data_109D
# 
_entry.id   109D 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.385 
_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   109D         pdb_0000109d 10.2210/pdb109d/pdb 
RCSB  GDL033       ?            ?                   
WWPDB D_1000170023 ?            ?                   
# 
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 1995-05-08 
2 'Structure model' 1 1 2008-05-22 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2024-02-07 
# 
_pdbx_audit_revision_details.ordinal             1 
_pdbx_audit_revision_details.revision_ordinal    1 
_pdbx_audit_revision_details.data_content_type   'Structure model' 
_pdbx_audit_revision_details.provider            repository 
_pdbx_audit_revision_details.type                'Initial release' 
_pdbx_audit_revision_details.description         ? 
_pdbx_audit_revision_details.details             ? 
# 
loop_
_pdbx_audit_revision_group.ordinal 
_pdbx_audit_revision_group.revision_ordinal 
_pdbx_audit_revision_group.data_content_type 
_pdbx_audit_revision_group.group 
1 2 'Structure model' 'Version format compliance' 
2 3 'Structure model' 'Version format compliance' 
3 4 'Structure model' 'Data collection'           
4 4 'Structure model' 'Database references'       
5 4 'Structure model' 'Derived calculations'      
# 
loop_
_pdbx_audit_revision_category.ordinal 
_pdbx_audit_revision_category.revision_ordinal 
_pdbx_audit_revision_category.data_content_type 
_pdbx_audit_revision_category.category 
1 4 'Structure model' chem_comp_atom         
2 4 'Structure model' chem_comp_bond         
3 4 'Structure model' database_2             
4 4 'Structure model' pdbx_struct_conn_angle 
5 4 'Structure model' struct_conn            
6 4 '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' '_database_2.pdbx_DOI'                      
2  4 'Structure model' '_database_2.pdbx_database_accession'       
3  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 
4  4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 
5  4 'Structure model' '_pdbx_struct_conn_angle.value'             
6  4 'Structure model' '_struct_conn.pdbx_dist_value'              
7  4 'Structure model' '_struct_conn.ptnr2_auth_seq_id'            
8  4 'Structure model' '_struct_site.pdbx_auth_asym_id'            
9  4 'Structure model' '_struct_site.pdbx_auth_comp_id'            
10 4 'Structure model' '_struct_site.pdbx_auth_seq_id'             
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        109D 
_pdbx_database_status.recvd_initial_deposition_date   1995-02-15 
_pdbx_database_status.deposit_site                    BNL 
_pdbx_database_status.process_site                    NDB 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Czarny, A.'   1 
'Boykin, D.W.' 2 
'Wood, A.A.'   3 
'Nunn, C.M.'   4 
'Neidle, S.'   5 
'Zhao, M.'     6 
'Wilson, W.D.' 7 
# 
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 
;Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
;
'Nucleic Acids Res.' 23  3678  3684 1995 NARHAD UK 0305-1048 0389 ? 7478996 10.1093/nar/23.18.3678 
1       
'Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA' 
J.Am.Chem.Soc.       117 4716  4717 1995 JACSAT US 0002-7863 0004 ? ?       ?                      
2       
;Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G
;
Biochemistry         30  10294 ?    1991 BICHAW US 0006-2960 0033 ? ?       ?                      
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Wood, A.A.'      1  ? 
primary 'Nunn, C.M.'      2  ? 
primary 'Czarny, A.'      3  ? 
primary 'Boykin, D.W.'    4  ? 
primary 'Neidle, S.'      5  ? 
1       'Czarny, A.'      6  ? 
1       'Boykin, D.W.'    7  ? 
1       'Wood, A.A.'      8  ? 
1       'Nunn, C.M.'      9  ? 
1       'Neidle, S.'      10 ? 
1       'Zhao, M.'        11 ? 
1       'Wilson, W.D.'    12 ? 
2       'Quintana, J.R.'  13 ? 
2       'Lipanov, A.A.'   14 ? 
2       'Dickerson, R.E.' 15 ? 
# 
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*AP*AP*TP*TP*CP*GP*CP*G)-3')
;
3663.392 2  ? ? ? ? 
2 non-polymer syn '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' 396.445  1  ? ? ? ? 
3 non-polymer syn 'MAGNESIUM ION'                                                            24.305   1  ? ? ? ? 
4 water       nat water                                                                      18.015   90 ? ? ? ? 
# 
_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)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' 
_entity_poly.pdbx_seq_one_letter_code_can   CGCGAATTCGCG 
_entity_poly.pdbx_strand_id                 A,B 
_entity_poly.pdbx_target_identifier         ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' IBB 
3 'MAGNESIUM ION'                                                            MG  
4 water                                                                      HOH 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  DC n 
1 2  DG n 
1 3  DC n 
1 4  DG n 
1 5  DA n 
1 6  DA n 
1 7  DT n 
1 8  DT n 
1 9  DC n 
1 10 DG n 
1 11 DC n 
1 12 DG n 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
DA  'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE"                                       ? 'C10 H14 N5 O6 P' 331.222 
DC  'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"                                        ? 'C9 H14 N3 O7 P'  307.197 
DG  'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE"                                       ? 'C10 H14 N5 O7 P' 347.221 
DT  'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE"                                               ? 'C10 H15 N2 O8 P' 322.208 
HOH non-polymer   . WATER                                                                      ? 'H2 O'            18.015  
IBB non-polymer   . '5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE' ? 'C23 H20 N6 O'    396.445 
MG  non-polymer   . 'MAGNESIUM ION'                                                            ? 'Mg 2'            24.305  
# 
loop_
_pdbx_poly_seq_scheme.asym_id 
_pdbx_poly_seq_scheme.entity_id 
_pdbx_poly_seq_scheme.seq_id 
_pdbx_poly_seq_scheme.mon_id 
_pdbx_poly_seq_scheme.ndb_seq_num 
_pdbx_poly_seq_scheme.pdb_seq_num 
_pdbx_poly_seq_scheme.auth_seq_num 
_pdbx_poly_seq_scheme.pdb_mon_id 
_pdbx_poly_seq_scheme.auth_mon_id 
_pdbx_poly_seq_scheme.pdb_strand_id 
_pdbx_poly_seq_scheme.pdb_ins_code 
_pdbx_poly_seq_scheme.hetero 
A 1 1  DC 1  1  1  DC C A . n 
A 1 2  DG 2  2  2  DG G A . n 
A 1 3  DC 3  3  3  DC C A . n 
A 1 4  DG 4  4  4  DG G A . n 
A 1 5  DA 5  5  5  DA A A . n 
A 1 6  DA 6  6  6  DA A A . n 
A 1 7  DT 7  7  7  DT T A . n 
A 1 8  DT 8  8  8  DT T A . n 
A 1 9  DC 9  9  9  DC C A . n 
A 1 10 DG 10 10 10 DG G A . n 
A 1 11 DC 11 11 11 DC C A . n 
A 1 12 DG 12 12 12 DG G A . n 
B 1 1  DC 1  13 13 DC C B . n 
B 1 2  DG 2  14 14 DG G B . n 
B 1 3  DC 3  15 15 DC C B . n 
B 1 4  DG 4  16 16 DG G B . n 
B 1 5  DA 5  17 17 DA A B . n 
B 1 6  DA 6  18 18 DA A B . n 
B 1 7  DT 7  19 19 DT T B . n 
B 1 8  DT 8  20 20 DT T B . n 
B 1 9  DC 9  21 21 DC C B . n 
B 1 10 DG 10 22 22 DG G B . n 
B 1 11 DC 11 23 23 DC C B . n 
B 1 12 DG 12 24 24 DG G B . n 
# 
loop_
_pdbx_nonpoly_scheme.asym_id 
_pdbx_nonpoly_scheme.entity_id 
_pdbx_nonpoly_scheme.mon_id 
_pdbx_nonpoly_scheme.ndb_seq_num 
_pdbx_nonpoly_scheme.pdb_seq_num 
_pdbx_nonpoly_scheme.auth_seq_num 
_pdbx_nonpoly_scheme.pdb_mon_id 
_pdbx_nonpoly_scheme.auth_mon_id 
_pdbx_nonpoly_scheme.pdb_strand_id 
_pdbx_nonpoly_scheme.pdb_ins_code 
C 2 IBB 1  25  25  IBB IBB A . 
