop_
_refine_ls_restr.type 
_refine_ls_restr.number 
_refine_ls_restr.dev_ideal 
_refine_ls_restr.weight 
_refine_ls_restr.dev_ideal_target 
_refine_ls_restr.pdbx_refine_id 
_refine_ls_restr.pdbx_restraint_function 
r_bond_refined_d      452 0.008 0.021 ? 'X-RAY DIFFRACTION' ? 
r_angle_refined_deg   694 1.822 3.000 ? 'X-RAY DIFFRACTION' ? 
r_chiral_restr        78  0.066 0.200 ? 'X-RAY DIFFRACTION' ? 
r_gen_planes_refined  208 0.006 0.020 ? 'X-RAY DIFFRACTION' ? 
r_nbd_refined         121 0.193 0.200 ? 'X-RAY DIFFRACTION' ? 
r_nbtor_refined       259 0.316 0.200 ? 'X-RAY DIFFRACTION' ? 
r_xyhbond_nbd_refined 28  0.325 0.200 ? 'X-RAY DIFFRACTION' ? 
# 
_struct.entry_id                  3GOM 
_struct.title                     'Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        3GOM 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'Holliday junction structure, 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 ? 
E N N 2 ? 
F N N 2 ? 
G N N 2 ? 
H N N 3 ? 
I N N 3 ? 
# 
_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 4 O6 ? ? ? 1_555 C BA  .  BA ? ? A DG 4  A BA  21 1_555 ? ? ? ? ? ? ?            2.562 ? ? 
metalc2  metalc ? ? C BA . BA ? ? ? 1_555 I HOH .  O  ? ? A BA 21 B HOH 48 1_555 ? ? ? ? ? ? ?            2.550 ? ? 
metalc3  metalc ? ? D BA . BA ? ? ? 1_555 I HOH .  O  ? ? A BA 23 B HOH 24 1_555 ? ? ? ? ? ? ?            3.124 ? ? 
metalc4  metalc ? ? D BA . BA ? ? ? 1_555 I HOH .  O  ? ? A BA 23 B HOH 65 1_555 ? ? ? ? ? ? ?            2.508 ? ? 
metalc5  metalc ? ? F BA . BA ? ? ? 1_555 I HOH .  O  ? ? B BA 25 B HOH 57 1_555 ? ? ? ? ? ? ?            2.642 ? ? 
hydrog1  hydrog ? ? A DT 1 N3 ? ? ? 1_555 B DA  10 N1 ? ? A DT 1  B DA  20 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ?     ? ? 
hydrog2  hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG  9  N1 ? ? A DC 2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG  9  O6 ? ? A DC 2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG  9  N2 ? ? A DC 2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC  7  N4 ? ? A DG 3  B DC  17 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ?     ? ? 
hydrog6  hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC  8  N3 ? ? A DG 3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC  8  O2 ? ? A DG 3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC  8  N4 ? ? A DG 3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC  7  N3 ? ? A DG 4  B DC  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC  7  O2 ? ? A DG 4  B DC  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC  7  N4 ? ? A DG 4  B DC  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG  6  N1 ? ? A DC 5  B DG  16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG  6  O6 ? ? A DC 5  B DG  16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG  6  N2 ? ? A DC 5  B DG  16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC  5  N3 ? ? A DG 6  B DC  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC  5  O2 ? ? A DG 6  B DC  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC  5  N4 ? ? A DG 6  B DC  15 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 BA 21 ? 6 'BINDING SITE FOR RESIDUE BA A 21' 
AC2 Software A BA 23 ? 1 'BINDING SITE FOR RESIDUE BA A 23' 
AC3 Software B BA 25 ? 2 'BINDING SITE FOR RESIDUE BA B 25' 
AC4 Software B BA 49 ? 1 'BINDING SITE FOR RESIDUE BA B 49' 
