data_1NZG
#
_entry.id 1NZG
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.386
_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 1NZG pdb_00001nzg 10.2210/pdb1nzg/pdb
NDB AD0029 ? ?
RCSB RCSB018385 ? ?
WWPDB D_1000018385 ? ?
#
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 2003-08-26
2 'Structure model' 1 1 2008-04-29
3 'Structure model' 1 2 2011-07-13
4 'Structure model' 1 3 2011-11-02
5 'Structure model' 1 4 2024-02-14
#
_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' 'Non-polymer description'
4 5 'Structure model' 'Data collection'
5 5 'Structure model' 'Database references'
6 5 '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 5 'Structure model' chem_comp_atom
2 5 'Structure model' chem_comp_bond
3 5 'Structure model' database_2
4 5 'Structure model' struct_conn
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 5 'Structure model' '_database_2.pdbx_DOI'
2 5 'Structure model' '_database_2.pdbx_database_accession'
3 5 'Structure model' '_struct_conn.pdbx_dist_value'
4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'
5 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id'
6 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id'
7 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id'
8 5 'Structure model' '_struct_conn.ptnr1_label_asym_id'
9 5 'Structure model' '_struct_conn.ptnr1_label_comp_id'
10 5 'Structure model' '_struct_conn.ptnr1_label_seq_id'
11 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id'
12 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id'
13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id'
14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id'
15 5 'Structure model' '_struct_conn.ptnr2_label_comp_id'
16 5 'Structure model' '_struct_conn.ptnr2_label_seq_id'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 1NZG
_pdbx_database_status.recvd_initial_deposition_date 2003-02-17
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.SG_entry .
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Prhavc, M.' 1
'Prakash, T.P.' 2
'Minasov, G.' 3
'Egli, M.' 4
'Manoharan, M.' 5
#
_citation.id primary
_citation.title
;2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects
;
_citation.journal_abbrev Org.Lett.
_citation.journal_volume 5
_citation.page_first 2017
_citation.page_last 2020
_citation.year 2003
_citation.journal_id_ASTM ?
_citation.country US
_citation.journal_id_ISSN 1523-7060
_citation.journal_id_CSD ?
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 12790517
_citation.pdbx_database_id_DOI 10.1021/ol0340991
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Prhavc, M.' 1 ?
primary 'Prakash, T.P.' 2 ?
primary 'Minasov, G.' 3 ?
primary 'Cook, P.D.' 4 ?
primary 'Egli, M.' 5 ?
primary 'Manoharan, M.' 6 ?
#
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(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'" 3176.178 2 ? ? ? ?
2 water nat water 18.015 101 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type polydeoxyribonucleotide
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(3ME)(DA)(DC)(DG)(DC)'
_entity_poly.pdbx_seq_one_letter_code_can GCGTAUACGC
_entity_poly.pdbx_strand_id A,B
_entity_poly.pdbx_target_identifier ?
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name water
_pdbx_entity_nonpoly.comp_id HOH
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 DG n
1 2 DC n
1 3 DG n
1 4 DT n
1 5 DA n
1 6 3ME n
1 7 DA n
1 8 DC n
1 9 DG n
1 10 DC 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
3ME 'RNA linking' n
;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
;
? 'C16 H28 N3 O10 P' 453.381
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P'
331.222
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P'
307.197
DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P'
347.221
DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P'
322.208
HOH non-polymer . WATER ? 'H2 O'
18.015
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 DG 1 1 1 DG G 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 DT 4 4 4 DT T A . n
A 1 5 DA 5 5 5 DA A A . n
A 1 6 3ME 6 6 6 3ME 3ME A . n
A 1 7 DA 7 7 7 DA A 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 DC 10 10 10 DC C A . n
B 1 1 DG 1 11 11 DG G 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 DT 4 14 14 DT T B . n
B 1 5 DA 5 15 15 DA A B . n
B 1 6 3ME 6 16 16 3ME 3ME B . n
B 1 7 DA 7 17 17 DA A 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 DC 10 20 20 DC C B . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 HOH 1 101 101 HOH HOH A .