D 3 MG  1  26  26  MG  MO6 A . 
E 4 HOH 1  29  29  HOH HOH A . 
E 4 HOH 2  30  30  HOH HOH A . 
E 4 HOH 3  31  31  HOH HOH A . 
E 4 HOH 4  33  33  HOH HOH A . 
E 4 HOH 5  34  34  HOH HOH A . 
E 4 HOH 6  37  37  HOH HOH A . 
E 4 HOH 7  38  38  HOH HOH A . 
E 4 HOH 8  40  40  HOH HOH A . 
E 4 HOH 9  41  41  HOH HOH A . 
E 4 HOH 10 42  42  HOH HOH A . 
E 4 HOH 11 43  43  HOH HOH A . 
E 4 HOH 12 44  44  HOH HOH A . 
E 4 HOH 13 45  45  HOH HOH A . 
E 4 HOH 14 47  47  HOH HOH A . 
E 4 HOH 15 49  49  HOH HOH A . 
E 4 HOH 16 50  50  HOH HOH A . 
E 4 HOH 17 52  52  HOH HOH A . 
E 4 HOH 18 54  54  HOH HOH A . 
E 4 HOH 19 55  55  HOH HOH A . 
E 4 HOH 20 58  58  HOH HOH A . 
E 4 HOH 21 60  60  HOH HOH A . 
E 4 HOH 22 62  62  HOH HOH A . 
E 4 HOH 23 63  63  HOH HOH A . 
E 4 HOH 24 65  65  HOH HOH A . 
E 4 HOH 25 66  66  HOH HOH A . 
E 4 HOH 26 67  67  HOH HOH A . 
E 4 HOH 27 69  69  HOH HOH A . 
E 4 HOH 28 70  70  HOH HOH A . 
E 4 HOH 29 72  72  HOH HOH A . 
E 4 HOH 30 75  75  HOH HOH A . 
E 4 HOH 31 76  76  HOH HOH A . 
E 4 HOH 32 78  78  HOH HOH A . 
E 4 HOH 33 79  79  HOH HOH A . 
E 4 HOH 34 80  80  HOH HOH A . 
E 4 HOH 35 83  83  HOH HOH A . 
E 4 HOH 36 86  86  HOH HOH A . 
E 4 HOH 37 87  87  HOH HOH A . 
E 4 HOH 38 88  88  HOH HOH A . 
E 4 HOH 39 89  89  HOH HOH A . 
E 4 HOH 40 90  90  HOH HOH A . 
E 4 HOH 41 91  91  HOH HOH A . 
E 4 HOH 42 92  92  HOH HOH A . 
E 4 HOH 43 93  93  HOH HOH A . 
E 4 HOH 44 94  94  HOH HOH A . 
E 4 HOH 45 95  95  HOH HOH A . 
E 4 HOH 46 100 100 HOH HOH A . 
E 4 HOH 47 101 101 HOH HOH A . 
E 4 HOH 48 102 102 HOH HOH A . 
E 4 HOH 49 103 103 HOH HOH A . 
E 4 HOH 50 104 104 HOH HOH A . 
E 4 HOH 51 105 105 HOH HOH A . 
E 4 HOH 52 106 106 HOH HOH A . 
E 4 HOH 53 107 107 HOH HOH A . 
E 4 HOH 54 108 108 HOH HOH A . 
E 4 HOH 55 109 109 HOH HOH A . 
E 4 HOH 56 111 26  HOH MO6 A . 
E 4 HOH 57 112 26  HOH MO6 A . 
E 4 HOH 58 113 26  HOH MO6 A . 
E 4 HOH 59 114 26  HOH MO6 A . 
E 4 HOH 60 115 26  HOH MO6 A . 
E 4 HOH 61 116 26  HOH MO6 A . 
F 4 HOH 1  27  27  HOH HOH B . 
F 4 HOH 2  28  28  HOH HOH B . 
F 4 HOH 3  32  32  HOH HOH B . 
F 4 HOH 4  35  35  HOH HOH B . 
F 4 HOH 5  36  36  HOH HOH B . 
F 4 HOH 6  39  39  HOH HOH B . 
F 4 HOH 7  46  46  HOH HOH B . 
F 4 HOH 8  48  48  HOH HOH B . 
F 4 HOH 9  51  51  HOH HOH B . 
F 4 HOH 10 53  53  HOH HOH B . 
F 4 HOH 11 56  56  HOH HOH B . 
F 4 HOH 12 57  57  HOH HOH B . 
F 4 HOH 13 59  59  HOH HOH B . 
F 4 HOH 14 61  61  HOH HOH B . 
F 4 HOH 15 64  64  HOH HOH B . 
F 4 HOH 16 68  68  HOH HOH B . 
F 4 HOH 17 71  71  HOH HOH B . 
F 4 HOH 18 73  73  HOH HOH B . 
F 4 HOH 19 74  74  HOH HOH B . 
F 4 HOH 20 77  77  HOH HOH B . 
F 4 HOH 21 81  81  HOH HOH B . 
F 4 HOH 22 82  82  HOH HOH B . 
F 4 HOH 23 84  84  HOH HOH B . 
F 4 HOH 24 85  85  HOH HOH B . 
F 4 HOH 25 96  96  HOH HOH B . 
F 4 HOH 26 97  97  HOH HOH B . 
F 4 HOH 27 98  98  HOH HOH B . 
F 4 HOH 28 99  99  HOH HOH B . 
F 4 HOH 29 110 110 HOH HOH B . 
# 
_software.name             X-PLOR 
_software.classification   refinement 
_software.version          . 
_software.citation_id      ? 
_software.pdbx_ordinal     1 
# 
_cell.entry_id           109D 
_cell.length_a           24.590 
_cell.length_b           40.440 
_cell.length_c           65.760 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        90.00 
_cell.Z_PDB              8 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         109D 
_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 
# 
_exptl.entry_id          109D 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   ? 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.23 
_exptl_crystal.density_percent_sol   44.88 
_exptl_crystal.description           ? 
# 
_diffrn.id                     1 
_diffrn.crystal_id             1 
_diffrn.ambient_temp           ? 
_diffrn.ambient_temp_details   ? 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               'AREA DETECTOR' 
_diffrn_detector.type                   XENTRONICS 
_diffrn_detector.pdbx_collection_date   ? 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   ? 
_diffrn_radiation.monochromator                    ? 
_diffrn_radiation.pdbx_diffrn_protocol             ? 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.5418 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'ROTATING ANODE' 
_diffrn_source.type                        ENRAF-NONIUS 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
_diffrn_source.pdbx_wavelength             1.5418 
_diffrn_source.pdbx_wavelength_list        ? 