# 
loop_
_struct_site_gen.id 
_struct_site_gen.site_id 
_struct_site_gen.pdbx_num_res 
_struct_site_gen.label_comp_id 
_struct_site_gen.label_asym_id 
_struct_site_gen.label_seq_id 
_struct_site_gen.pdbx_auth_ins_code 
_struct_site_gen.auth_comp_id 
_struct_site_gen.auth_asym_id 
_struct_site_gen.auth_seq_id 
_struct_site_gen.label_atom_id 
_struct_site_gen.label_alt_id 
_struct_site_gen.symmetry 
_struct_site_gen.details 
1  AC1 6 DG  A 3 ? DG  A 3  . ? 1_555 ? 
2  AC1 6 DG  A 4 ? DG  A 4  . ? 1_555 ? 
3  AC1 6 HOH H . ? HOH A 28 . ? 1_555 ? 
4  AC1 6 HOH H . ? HOH A 29 . ? 1_555 ? 
5  AC1 6 HOH H . ? HOH A 53 . ? 1_555 ? 
6  AC1 6 HOH I . ? HOH B 48 . ? 1_555 ? 
7  AC2 1 HOH I . ? HOH B 65 . ? 1_555 ? 
8  AC3 2 HOH I . ? HOH B 57 . ? 1_555 ? 
9  AC3 2 HOH I . ? HOH B 62 . ? 1_555 ? 
10 AC4 1 HOH I . ? HOH B 50 . ? 1_555 ? 
# 
_atom_sites.entry_id                    3GOM 
_atom_sites.fract_transf_matrix[1][1]   0.0153 
_atom_sites.fract_transf_matrix[1][2]   0.0000 
_atom_sites.fract_transf_matrix[1][3]   0.0056 
_atom_sites.fract_transf_matrix[2][1]   0.0000 
_atom_sites.fract_transf_matrix[2][2]   0.0420 
_atom_sites.fract_transf_matrix[2][3]   0.0000 
_atom_sites.fract_transf_matrix[3][1]   0.0000 
_atom_sites.fract_transf_matrix[3][2]   0.0000 
_atom_sites.fract_transf_matrix[3][3]   0.0284 
_atom_sites.fract_transf_vector[1]      0.0000 
_atom_sites.fract_transf_vector[2]      0.0000 
_atom_sites.fract_transf_vector[3]      0.0000 
# 
loop_
_atom_type.symbol 
BA 
C  
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  DT 1  1  1  DT T 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  DG 4  4  4  DG G A . n 
A 1 5  DC 5  5  5  DC C A . n 
A 1 6  DG 6  6  6  DG G A . n 
A 1 7  DC 7  7  7  DC C 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 DA 10 10 10 DA A A . n 
B 1 1  DT 1  11 11 DT T 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  DG 4  14 14 DG G B . n 
B 1 5  DC 5  15 15 DC C B . n 
B 1 6  DG 6  16 16 DG G B . n 
B 1 7  DC 7  17 17 DC C 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 DA 10 20 20 DA A 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 BA  1  21 21 BA  BA  A . 
D 2 BA  1  23 23 BA  BA  A . 
E 2 BA  1  22 22 BA  BA  B . 
F 2 BA  1  25 25 BA  BA  B . 
G 2 BA  1  49 49 BA  BA  B . 
H 3 HOH 1  28 28 HOH HOH A . 
H 3 HOH 2  29 29 HOH HOH A . 
H 3 HOH 3  30 30 HOH HOH A . 
H 3 HOH 4  31 31 HOH HOH A . 
H 3 HOH 5  32 32 HOH HOH A . 
H 3 HOH 6  33 33 HOH HOH A . 
H 3 HOH 7  40 40 HOH HOH A . 
H 3 HOH 8  41 41 HOH HOH A . 
H 3 HOH 9  43 43 HOH HOH A . 
H 3 HOH 10 44 44 HOH HOH A . 
H 3 HOH 11 52 52 HOH HOH A . 
H 3 HOH 12 53 53 HOH HOH A . 