C 2 HOH 2 102 102 HOH HOH A .
C 2 HOH 3 104 104 HOH HOH A .
C 2 HOH 4 106 106 HOH HOH A .
C 2 HOH 5 108 108 HOH HOH A .
C 2 HOH 6 109 109 HOH HOH A .
C 2 HOH 7 111 111 HOH HOH A .
C 2 HOH 8 112 112 HOH HOH A .
C 2 HOH 9 113 113 HOH HOH A .
C 2 HOH 10 114 114 HOH HOH A .
C 2 HOH 11 115 115 HOH HOH A .
C 2 HOH 12 116 116 HOH HOH A .
C 2 HOH 13 118 118 HOH HOH A .
C 2 HOH 14 119 119 HOH HOH A .
C 2 HOH 15 120 120 HOH HOH A .
C 2 HOH 16 121 121 HOH HOH A .
C 2 HOH 17 123 123 HOH HOH A .
C 2 HOH 18 126 126 HOH HOH A .
C 2 HOH 19 127 127 HOH HOH A .
C 2 HOH 20 128 128 HOH HOH A .
C 2 HOH 21 131 131 HOH HOH A .
C 2 HOH 22 133 133 HOH HOH A .
C 2 HOH 23 134 134 HOH HOH A .
C 2 HOH 24 135 135 HOH HOH A .
C 2 HOH 25 136 136 HOH HOH A .
C 2 HOH 26 138 138 HOH HOH A .
C 2 HOH 27 142 142 HOH HOH A .
C 2 HOH 28 143 143 HOH HOH A .
C 2 HOH 29 144 144 HOH HOH A .
C 2 HOH 30 145 145 HOH HOH A .
C 2 HOH 31 148 148 HOH HOH A .
C 2 HOH 32 149 149 HOH HOH A .
C 2 HOH 33 150 150 HOH HOH A .
C 2 HOH 34 151 151 HOH HOH A .
C 2 HOH 35 152 152 HOH HOH A .
C 2 HOH 36 153 153 HOH HOH A .
C 2 HOH 37 154 154 HOH HOH A .
C 2 HOH 38 159 159 HOH HOH A .
C 2 HOH 39 160 160 HOH HOH A .
C 2 HOH 40 161 161 HOH HOH A .
C 2 HOH 41 163 163 HOH HOH A .
C 2 HOH 42 164 164 HOH HOH A .
C 2 HOH 43 165 165 HOH HOH A .
C 2 HOH 44 166 166 HOH HOH A .
C 2 HOH 45 167 167 HOH HOH A .
C 2 HOH 46 168 168 HOH HOH A .
C 2 HOH 47 169 169 HOH HOH A .
C 2 HOH 48 173 173 HOH HOH A .
C 2 HOH 49 175 175 HOH HOH A .
C 2 HOH 50 177 177 HOH HOH A .
C 2 HOH 51 178 178 HOH HOH A .
C 2 HOH 52 180 180 HOH HOH A .
C 2 HOH 53 184 184 HOH HOH A .
C 2 HOH 54 186 186 HOH HOH A .
C 2 HOH 55 187 187 HOH HOH A .
C 2 HOH 56 191 191 HOH HOH A .
C 2 HOH 57 195 195 HOH HOH A .
C 2 HOH 58 196 196 HOH HOH A .
C 2 HOH 59 197 197 HOH HOH A .
C 2 HOH 60 199 199 HOH HOH A .
C 2 HOH 61 201 201 HOH HOH A .
C 2 HOH 62 204 204 HOH HOH A .
D 2 HOH 1 103 103 HOH HOH B .
D 2 HOH 2 105 105 HOH HOH B .
D 2 HOH 3 107 107 HOH HOH B .
D 2 HOH 4 110 110 HOH HOH B .
D 2 HOH 5 117 117 HOH HOH B .
D 2 HOH 6 122 122 HOH HOH B .
D 2 HOH 7 125 125 HOH HOH B .
D 2 HOH 8 129 129 HOH HOH B .
D 2 HOH 9 130 130 HOH HOH B .