# 
_reflns.entry_id                     109D 
_reflns.observed_criterion_sigma_I   ? 
_reflns.observed_criterion_sigma_F   ? 
_reflns.d_resolution_low             ? 
_reflns.d_resolution_high            ? 
_reflns.number_obs                   ? 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         87.000 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_refine.entry_id                                 109D 
_refine.ls_number_reflns_obs                     4016 
_refine.ls_number_reflns_all                     ? 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          2.000 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             8.000 
_refine.ls_d_res_high                            2.000 
_refine.ls_percent_reflns_obs                    ? 
_refine.ls_R_factor_obs                          0.1970000 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.1970000 
_refine.ls_R_factor_R_free                       ? 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 ? 
_refine.ls_number_reflns_R_free                  ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_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                    ? 
_refine.solvent_model_param_ksol                 ? 
_refine.solvent_model_param_bsol                 ? 
_refine.pdbx_ls_cross_valid_method               ? 
_refine.details                                  ? 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          ? 
_refine.pdbx_isotropic_thermal_model             ? 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.overall_SU_ML                            ? 
_refine.overall_SU_B                             ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.pdbx_overall_phase_error                 ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_hist.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_hist.cycle_id                         LAST 
_refine_hist.pdbx_number_atoms_protein        0 
_refine_hist.pdbx_number_atoms_nucleic_acid   486 
_refine_hist.pdbx_number_atoms_ligand         37 
_refine_hist.number_atoms_solvent             84 
_refine_hist.number_atoms_total               607 
_refine_hist.d_res_high                       2.000 
_refine_hist.d_res_low                        8.000 
# 
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 
x_bond_d                0.020 ? ? ? 'X-RAY DIFFRACTION' ? 
x_bond_d_na             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_bond_d_prot           ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d               ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d_na            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d_prot          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg             4.30  ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg_na          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg_prot        ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d      ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d      ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_mcbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_mcangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_scbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_scangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_database_PDB_matrix.entry_id          109D 
_database_PDB_matrix.origx[1][1]       1.000000 
_database_PDB_matrix.origx[1][2]       0.000000 
_database_PDB_matrix.origx[1][3]       0.000000 
_database_PDB_matrix.origx[2][1]       0.000000 
_database_PDB_matrix.origx[2][2]       1.000000 
_database_PDB_matrix.origx[2][3]       0.000000 
_database_PDB_matrix.origx[3][1]       0.000000 
_database_PDB_matrix.origx[3][2]       0.000000 
_database_PDB_matrix.origx[3][3]       1.000000 
_database_PDB_matrix.origx_vector[1]   0.00000 
_database_PDB_matrix.origx_vector[2]   0.00000 
_database_PDB_matrix.origx_vector[3]   0.00000 
# 
_struct.entry_id                  109D 
_struct.title                     
;VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2
;
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        109D 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, 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_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    109D 
_struct_ref.pdbx_db_accession          109D 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
loop_
_struct_ref_seq.align_id 
_struct_ref_seq.ref_id 
_struct_ref_seq.pdbx_PDB_id_code 
_struct_ref_seq.pdbx_strand_id 
_struct_ref_seq.seq_align_beg 
_struct_ref_seq.pdbx_seq_align_beg_ins_code 
_struct_ref_seq.seq_align_end 
_struct_ref_seq.pdbx_seq_align_end_ins_code 
_struct_ref_seq.pdbx_db_accession 
_struct_ref_seq.db_align_beg 
_struct_ref_seq.pdbx_db_align_beg_ins_code 
_struct_ref_seq.db_align_end 
_struct_ref_seq.pdbx_db_align_end_ins_code 
_struct_ref_seq.pdbx_auth_seq_align_beg 
_struct_ref_seq.pdbx_auth_seq_align_end 
1 1 109D A 1 ? 12 ? 109D 1  ? 12 ? 1  12 
2 1 109D B 1 ? 12 ? 109D 13 ? 24 ? 13 24 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   dimeric 
_pdbx_struct_assembly.oligomeric_count     2 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D,E,F 
# 
_pdbx_struct_oper_list.id                   1 
_pdbx_struct_oper_list.type                 'identity operation' 
_pdbx_struct_oper_list.name                 1_555 
_pdbx_struct_oper_list.symmetry_operation   x,y,z 
_pdbx_struct_oper_list.matrix[1][1]         1.0000000000 
_pdbx_struct_oper_list.matrix[1][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[1][3]         0.0000000000 
_pdbx_struct_oper_list.vector[1]            0.0000000000 
_pdbx_struct_oper_list.matrix[2][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[2][2]         1.0000000000 
_pdbx_struct_oper_list.matrix[2][3]         0.0000000000 
_pdbx_struct_oper_list.vector[2]            0.0000000000 
_pdbx_struct_oper_list.matrix[3][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
_pdbx_struct_oper_list.vector[3]            0.0000000000 
# 
_struct_biol.id   1 
# 
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 ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 111 1_555 ? ? ? ? ? ? ?               2.179 ? ? 
metalc2  metalc ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 112 1_555 ? ? ? ? ? ? ?               2.192 ? ? 
metalc3  metalc ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 113 1_555 ? ? ? ? ? ? ?               2.200 ? ? 
metalc4  metalc ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 114 1_555 ? ? ? ? ? ? ?               2.305 ? ? 
metalc5  metalc ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 115 1_555 ? ? ? ? ? ? ?               2.206 ? ? 
metalc6  metalc ? ? D MG .  MG ? ? ? 1_555 E HOH .  O  ? ? A MG 26 A HOH 116 1_555 ? ? ? ? ? ? ?               2.251 ? ? 
hydrog1  hydrog ? ? A DC 1  N3 ? ? ? 1_555 B DG  12 N1 ? ? A DC 1  B DG  24  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog2  hydrog ? ? A DC 1  N4 ? ? ? 1_555 B DG  12 O6 ? ? A DC 1  B DG  24  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog3  hydrog ? ? A DC 1  O2 ? ? ? 1_555 B DG  12 N2 ? ? A DC 1  B DG  24  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog4  hydrog ? ? A DG 2  N1 ? ? ? 1_555 B DC  11 N3 ? ? A DG 2  B DC  23  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog5  hydrog ? ? A DG 2  N2 ? ? ? 1_555 B DC  11 O2 ? ? A DG 2  B DC  23  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog6  hydrog ? ? A DG 2  O6 ? ? ? 1_555 B DC  11 N4 ? ? A DG 2  B DC  23  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog7  hydrog ? ? A DC 3  N3 ? ? ? 1_555 B DG  10 N1 ? ? A DC 3  B DG  22  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog8  hydrog ? ? A DC 3  N4 ? ? ? 1_555 B DG  10 O6 ? ? A DC 3  B DG  22  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog9  hydrog ? ? A DC 3  O2 ? ? ? 1_555 B DG  10 N2 ? ? A DC 3  B DG  22  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog10 hydrog ? ? A DG 4  N1 ? ? ? 1_555 B DC  9  N3 ? ? A DG 4  B DC  21  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog11 hydrog ? ? A DG 4  N2 ? ? ? 1_555 B DC  9  O2 ? ? A DG 4  B DC  21  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog12 hydrog ? ? A DG 4  O6 ? ? ? 1_555 B DC  9  N4 ? ? A DG 4  B DC  21  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog13 hydrog ? ? A DA 5  N1 ? ? ? 1_555 B DT  8  N3 ? ? A DA 5  B DT  20  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog14 hydrog ? ? A DA 5  N6 ? ? ? 1_555 B DT  8  O4 ? ? A DA 5  B DT  20  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog15 hydrog ? ? A DA 6  N6 ? ? ? 1_555 B DA  6  N1 ? ? A DA 6  B DA  18  1_555 ? ? ? ? ? ? 'DA-DA MISPAIR' ?     ? ? 