H 3 HOH 13 55 55 HOH HOH A . 
H 3 HOH 14 56 56 HOH HOH A . 
H 3 HOH 15 58 58 HOH HOH A . 
H 3 HOH 16 60 60 HOH HOH A . 
I 3 HOH 1  24 24 HOH HOH B . 
I 3 HOH 2  34 34 HOH HOH B . 
I 3 HOH 3  35 35 HOH HOH B . 
I 3 HOH 4  36 36 HOH HOH B . 
I 3 HOH 5  37 37 HOH HOH B . 
I 3 HOH 6  38 38 HOH HOH B . 
I 3 HOH 7  39 39 HOH HOH B . 
I 3 HOH 8  45 45 HOH HOH B . 
I 3 HOH 9  46 46 HOH HOH B . 
I 3 HOH 10 47 47 HOH HOH B . 
I 3 HOH 11 48 48 HOH HOH B . 
I 3 HOH 12 50 50 HOH HOH B . 
I 3 HOH 13 51 51 HOH HOH B . 
I 3 HOH 14 57 57 HOH HOH B . 
I 3 HOH 15 59 59 HOH HOH B . 
I 3 HOH 16 61 61 HOH HOH B . 
I 3 HOH 17 62 62 HOH HOH B . 
I 3 HOH 18 63 63 HOH HOH B . 
I 3 HOH 19 64 64 HOH HOH B . 
I 3 HOH 20 65 65 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   tetrameric 
_pdbx_struct_assembly.oligomeric_count     4 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1,2 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D,E,F,G,H,I 
# 
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)' 5740 ? 
1 MORE         -98  ? 
1 'SSA (A^2)'  6090 ? 
# 
loop_
_pdbx_struct_oper_list.id 
_pdbx_struct_oper_list.type 
_pdbx_struct_oper_list.name 
_pdbx_struct_oper_list.symmetry_operation 
_pdbx_struct_oper_list.matrix[1][1] 
_pdbx_struct_oper_list.matrix[1][2] 
_pdbx_struct_oper_list.matrix[1][3] 
_pdbx_struct_oper_list.vector[1] 
_pdbx_struct_oper_list.matrix[2][1] 
_pdbx_struct_oper_list.matrix[2][2] 
_pdbx_struct_oper_list.matrix[2][3] 
_pdbx_struct_oper_list.vector[2] 
_pdbx_struct_oper_list.matrix[3][1] 
_pdbx_struct_oper_list.matrix[3][2] 
_pdbx_struct_oper_list.matrix[3][3] 
_pdbx_struct_oper_list.vector[3] 
1 'identity operation'         1_555 x,y,z   1.0000000000  0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000  0.0000000000 
2 'crystal symmetry operation' 2_555 -x,y,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 
# 
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 O6 ? A DG  4 ? A DG  4  ? 1_555 BA ? C BA . ? A BA 21 ? 1_555 O ? I HOH . ? B HOH 48 ? 1_555 101.5 ? 