D 2 HOH 10 132 132 HOH HOH B .
D 2 HOH 11 137 137 HOH HOH B .
D 2 HOH 12 139 139 HOH HOH B .
D 2 HOH 13 140 140 HOH HOH B .
D 2 HOH 14 141 141 HOH HOH B .
D 2 HOH 15 146 146 HOH HOH B .
D 2 HOH 16 147 147 HOH HOH B .
D 2 HOH 17 155 155 HOH HOH B .
D 2 HOH 18 156 156 HOH HOH B .
D 2 HOH 19 157 157 HOH HOH B .
D 2 HOH 20 158 158 HOH HOH B .
D 2 HOH 21 162 162 HOH HOH B .
D 2 HOH 22 170 170 HOH HOH B .
D 2 HOH 23 171 171 HOH HOH B .
D 2 HOH 24 172 172 HOH HOH B .
D 2 HOH 25 174 174 HOH HOH B .
D 2 HOH 26 176 176 HOH HOH B .
D 2 HOH 27 181 181 HOH HOH B .
D 2 HOH 28 182 182 HOH HOH B .
D 2 HOH 29 185 185 HOH HOH B .
D 2 HOH 30 188 188 HOH HOH B .
D 2 HOH 31 189 189 HOH HOH B .
D 2 HOH 32 190 190 HOH HOH B .
D 2 HOH 33 192 192 HOH HOH B .
D 2 HOH 34 193 193 HOH HOH B .
D 2 HOH 35 194 194 HOH HOH B .
D 2 HOH 36 198 198 HOH HOH B .
D 2 HOH 37 203 203 HOH HOH B .
D 2 HOH 38 206 206 HOH HOH B .
D 2 HOH 39 208 208 HOH HOH B .
#
loop_
_software.name
_software.classification
_software.version
_software.citation_id
_software.pdbx_ordinal
DENZO 'data reduction' . ? 1
SCALEPACK 'data scaling' . ? 2
AMoRE phasing . ? 3
CNS refinement . ? 4
#
_cell.entry_id 1NZG
_cell.length_a 25.260
_cell.length_b 44.110
_cell.length_c 45.530
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.Z_PDB 8
_cell.pdbx_unique_axis ?
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.entry_id 1NZG
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 19
_symmetry.space_group_name_Hall ?
#
_exptl.entry_id 1NZG
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 1.71
_exptl_crystal.density_percent_sol 27.47
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP'
_exptl_crystal_grow.temp 295.0
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 6.0
_exptl_crystal_grow.pdbx_details
'MPD, Sodium Cacodylate, Spermine, Sodium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K'
_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.volume
_exptl_crystal_grow_comp.conc
_exptl_crystal_grow_comp.details
1 1 1 MPD ? ? ?
1 2 1 'Sodium Cacodylate' ? ? ?
1 3 1 Spermine ? ? ?
1 4 1 'Sodium Chloride' ? ? ?
1 5 2 MPD ? ? ?
1 6 2 'Sodium Chloride' ? ? ?
#
_diffrn.id 1
_diffrn.ambient_temp 100.0
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type MARRESEARCH
_diffrn_detector.pdbx_collection_date 1999-06-08
_diffrn_detector.details Mirrors
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator Graphite
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.00000
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'APS BEAMLINE 5ID-B'
_diffrn_source.pdbx_synchrotron_site APS
_diffrn_source.pdbx_synchrotron_beamline 5ID-B
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 1.00000
#
_reflns.entry_id 1NZG
_reflns.observed_criterion_sigma_F ?
_reflns.observed_criterion_sigma_I -3.0
_reflns.d_resolution_high 1.60
_reflns.d_resolution_low 20.0
_reflns.number_all 7031
_reflns.number_obs 7031
_reflns.percent_possible_obs 97.6
_reflns.pdbx_Rmerge_I_obs 0.063
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 22.9
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 8.2
_reflns.R_free_details ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
#
_reflns_shell.d_res_high 1.60
_reflns_shell.d_res_low 1.66
_reflns_shell.percent_possible_all 82.9
_reflns_shell.Rmerge_I_obs 0.182
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 6.5
_reflns_shell.pdbx_redundancy 4.9
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all 575
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_unique_obs ?