hydrog16 hydrog ? ? A DA 6  N1 ? ? ? 1_555 B DT  7  N3 ? ? A DA 6  B DT  19  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog17 hydrog ? ? A DA 6  N6 ? ? ? 1_555 B DT  7  O4 ? ? A DA 6  B DT  19  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog18 hydrog ? ? A DT 7  N3 ? ? ? 1_555 B DA  6  N1 ? ? A DT 7  B DA  18  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog19 hydrog ? ? A DT 7  O4 ? ? ? 1_555 B DA  6  N6 ? ? A DT 7  B DA  18  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog20 hydrog ? ? A DT 8  N3 ? ? ? 1_555 B DA  5  N1 ? ? A DT 8  B DA  17  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog21 hydrog ? ? A DT 8  O4 ? ? ? 1_555 B DA  5  N6 ? ? A DT 8  B DA  17  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog22 hydrog ? ? A DC 9  N3 ? ? ? 1_555 B DG  4  N1 ? ? A DC 9  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog23 hydrog ? ? A DC 9  N4 ? ? ? 1_555 B DG  4  O6 ? ? A DC 9  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog24 hydrog ? ? A DC 9  O2 ? ? ? 1_555 B DG  4  N2 ? ? A DC 9  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog25 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC  3  N3 ? ? A DG 10 B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog26 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC  3  O2 ? ? A DG 10 B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog27 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC  3  N4 ? ? A DG 10 B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog28 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG  2  N1 ? ? A DC 11 B DG  14  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog29 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG  2  O6 ? ? A DC 11 B DG  14  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog30 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG  2  N2 ? ? A DC 11 B DG  14  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog31 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC  1  N3 ? ? A DG 12 B DC  13  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog32 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC  1  O2 ? ? A DG 12 B DC  13  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog33 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC  1  N4 ? ? A DG 12 B DC  13  1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
metalc ? ? 
hydrog ? ? 
# 
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  O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 112 ? 1_555 93.1  ? 
2  O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 113 ? 1_555 95.5  ? 
3  O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 113 ? 1_555 87.0  ? 
4  O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 174.7 ? 
5  O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 91.3  ? 
6  O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 114 ? 1_555 87.5  ? 
7  O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 90.9  ? 
8  O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 171.6 ? 
9  O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 85.3  ? 
10 O ? E HOH . ? A HOH 114 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 115 ? 1_555 85.0  ? 
11 O ? E HOH . ? A HOH 111 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 93.6  ? 
12 O ? E HOH . ? A HOH 112 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 91.1  ? 
13 O ? E HOH . ? A HOH 113 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 170.7 ? 
14 O ? E HOH . ? A HOH 114 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 83.5  ? 
15 O ? E HOH . ? A HOH 115 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 96.0  ? 
# 
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 IBB 25 ? 12 'BINDING SITE FOR RESIDUE IBB A 25' 
AC2 Software A MG  26 ? 6  'BINDING SITE FOR RESIDUE MG A 26'  
1   ?        ? ?   ?  ? ?  ?                                   
# 
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 12 DA  A 5 ? DA  A 5   . ? 1_555 ? 
2  AC1 12 DA  A 6 ? DA  A 6   . ? 1_555 ? 
3  AC1 12 DT  A 7 ? DT  A 7   . ? 1_555 ? 
4  AC1 12 DT  A 8 ? DT  A 8   . ? 1_555 ? 
5  AC1 12 DC  A 9 ? DC  A 9   . ? 1_555 ? 
6  AC1 12 HOH E . ? HOH A 40  . ? 1_555 ? 
7  AC1 12 HOH E . ? HOH A 62  . ? 1_555 ? 
8  AC1 12 HOH E . ? HOH A 66  . ? 1_555 ? 
9  AC1 12 DA  B 6 ? DA  B 18  . ? 1_555 ? 
10 AC1 12 DT  B 7 ? DT  B 19  . ? 1_555 ? 
11 AC1 12 DT  B 8 ? DT  B 20  . ? 1_555 ? 
12 AC1 12 DC  B 9 ? DC  B 21  . ? 1_555 ? 
13 AC2 6  HOH E . ? HOH A 111 . ? 1_555 ? 
14 AC2 6  HOH E . ? HOH A 112 . ? 1_555 ? 
15 AC2 6  HOH E . ? HOH A 113 . ? 1_555 ? 
16 AC2 6  HOH E . ? HOH A 114 . ? 1_555 ? 
17 AC2 6  HOH E . ? HOH A 115 . ? 1_555 ? 
18 AC2 6  HOH E . ? HOH A 116 . ? 1_555 ? 
# 
loop_
_pdbx_validate_rmsd_bond.id 
_pdbx_validate_rmsd_bond.PDB_model_num 
_pdbx_validate_rmsd_bond.auth_atom_id_1 
_pdbx_validate_rmsd_bond.auth_asym_id_1 
_pdbx_validate_rmsd_bond.auth_comp_id_1 
_pdbx_validate_rmsd_bond.auth_seq_id_1 