2 O  ? I HOH . ? B HOH 24 ? 1_555 BA ? D BA . ? A BA 23 ? 1_555 O ? I HOH . ? B HOH 65 ? 1_555 47.7  ? 
# 
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 2009-04-07 
2 'Structure model' 1 1 2011-07-13 
3 'Structure model' 1 2 2011-11-02 
4 'Structure model' 1 3 2017-11-01 
5 'Structure model' 1 4 2018-04-04 
6 'Structure model' 1 5 2023-09-06 
# 
_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' 'Database references'       
3 4 'Structure model' 'Refinement description'    
4 5 'Structure model' 'Data collection'           
5 6 'Structure model' 'Data collection'           
6 6 'Structure model' 'Database references'       
7 6 'Structure model' 'Derived calculations'      
8 6 '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' software                      
2 5 'Structure model' diffrn_source                 
3 6 'Structure model' chem_comp_atom                
4 6 'Structure model' chem_comp_bond                
5 6 'Structure model' database_2                    
6 6 'Structure model' pdbx_initial_refinement_model 
7 6 'Structure model' pdbx_struct_conn_angle        
8 6 'Structure model' struct_conn                   
9 6 'Structure model' struct_site                   
# 
loop_
_pdbx_audit_revision_item.ordinal 
_pdbx_audit_revision_item.revision_ordinal 
_pdbx_audit_revision_item.data_content_type 
_pdbx_audit_revision_item.item 
1  4 'Structure model' '_software.name'                              
2  5 'Structure model' '_diffrn_source.type'                         
3  6 'Structure model' '_database_2.pdbx_DOI'                        
4  6 'Structure model' '_database_2.pdbx_database_accession'         
5  6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id'  
6  6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id'  
7  6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id'   
8  6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 
9  6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 
10 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 
11 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id'  
12 6 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id'   
13 6 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 
14 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id'  
15 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id'  
16 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id'   
17 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 
18 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 
19 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 
20 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id'  
21 6 'Structure model' '_pdbx_struct_conn_angle.value'               
22 6 'Structure model' '_struct_conn.pdbx_dist_value'                
23 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id'             
24 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id'             
25 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id'              
26 6 'Structure model' '_struct_conn.ptnr1_label_asym_id'            
27 6 'Structure model' '_struct_conn.ptnr1_label_atom_id'            
28 6 'Structure model' '_struct_conn.ptnr1_label_comp_id'            
29 6 'Structure model' '_struct_conn.ptnr1_label_seq_id'             
30 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id'             
31 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id'             
32 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id'              
33 6 'Structure model' '_struct_conn.ptnr2_label_asym_id'            