_pdbx_validate_rmsd_bond.PDB_ins_code_1 
_pdbx_validate_rmsd_bond.label_alt_id_1 
_pdbx_validate_rmsd_bond.auth_atom_id_2 
_pdbx_validate_rmsd_bond.auth_asym_id_2 
_pdbx_validate_rmsd_bond.auth_comp_id_2 
_pdbx_validate_rmsd_bond.auth_seq_id_2 
_pdbx_validate_rmsd_bond.PDB_ins_code_2 
_pdbx_validate_rmsd_bond.label_alt_id_2 
_pdbx_validate_rmsd_bond.bond_value 
_pdbx_validate_rmsd_bond.bond_target_value 
_pdbx_validate_rmsd_bond.bond_deviation 
_pdbx_validate_rmsd_bond.bond_standard_deviation 
_pdbx_validate_rmsd_bond.linker_flag 
1  1 "C3'" A DC 3  ? ? "C2'" A DC 3  ? ? 1.464 1.516 -0.052 0.008 N 
2  1 C5    A DG 4  ? ? N7    A DG 4  ? ? 1.347 1.388 -0.041 0.006 N 
3  1 C6    A DA 6  ? ? N1    A DA 6  ? ? 1.414 1.351 0.063  0.007 N 
4  1 N9    A DA 6  ? ? C4    A DA 6  ? ? 1.416 1.374 0.042  0.006 N 
5  1 C5    A DG 10 ? ? N7    A DG 10 ? ? 1.351 1.388 -0.037 0.006 N 
6  1 N1    B DA 18 ? ? C2    B DA 18 ? ? 1.225 1.339 -0.114 0.009 N 
7  1 C2    B DA 18 ? ? N3    B DA 18 ? ? 1.174 1.331 -0.157 0.009 N 
8  1 N3    B DA 18 ? ? C4    B DA 18 ? ? 1.470 1.344 0.126  0.006 N 
9  1 C6    B DA 18 ? ? N1    B DA 18 ? ? 1.275 1.351 -0.076 0.007 N 
10 1 C5    B DA 18 ? ? N7    B DA 18 ? ? 1.348 1.388 -0.040 0.006 N 
11 1 N9    B DA 18 ? ? C4    B DA 18 ? ? 1.473 1.374 0.099  0.006 N 
12 1 C5    B DG 22 ? ? N7    B DG 22 ? ? 1.345 1.388 -0.043 0.006 N 
13 1 C5    B DG 24 ? ? N7    B DG 24 ? ? 1.345 1.388 -0.043 0.006 N 
# 
loop_
_pdbx_validate_rmsd_angle.id 
_pdbx_validate_rmsd_angle.PDB_model_num 
_pdbx_validate_rmsd_angle.auth_atom_id_1 
_pdbx_validate_rmsd_angle.auth_asym_id_1 
_pdbx_validate_rmsd_angle.auth_comp_id_1 
_pdbx_validate_rmsd_angle.auth_seq_id_1 
_pdbx_validate_rmsd_angle.PDB_ins_code_1 
_pdbx_validate_rmsd_angle.label_alt_id_1 
_pdbx_validate_rmsd_angle.auth_atom_id_2 
_pdbx_validate_rmsd_angle.auth_asym_id_2 
_pdbx_validate_rmsd_angle.auth_comp_id_2 
_pdbx_validate_rmsd_angle.auth_seq_id_2 
_pdbx_validate_rmsd_angle.PDB_ins_code_2 
_pdbx_validate_rmsd_angle.label_alt_id_2 
_pdbx_validate_rmsd_angle.auth_atom_id_3 
_pdbx_validate_rmsd_angle.auth_asym_id_3 
_pdbx_validate_rmsd_angle.auth_comp_id_3 
_pdbx_validate_rmsd_angle.auth_seq_id_3 
_pdbx_validate_rmsd_angle.PDB_ins_code_3 
_pdbx_validate_rmsd_angle.label_alt_id_3 
_pdbx_validate_rmsd_angle.angle_value 
_pdbx_validate_rmsd_angle.angle_target_value 
_pdbx_validate_rmsd_angle.angle_deviation 
_pdbx_validate_rmsd_angle.angle_standard_deviation 
_pdbx_validate_rmsd_angle.linker_flag 
1  1 "O4'" A DC 1  ? ? "C1'" A DC 1  ? ? N1    A DC 1  ? ? 103.46 108.00 -4.54  0.70 N 
2  1 "C3'" A DG 2  ? ? "O3'" A DG 2  ? ? P     A DC 3  ? ? 128.57 119.70 8.87   1.20 Y 
3  1 P     A DC 3  ? ? "O5'" A DC 3  ? ? "C5'" A DC 3  ? ? 109.68 120.90 -11.22 1.60 N 
4  1 "O4'" A DC 3  ? ? "C1'" A DC 3  ? ? "C2'" A DC 3  ? ? 99.90  105.90 -6.00  0.80 N 
5  1 "O4'" A DC 3  ? ? "C1'" A DC 3  ? ? N1    A DC 3  ? ? 113.26 108.30 4.96   0.30 N 
6  1 "O4'" A DA 6  ? ? "C4'" A DA 6  ? ? "C3'" A DA 6  ? ? 101.02 104.50 -3.48  0.40 N 
7  1 "C1'" A DA 6  ? ? "O4'" A DA 6  ? ? "C4'" A DA 6  ? ? 116.89 110.30 6.59   0.70 N 
8  1 "O4'" A DA 6  ? ? "C1'" A DA 6  ? ? "C2'" A DA 6  ? ? 99.87  105.90 -6.03  0.80 N 
9  1 "O4'" A DA 6  ? ? "C1'" A DA 6  ? ? N9    A DA 6  ? ? 111.39 108.30 3.09   0.30 N 
10 1 C6    A DA 6  ? ? N1    A DA 6  ? ? C2    A DA 6  ? ? 105.50 118.60 -13.10 0.60 N 
11 1 N1    A DA 6  ? ? C2    A DA 6  ? ? N3    A DA 6  ? ? 136.72 129.30 7.42   0.50 N 
12 1 N3    A DA 6  ? ? C4    A DA 6  ? ? C5    A DA 6  ? ? 121.93 126.80 -4.87  0.70 N 
13 1 C5    A DA 6  ? ? C6    A DA 6  ? ? N1    A DA 6  ? ? 124.46 117.70 6.76   0.50 N 
14 1 C5    A DA 6  ? ? N7    A DA 6  ? ? C8    A DA 6  ? ? 107.41 103.90 3.51   0.50 N 
15 1 N9    A DA 6  ? ? C4    A DA 6  ? ? C5    A DA 6  ? ? 108.20 105.80 2.40   0.40 N 
16 1 C5    A DA 6  ? ? C6    A DA 6  ? ? N6    A DA 6  ? ? 117.36 123.70 -6.34  0.80 N 
17 1 "C3'" A DA 6  ? ? "O3'" A DA 6  ? ? P     A DT 7  ? ? 129.35 119.70 9.65   1.20 Y 
18 1 "O4'" A DT 7  ? ? "C4'" A DT 7  ? ? "C3'" A DT 7  ? ? 101.04 104.50 -3.46  0.40 N 
19 1 "O4'" A DT 7  ? ? "C1'" A DT 7  ? ? N1    A DT 7  ? ? 113.53 108.30 5.23   0.30 N 
20 1 C6    A DT 7  ? ? N1    A DT 7  ? ? C2    A DT 7  ? ? 118.05 121.30 -3.25  0.50 N 
21 1 N3    A DT 7  ? ? C4    A DT 7  ? ? C5    A DT 7  ? ? 109.49 115.20 -5.71  0.60 N 
22 1 C4    A DT 7  ? ? C5    A DT 7  ? ? C6    A DT 7  ? ? 124.03 118.00 6.03   0.60 N 
23 1 N3    A DT 7  ? ? C2    A DT 7  ? ? O2    A DT 7  ? ? 115.73 122.30 -6.57  0.60 N 
24 1 C6    A DT 7  ? ? C5    A DT 7  ? ? C7    A DT 7  ? ? 116.75 122.90 -6.15  0.60 N 
25 1 "O4'" A DT 8  ? ? "C4'" A DT 8  ? ? "C3'" A DT 8  ? ? 101.84 104.50 -2.66  0.40 N 
26 1 N1    A DT 8  ? ? C2    A DT 8  ? ? N3    A DT 8  ? ? 118.41 114.60 3.81   0.60 N 
27 1 C4    A DT 8  ? ? C5    A DT 8  ? ? C6    A DT 8  ? ? 122.77 118.00 4.77   0.60 N 
28 1 N3    A DT 8  ? ? C2    A DT 8  ? ? O2    A DT 8  ? ? 118.14 122.30 -4.16  0.60 N 
29 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1    A DC 11 ? ? 101.07 108.00 -6.93  0.70 N 
30 1 "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? 101.56 104.50 -2.94  0.40 N 
31 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P     B DG 14 ? ? 127.56 119.70 7.86   1.20 Y 
32 1 "O4'" B DC 15 ? ? "C4'" B DC 15 ? ? "C3'" B DC 15 ? ? 101.34 104.50 -3.16  0.40 N 
33 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? "C2'" B DC 15 ? ? 100.85 105.90 -5.05  0.80 N 
34 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1    B DC 15 ? ? 110.88 108.30 2.58   0.30 N 
35 1 C2    B DC 15 ? ? N3    B DC 15 ? ? C4    B DC 15 ? ? 124.02 119.90 4.12   0.50 N 
36 1 N3    B DC 15 ? ? C4    B DC 15 ? ? C5    B DC 15 ? ? 118.42 121.90 -3.48  0.40 N 
37 1 "C3'" B DA 17 ? ? "O3'" B DA 17 ? ? P     B DA 18 ? ? 131.17 119.70 11.47  1.20 Y 
38 1 "C1'" B DA 18 ? ? "O4'" B DA 18 ? ? "C4'" B DA 18 ? ? 118.54 110.30 8.24   0.70 N 
39 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? "C2'" B DA 18 ? ? 95.20  105.90 -10.70 0.80 N 
40 1 C6    B DA 18 ? ? N1    B DA 18 ? ? C2    B DA 18 ? ? 132.96 118.60 14.36  0.60 N 
41 1 N1    B DA 18 ? ? C2    B DA 18 ? ? N3    B DA 18 ? ? 120.94 129.30 -8.36  0.50 N 
42 1 C2    B DA 18 ? ? N3    B DA 18 ? ? C4    B DA 18 ? ? 116.87 110.60 6.27   0.50 N 
43 1 N3    B DA 18 ? ? C4    B DA 18 ? ? C5    B DA 18 ? ? 121.41 126.80 -5.39  0.70 N 
44 1 C4    B DA 18 ? ? C5    B DA 18 ? ? C6    B DA 18 ? ? 111.72 117.00 -5.28  0.50 N 
45 1 N9    B DA 18 ? ? C4    B DA 18 ? ? C5    B DA 18 ? ? 100.33 105.80 -5.47  0.40 N 
46 1 N3    B DA 18 ? ? C4    B DA 18 ? ? N9    B DA 18 ? ? 138.24 127.40 10.84  0.80 N 
47 1 N1    B DA 18 ? ? C6    B DA 18 ? ? N6    B DA 18 ? ? 106.90 118.60 -11.70 0.60 N 
48 1 C5    B DA 18 ? ? C6    B DA 18 ? ? N6    B DA 18 ? ? 137.03 123.70 13.33  0.80 N 
49 1 P     B DT 19 ? ? "O5'" B DT 19 ? ? "C5'" B DT 19 ? ? 108.26 120.90 -12.64 1.60 N 
50 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1    B DT 19 ? ? 110.93 108.30 2.63   0.30 N 
51 1 N3    B DT 19 ? ? C4    B DT 19 ? ? C5    B DT 19 ? ? 110.65 115.20 -4.55  0.60 N 
52 1 C4    B DT 19 ? ? C5    B DT 19 ? ? C6    B DT 19 ? ? 122.15 118.00 4.15   0.60 N 
53 1 "O4'" B DT 20 ? ? "C4'" B DT 20 ? ? "C3'" B DT 20 ? ? 100.26 104.50 -4.24  0.40 N 
54 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1    B DT 20 ? ? 102.92 108.00 -5.08  0.70 N 
55 1 P     B DC 21 ? ? "O5'" B DC 21 ? ? "C5'" B DC 21 ? ? 111.19 120.90 -9.71  1.60 N 
56 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1    B DC 21 ? ? 102.63 108.00 -5.37  0.70 N 
57 1 N1    B DC 21 ? ? C2    B DC 21 ? ? O2    B DC 21 ? ? 122.51 118.90 3.61   0.60 N 
58 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9    B DG 22 ? ? 111.21 108.30 2.91   0.30 N 
59 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1    B DC 23 ? ? 111.96 108.30 3.66   0.30 N 
60 1 N9    B DG 24 ? ? "C1'" B DG 24 ? ? "C2'" B DG 24 ? ? 100.93 112.60 -11.67 1.90 N 
61 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9    B DG 24 ? ? 116.31 108.30 8.01   0.30 N 
62 1 N7    B DG 24 ? ? C8    B DG 24 ? ? N9    B DG 24 ? ? 116.65 113.10 3.55   0.50 N 
63 1 C8    B DG 24 ? ? N9    B DG 24 ? ? C4    B DG 24 ? ? 103.30 106.40 -3.10  0.40 N 
64 1 N3    B DG 24 ? ? C2    B DG 24 ? ? N2    B DG 24 ? ? 114.82 119.90 -5.08  0.70 N 
65 1 N1    B DG 24 ? ? C6    B DG 24 ? ? O6    B DG 24 ? ? 123.63 119.90 3.73   0.60 N 
# 
_struct_site_keywords.site_id   1 
_struct_site_keywords.text      'MINOR GROOVE BINDER' 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_ordinal 
DA  OP3    O  N N 1   
DA  P      P  N N 2   
DA  OP1    O  N N 3   
DA  OP2    O  N N 4   
DA  "O5'"  O  N N 5   
DA  "C5'"  C  N N 6   
DA  "C4'"  C  N R 7   
DA  "O4'"  O  N N 8   
DA  "C3'"  C  N S 9   
DA  "O3'"  O  N N 10  
DA  "C2'"  C  N N 11  
DA  "C1'"  C  N R 12  
DA  N9     N  Y N 13  
DA  C8     C  Y N 14  
DA  N7     N  Y N 15  
DA  C5     C  Y N 16  
DA  C6     C  Y N 17  
DA  N6     N  N N 18  
DA  N1     N  Y N 19  
DA  C2     C  Y N 20  
DA  N3     N  Y N 21  
DA  C4     C  Y N 22  
DA  HOP3   H  N N 23  
DA  HOP2   H  N N 24  
DA  "H5'"  H  N N 25  
DA  "H5''" H  N N 26  
DA  "H4'"  H  N N 27  
DA  "H3'"  H  N N 28  
DA  "HO3'" H  N N 29  
DA  "H2'"  H  N N 30  
DA  "H2''" H  N N 31  
DA  "H1'"  H  N N 32  
DA  H8     H  N N 33  
DA  H61    H  N N 34  
DA  H62    H  N N 35  
DA  H2     H  N N 36  
DC  OP3    O  N N 37  
DC  P      P  N N 38  
DC  OP1    O  N N 39  
DC  OP2    O  N N 40  
DC  "O5'"  O  N N 41  
DC  "C5'"  C  N N 42  
DC  "C4'"  C  N R 43  
DC  "O4'"  O  N N 44  
DC  "C3'"  C  N S 45  
DC  "O3'"  O  N N 46  
DC  "C2'"  C  N N 47  
DC  "C1'"  C  N R 48  
DC  N1     N  N N 49  
DC  C2     C  N N 50  
DC  O2     O  N N 51  
DC  N3     N  N N 52  
DC  C4     C  N N 53  
DC  N4     N  N N 54  
DC  C5     C  N N 55  
DC  C6     C  N N 56  
DC  HOP3   H  N N 57  
DC  HOP2   H  N N 58  
DC  "H5'"  H  N N 59  
DC  "H5''" H  N N 60  
DC  "H4'"  H  N N 61  
DC  "H3'"  H  N N 62  