34 6 'Structure model' '_struct_conn.ptnr2_label_atom_id'            
35 6 'Structure model' '_struct_conn.ptnr2_label_comp_id'            
36 6 'Structure model' '_struct_site.pdbx_auth_asym_id'              
37 6 'Structure model' '_struct_site.pdbx_auth_comp_id'              
38 6 'Structure model' '_struct_site.pdbx_auth_seq_id'               
# 
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 
REFMAC      .     ?               program 'Murshudov, G.N.' ccp4@dl.ac.uk            refinement        
http://www.ccp4.ac.uk/main.html  Fortran ? 1 
PDB_EXTRACT 1.401 'March 3, 2004' program H.Yang            sw-help@rcsb.rutgers.edu 'data extraction' 
http://pdb.rutgers.edu/software/ C/C++   ? 2 
CrysalisPro Red   ?               ?       ?                 ?                        'data collection' ? ?       ? 3 
CrysalisPro Red   ?               ?       ?                 ?                        'data reduction'  ? ?       ? 4 
CrysalisPro Red   ?               ?       ?                 ?                        'data scaling'    ? ?       ? 5 
MOLREP      .     ?               ?       ?                 ?                        phasing           ? ?       ? 6 
# 
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 OP2 B DG  16 ? ? O B HOH 51 ? ? 1.94 
2 1 O   A HOH 28 ? ? O B HOH 48 ? ? 2.06 
# 
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 "C3'" A DG 4  ? ? "C2'" A DG 4  ? ? "C1'" A DG 4  ? ? 97.22  102.40 -5.18 0.80 N 
2 1 "O4'" A DG 4  ? ? "C1'" A DG 4  ? ? N9    A DG 4  ? ? 110.81 108.30 2.51  0.30 N 
3 1 "O4'" A DG 9  ? ? "C1'" A DG 9  ? ? N9    A DG 9  ? ? 110.80 108.30 2.50  0.30 N 
4 1 "O4'" B DG 16 ? ? "C1'" B DG 16 ? ? N9    B DG 16 ? ? 102.05 108.00 -5.95 0.70 N 
5 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1    B DC 18 ? ? 110.12 108.30 1.82  0.30 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 
BA  BA     BA N N 1   
DA  OP3    O  N N 2   
DA  P      P  N N 3   
DA  OP1    O  N N 4   
DA  OP2    O  N N 5   
DA  "O5'"  O  N N 6   
DA  "C5'"  C  N N 7   
DA  "C4'"  C  N R 8   
DA  "O4'"  O  N N 9   
DA  "C3'"  C  N S 10  
DA  "O3'"  O  N N 11  
DA  "C2'"  C  N N 12  
DA  "C1'"  C  N R 13  
DA  N9     N  Y N 14  
DA  C8     C  Y N 15  
DA  N7     N  Y N 16  
DA  C5     C  Y N 17  
DA  C6     C  Y N 18  
DA  N6     N  N N 19  
DA  N1     N  Y N 20  
DA  C2     C  Y N 21  
DA  N3     N  Y N 22  
DA  C4     C  Y N 23  
DA  HOP3   H  N N 24  
DA  HOP2   H  N N 25  
DA  "H5'"  H  N N 26  
DA  "H5''" H  N N 27  
DA  "H4'"  H  N N 28  
DA  "H3'"  H  N N 29  
DA  "HO3'" H  N N 30  
DA  "H2'"  H  N N 31  
DA  "H2''" H  N N 32  
DA  "H1'"  H  N N 33  
DA  H8     H  N N 34  
DA  H61    H  N N 35  
DA  H62    H  N N 36  
DA  H2     H  N N 37  
DC  OP3    O  N N 38  
DC  P      P  N N 39  
DC  OP1    O  N N 40  
DC  OP2    O  N N 41  
DC  "O5'"  O  N N 42  
DC  "C5'"  C  N N 43  
DC  "C4'"  C  N R 44  
DC  "O4'"  O  N N 45  
DC  "C3'"  C  N S 46  
DC  "O3'"  O  N N 47  
DC  "C2'"  C  N N 48  
DC  "C1'"  C  N R 49  
DC  N1     N  N N 50  
DC  C2     C  N N 51  
DC  O2     O  N N 52  
DC  N3     N  N N 53  
DC  C4     C  N N 54  
DC  N4     N  N N 55  
DC  C5     C  N N 56  
DC  C6     C  N N 57  
DC  HOP3   H  N N 58  
DC  HOP2   H  N N 59  
DC  "H5'"  H  N N 60  
DC  "H5''" H  N N 61  
DC  "H4'"  H  N N 62  
DC  "H3'"  H  N N 63  
DC  "HO3'" H  N N 64  
DC  "H2'"  H  N N 65  
DC  "H2''" H  N N 66  
DC  "H1'"  H  N N 67  
DC  H41    H  N N 68  
DC  H42    H  N N 69  
DC  H5     H  N N 70  
DC  H6     H  N N 71  
DG  OP3    O  N N 72  
DG  P      P  N N 73  
DG  OP1    O  N N 74  
DG  OP2    O  N N 75  