DC  "HO3'" H  N N 63  
DC  "H2'"  H  N N 64  
DC  "H2''" H  N N 65  
DC  "H1'"  H  N N 66  
DC  H41    H  N N 67  
DC  H42    H  N N 68  
DC  H5     H  N N 69  
DC  H6     H  N N 70  
DG  OP3    O  N N 71  
DG  P      P  N N 72  
DG  OP1    O  N N 73  
DG  OP2    O  N N 74  
DG  "O5'"  O  N N 75  
DG  "C5'"  C  N N 76  
DG  "C4'"  C  N R 77  
DG  "O4'"  O  N N 78  
DG  "C3'"  C  N S 79  
DG  "O3'"  O  N N 80  
DG  "C2'"  C  N N 81  
DG  "C1'"  C  N R 82  
DG  N9     N  Y N 83  
DG  C8     C  Y N 84  
DG  N7     N  Y N 85  
DG  C5     C  Y N 86  
DG  C6     C  N N 87  
DG  O6     O  N N 88  
DG  N1     N  N N 89  
DG  C2     C  N N 90  
DG  N2     N  N N 91  
DG  N3     N  N N 92  
DG  C4     C  Y N 93  
DG  HOP3   H  N N 94  
DG  HOP2   H  N N 95  
DG  "H5'"  H  N N 96  
DG  "H5''" H  N N 97  
DG  "H4'"  H  N N 98  
DG  "H3'"  H  N N 99  
DG  "HO3'" H  N N 100 
DG  "H2'"  H  N N 101 
DG  "H2''" H  N N 102 
DG  "H1'"  H  N N 103 
DG  H8     H  N N 104 
DG  H1     H  N N 105 
DG  H21    H  N N 106 
DG  H22    H  N N 107 
DT  OP3    O  N N 108 
DT  P      P  N N 109 
DT  OP1    O  N N 110 
DT  OP2    O  N N 111 
DT  "O5'"  O  N N 112 
DT  "C5'"  C  N N 113 
DT  "C4'"  C  N R 114 
DT  "O4'"  O  N N 115 
DT  "C3'"  C  N S 116 
DT  "O3'"  O  N N 117 
DT  "C2'"  C  N N 118 
DT  "C1'"  C  N R 119 
DT  N1     N  N N 120 
DT  C2     C  N N 121 
DT  O2     O  N N 122 
DT  N3     N  N N 123 
DT  C4     C  N N 124 
DT  O4     O  N N 125 
DT  C5     C  N N 126 
DT  C7     C  N N 127 
DT  C6     C  N N 128 
DT  HOP3   H  N N 129 
DT  HOP2   H  N N 130 
DT  "H5'"  H  N N 131 
DT  "H5''" H  N N 132 
DT  "H4'"  H  N N 133 
DT  "H3'"  H  N N 134 
DT  "HO3'" H  N N 135 
DT  "H2'"  H  N N 136 
DT  "H2''" H  N N 137 
DT  "H1'"  H  N N 138 
DT  H3     H  N N 139 
DT  H71    H  N N 140 
DT  H72    H  N N 141 
DT  H73    H  N N 142 
DT  H6     H  N N 143 
HOH O      O  N N 144 
HOH H1     H  N N 145 
HOH H2     H  N N 146 
IBB C1     C  N N 147 
IBB C2     C  N N 148 
IBB C3     C  N N 149 
IBB C4     C  Y N 150 
IBB C5     C  Y N 151 
IBB C6     C  Y N 152 
IBB C7     C  Y N 153 
IBB C8     C  Y N 154 
IBB C9     C  Y N 155 
IBB C10    C  Y N 156 
IBB C11    C  Y N 157 
IBB C12    C  Y N 158 
IBB C13    C  Y N 159 
IBB C14    C  Y N 160 
IBB C15    C  Y N 161 
IBB C16    C  Y N 162 
IBB C17    C  Y N 163 
IBB C18    C  Y N 164 
IBB C19    C  Y N 165 
IBB C20    C  Y N 166 
IBB C21    C  Y N 167 
IBB C22    C  Y N 168 
IBB C23    C  Y N 169 
IBB N1     N  N N 170 
IBB N2     N  N N 171 
IBB N3     N  Y N 172 
IBB N4     N  Y N 173 
IBB N5     N  Y N 174 
IBB N6     N  Y N 175 
IBB O1     O  N N 176 
IBB H1     H  N N 177 
IBB H21A   H  N N 178 
IBB H22    H  N N 179 
IBB H31    H  N N 180 
IBB H32    H  N N 181 
IBB H5     H  N N 182 
IBB H6     H  N N 183 
IBB H9     H  N N 184 
IBB H13    H  N N 185 
IBB H14    H  N N 186 
IBB H17    H  N N 187 
IBB H18    H  N N 188 
IBB H20    H  N N 189 
IBB H21    H  N N 190 
IBB H23    H  N N 191 
IBB HN1    H  N N 192 
IBB HN2    H  N N 193 
IBB HN3    H  N N 194 
IBB HN6    H  N N 195 
IBB HO1    H  N N 196 
MG  MG     MG N N 197 
# 
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 
IBB C1    C4     sing N N 152 
IBB C1    N1     sing N N 153 
IBB C1    N2     sing N N 154 
IBB C1    H1     sing N N 155 
IBB C2    C3     sing N N 156 
IBB C2    N1     sing N N 157 
IBB C2    H21A   sing N N 158 
IBB C2    H22    sing N N 159 
IBB C3    N2     sing N N 160 
IBB C3    H31    sing N N 161 
IBB C3    H32    sing N N 162 
IBB C4    C5     sing Y N 163 
IBB C4    C9     doub Y N 164 
IBB C5    C6     doub Y N 165 
IBB C5    H5     sing N N 166 
IBB C6    C7     sing Y N 167 
IBB C6    H6     sing N N 168 
IBB C7    C8     doub Y N 169 
IBB C7    N4     sing Y N 170 
IBB C8    C9     sing Y N 171 
IBB C8    N3     sing Y N 172 
IBB C9    H9     sing N N 173 
IBB C10   C22    sing Y N 174 
IBB C10   N3     sing Y N 175 
IBB C10   N4     doub Y N 176 
IBB C11   C12    doub Y N 177 
IBB C11   C23    sing Y N 178 
IBB C11   N6     sing Y N 179 
IBB C12   C13    sing Y N 180 
IBB C12   N5     sing Y N 181 
IBB C13   C14    doub Y N 182 
IBB C13   H13    sing N N 183 
IBB C14   C22    sing Y N 184 
IBB C14   H14    sing N N 185 
IBB C15   C16    sing Y N 186 
IBB C15   N5     doub Y N 187 
IBB C15   N6     sing Y N 188 
IBB C16   C17    sing Y N 189 
IBB C16   C21    doub Y N 190 
IBB C17   C18    doub Y N 191 
IBB C17   H17    sing N N 192 
IBB C18   C19    sing Y N 193 
IBB C18   H18    sing N N 194 
IBB C19   C20    doub Y N 195 
IBB C19   O1     sing N N 196 
IBB C20   C21    sing Y N 197 
IBB C20   H20    sing N N 198 
IBB C21   H21    sing N N 199 
IBB C22   C23    doub Y N 200 
IBB C23   H23    sing N N 201 
IBB N1    HN1    sing N N 202 
IBB N2    HN2    sing N N 203 
IBB N3    HN3    sing N N 204 
IBB N6    HN6    sing N N 205 
IBB O1    HO1    sing N N 206 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
109D 'double helix'         
109D 'b-form double helix'  
109D 'mismatched base pair' 
# 
loop_
_ndb_struct_na_base_pair.model_number 
_ndb_struct_na_base_pair.i_label_asym_id 
_ndb_struct_na_base_pair.i_label_comp_id 
_ndb_struct_na_base_pair.i_label_seq_id 
_ndb_struct_na_base_pair.i_symmetry 
_ndb_struct_na_base_pair.j_label_asym_id 
_ndb_struct_na_base_pair.j_label_comp_id 
_ndb_struct_na_base_pair.j_label_seq_id 
_ndb_struct_na_base_pair.j_symmetry 
_ndb_struct_na_base_pair.shear 
_ndb_struct_na_base_pair.stretch 
_ndb_struct_na_base_pair.stagger 
_ndb_struct_na_base_pair.buckle 
_ndb_struct_na_base_pair.propeller 
_ndb_struct_na_base_pair.opening 
_ndb_struct_na_base_pair.pair_number 
_ndb_struct_na_base_pair.pair_name 
_ndb_struct_na_base_pair.i_auth_asym_id 
_ndb_struct_na_base_pair.i_auth_seq_id 
_ndb_struct_na_base_pair.i_PDB_ins_code 
_ndb_struct_na_base_pair.j_auth_asym_id 
_ndb_struct_na_base_pair.j_auth_seq_id 
_ndb_struct_na_base_pair.j_PDB_ins_code 
_ndb_struct_na_base_pair.hbond_type_28 
_ndb_struct_na_base_pair.hbond_type_12 
1 A DC 1  1_555 B DG 12 1_555 0.227  -0.183 -0.224 5.955   -13.604 -0.490 1  A_DC1:DG24_B  A 1  ? B 24 ? 19 1 
1 A DG 2  1_555 B DC 11 1_555 -0.035 -0.233 0.260  -0.896  -8.828  -3.452 2  A_DG2:DC23_B  A 2  ? B 23 ? 19 1 
1 A DC 3  1_555 B DG 10 1_555 0.013  -0.140 -0.005 -0.627  -5.057  -1.400 3  A_DC3:DG22_B  A 3  ? B 22 ? 19 1 
1 A DG 4  1_555 B DC 9  1_555 -0.152 -0.038 -0.025 11.866  -4.328  -2.655 4  A_DG4:DC21_B  A 4  ? B 21 ? 19 1 
1 A DA 5  1_555 B DT 8  1_555 0.096  -0.068 -0.197 6.887   -19.745 0.156  5  A_DA5:DT20_B  A 5  ? B 20 ? 20 1 
1 A DA 6  1_555 B DT 7  1_555 0.047  -0.226 0.554  -6.398  -17.803 2.897  6  A_DA6:DT19_B  A 6  ? B 19 ? 20 1 
1 A DT 7  1_555 B DA 6  1_555 -0.656 -0.184 0.761  0.750   -7.168  18.116 7  A_DT7:DA18_B  A 7  ? B 18 ? 20 1 
1 A DT 8  1_555 B DA 5  1_555 -0.151 -0.194 -0.063 -7.253  -18.250 -2.478 8  A_DT8:DA17_B  A 8  ? B 17 ? 20 1 
1 A DC 9  1_555 B DG 4  1_555 -0.013 -0.113 -0.006 -10.992 -8.317  -1.696 9  A_DC9:DG16_B  A 9  ? B 16 ? 19 1 
1 A DG 10 1_555 B DC 3  1_555 -0.011 -0.210 0.087  4.340   -1.819  -0.710 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 
1 A DC 11 1_555 B DG 2  1_555 0.076  -0.146 0.098  5.431   -19.539 -2.624 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 
1 A DG 12 1_555 B DC 1  1_555 -0.154 -0.212 -0.283 4.047   8.262   -4.384 12 A_DG12:DC13_B A 12 ? B 13 ? 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 12 1_555 A DG 2  1_555 B DC 11 1_555 -0.289 0.288  3.562 -4.363 9.194   36.811 -0.845 -0.168 3.541 14.228  
6.753   38.145 1  AA_DC1DG2:DC23DG24_BB   A 1  ? B 24 ? A 2  ? B 23 ? 
1 A DG 2  1_555 B DC 11 1_555 A DC 3  1_555 B DG 10 1_555 0.633  0.487  3.438 3.367  -6.420  38.769 1.517  -0.521 3.360 -9.569  
-5.019  39.416 2  AA_DG2DC3:DG22DC23_BB   A 2  ? B 23 ? A 3  ? B 22 ? 
1 A DC 3  1_555 B DG 10 1_555 A DG 4  1_555 B DC 9  1_555 -0.189 0.650  3.158 1.357  7.390   29.638 -0.217 0.625  3.211 14.162  
-2.600  30.555 3  AA_DC3DG4:DC21DG22_BB   A 3  ? B 22 ? A 4  ? B 21 ? 
1 A DG 4  1_555 B DC 9  1_555 A DA 5  1_555 B DT 8  1_555 0.041  0.217  3.495 2.883  1.794   36.423 0.081  0.359  3.495 2.863   
-4.599  36.576 4  AA_DG4DA5:DT20DC21_BB   A 4  ? B 21 ? A 5  ? B 20 ? 
1 A DA 5  1_555 B DT 8  1_555 A DA 6  1_555 B DT 7  1_555 0.315  -0.697 3.505 -7.700 6.367   38.355 -1.811 -1.410 3.233 9.496   
11.483  39.587 5  AA_DA5DA6:DT19DT20_BB   A 5  ? B 20 ? A 6  ? B 19 ? 
1 A DA 6  1_555 B DT 7  1_555 A DT 7  1_555 B DA 6  1_555 0.833  -0.212 3.120 1.365  -10.896 26.250 2.009  -1.391 3.006 -22.765 
-2.853  28.417 6  AA_DA6DT7:DA18DT19_BB   A 6  ? B 19 ? A 7  ? B 18 ? 
1 A DT 7  1_555 B DA 6  1_555 A DT 8  1_555 B DA 5  1_555 -0.831 -0.433 3.311 8.910  10.172  39.651 -1.645 2.073  2.877 14.494  
-12.695 41.805 7  AA_DT7DT8:DA17DA18_BB   A 7  ? B 18 ? A 8  ? B 17 ? 
1 A DT 8  1_555 B DA 5  1_555 A DC 9  1_555 B DG 4  1_555 -0.016 0.373  3.494 -0.219 0.347   41.030 0.492  -0.003 3.497 0.495   
0.312   41.032 8  AA_DT8DC9:DG16DA17_BB   A 8  ? B 17 ? A 9  ? B 16 ? 
1 A DC 9  1_555 B DG 4  1_555 A DG 10 1_555 B DC 3  1_555 0.182  1.181  3.202 -2.888 3.333   29.498 1.604  -0.952 3.280 6.499   
5.632   29.819 9  AA_DC9DG10:DC15DG16_BB  A 9  ? B 16 ? A 10 ? B 15 ? 
1 A DG 10 1_555 B DC 3  1_555 A DC 11 1_555 B DG 2  1_555 -0.913 0.915  3.445 -1.243 -13.319 39.261 2.744  1.156  3.019 -19.159 
1.788   41.392 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 
1 A DC 11 1_555 B DG 2  1_555 A DG 12 1_555 B DC 1  1_555 0.879  0.906  3.637 4.677  -4.249  39.507 1.867  -0.687 3.601 -6.238  
-6.865  39.989 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? 
# 
_atom_sites.entry_id                    109D 
_atom_sites.fract_transf_matrix[1][1]   0.040667 
_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]   0.024728 
_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]   0.015207 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
loop_
_atom_type.symbol 
C  
MG 
N  
O  
P  
# 
loop_