DG  "O5'"  O  N N 76  
DG  "C5'"  C  N N 77  
DG  "C4'"  C  N R 78  
DG  "O4'"  O  N N 79  
DG  "C3'"  C  N S 80  
DG  "O3'"  O  N N 81  
DG  "C2'"  C  N N 82  
DG  "C1'"  C  N R 83  
DG  N9     N  Y N 84  
DG  C8     C  Y N 85  
DG  N7     N  Y N 86  
DG  C5     C  Y N 87  
DG  C6     C  N N 88  
DG  O6     O  N N 89  
DG  N1     N  N N 90  
DG  C2     C  N N 91  
DG  N2     N  N N 92  
DG  N3     N  N N 93  
DG  C4     C  Y N 94  
DG  HOP3   H  N N 95  
DG  HOP2   H  N N 96  
DG  "H5'"  H  N N 97  
DG  "H5''" H  N N 98  
DG  "H4'"  H  N N 99  
DG  "H3'"  H  N N 100 
DG  "HO3'" H  N N 101 
DG  "H2'"  H  N N 102 
DG  "H2''" H  N N 103 
DG  "H1'"  H  N N 104 
DG  H8     H  N N 105 
DG  H1     H  N N 106 
DG  H21    H  N N 107 
DG  H22    H  N N 108 
DT  OP3    O  N N 109 
DT  P      P  N N 110 
DT  OP1    O  N N 111 
DT  OP2    O  N N 112 
DT  "O5'"  O  N N 113 
DT  "C5'"  C  N N 114 
DT  "C4'"  C  N R 115 
DT  "O4'"  O  N N 116 
DT  "C3'"  C  N S 117 
DT  "O3'"  O  N N 118 
DT  "C2'"  C  N N 119 
DT  "C1'"  C  N R 120 
DT  N1     N  N N 121 
DT  C2     C  N N 122 
DT  O2     O  N N 123 
DT  N3     N  N N 124 
DT  C4     C  N N 125 
DT  O4     O  N N 126 
DT  C5     C  N N 127 
DT  C7     C  N N 128 
DT  C6     C  N N 129 
DT  HOP3   H  N N 130 
DT  HOP2   H  N N 131 
DT  "H5'"  H  N N 132 
DT  "H5''" H  N N 133 
DT  "H4'"  H  N N 134 
DT  "H3'"  H  N N 135 
DT  "HO3'" H  N N 136 
DT  "H2'"  H  N N 137 
DT  "H2''" H  N N 138 
DT  "H1'"  H  N N 139 
DT  H3     H  N N 140 
DT  H71    H  N N 141 
DT  H72    H  N N 142 
DT  H73    H  N N 143 
DT  H6     H  N N 144 
HOH O      O  N N 145 
HOH H1     H  N N 146 
HOH H2     H  N N 147 
# 
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   3GOM 
_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 DT 1 1_555 B DA 10 1_555 0.413  0.138  0.290 -2.410 -15.787 5.979  1 A_DT1:DA20_B A 1 ? B 20 ? ?  ? 
1 A DC 2 1_555 B DG 9  1_555 0.043  -0.115 0.291 5.381  -7.201  -0.312 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 
1 A DG 3 1_555 B DC 8  1_555 0.136  -0.238 0.252 -3.311 -12.242 -2.592 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 
1 A DG 4 1_555 B DC 7  1_555 0.142  -0.389 0.769 12.289 -8.972  -2.291 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 
1 A DC 5 1_555 B DG 6  1_555 -0.942 -0.023 0.062 -2.435 -15.298 -5.603 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 
1 A DG 6 1_555 B DC 5  1_555 -0.393 -0.148 0.182 -0.288 -14.743 -5.071 6 A_DG6:DC15_B A 6 ? B 15 ? 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 DT 1 1_555 B DA 10 1_555 A DC 2 1_555 B DG 9 1_555 0.102  2.089 3.335 5.301  5.242  37.010 2.508 0.572  3.568 8.156  -8.248 
37.728 1 AA_DT1DC2:DG19DA20_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 -0.714 2.531 3.585 -2.823 -2.313 44.359 3.573 0.661  3.493 -3.057 3.732  
44.502 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 DG 4 1_555 B DC 7 1_555 0.425  0.651 2.927 -4.537 2.859  29.428 0.731 -1.666 2.879 5.569  8.838  
29.902 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 
1 A DG 4 1_555 B DC 7  1_555 A DC 5 1_555 B DG 6 1_555 -0.568 0.402 3.592 4.662  -4.385 36.689 1.259 1.560  3.428 -6.901 -7.337 
37.224 4 AA_DG4DC5:DG16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 
1 A DC 5 1_555 B DG 6  1_555 A DG 6 1_555 B DC 5 1_555 0.481  0.746 3.354 0.454  5.194  37.346 0.454 -0.683 3.429 8.064  -0.704 
37.695 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 'BARIUM ION' BA  
3 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   1NVY 
_pdbx_initial_refinement_model.details          'PDB entry 1NVY' 
#