_reflns_shell.pdbx_chi_squared ?
#
_refine.entry_id 1NZG
_refine.ls_d_res_high 1.60
_refine.ls_d_res_low 20.0
_refine.pdbx_ls_sigma_F 0.0
_refine.pdbx_ls_sigma_I 0.0
_refine.ls_number_reflns_all 7114
_refine.ls_number_reflns_obs 6676
_refine.ls_number_reflns_R_free 687
_refine.ls_percent_reflns_obs 93.8
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_R_work 0.192
_refine.ls_R_factor_R_free 0.224
_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_percent_reflns_R_free ?
_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 ?
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_R_Free_selection_details Random
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_stereochemistry_target_values 'PARKINSON ET AL.'
_refine.solvent_model_details ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.occupancy_max ?
_refine.occupancy_min ?
_refine.pdbx_isotropic_thermal_model Isotropic
_refine.B_iso_mean ?
_refine.aniso_B[1][1] 2.756
_refine.aniso_B[1][2] 0.000
_refine.aniso_B[1][3] 0.000
_refine.aniso_B[2][2] -10.058
_refine.aniso_B[2][3] 0.000
_refine.aniso_B[3][3] 7.302
_refine.details ?
_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.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.overall_SU_B ?
_refine.overall_SU_ML ?
_refine.pdbx_overall_ESU_R_Free ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.pdbx_diffrn_id 1
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_overall_phase_error ?
_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_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 422
_refine_hist.pdbx_number_atoms_ligand 0
_refine_hist.number_atoms_solvent 101
_refine_hist.number_atoms_total 523
_refine_hist.d_res_high 1.60
_refine_hist.d_res_low 20.0
#
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
c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ?
c_angle_deg 1.30 ? ? ? 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.pdbx_total_number_of_bins_used ?
_refine_ls_shell.d_res_high 1.60
_refine_ls_shell.d_res_low 1.64
_refine_ls_shell.number_reflns_R_work ?
_refine_ls_shell.R_factor_R_work 0.312
_refine_ls_shell.percent_reflns_obs 80.1
_refine_ls_shell.R_factor_R_free 0.353
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 35
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.R_factor_all ?
#
_database_PDB_matrix.entry_id 1NZG
_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 1NZG
_struct.title 'Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 1NZG
_struct_keywords.pdbx_keywords DNA
_struct_keywords.text
;A-DNA, 2'-modified oligonucleotides, DNA
;
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
C N N 2 ?
D N N 2 ?
#
_struct_ref.id 1
_struct_ref.entity_id 1
_struct_ref.db_name PDB
_struct_ref.db_code 1NZG
_struct_ref.pdbx_db_accession 1NZG
_struct_ref.pdbx_align_begin ?
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_db_isoform ?
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 1NZG A 1 ? 10 ? 1NZG 1 ? 10 ? 1 10
2 1 1NZG B 1 ? 10 ? 1NZG 11 ? 20 ? 11 20
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_defined_assembly
_pdbx_struct_assembly.method_details ?
_pdbx_struct_assembly.oligomeric_details dimeric
_pdbx_struct_assembly.oligomeric_count 2
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B,C,D
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
_struct_biol.id 1
_struct_biol.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
covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A 3ME 6 P ? ? A DA 5 A 3ME 6 1_555 ? ? ? ? ? ? ? 1.605 ? ?
covale2 covale both ? A 3ME 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 3ME 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.597 ? ?
covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 3ME 6 P ? ? B DA 15 B 3ME 16 1_555 ? ? ? ? ? ? ? 1.604 ? ?
covale4 covale both ? B 3ME 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 3ME 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.607 ? ?
hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B 3ME 6 N3 ? ? A DA 5 B 3ME 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 3ME 6 O4 ? ? A DA 5 B 3ME 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog14 hydrog ? ? A 3ME 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 3ME 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog15 hydrog ? ? A 3ME 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 3ME 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ?
#
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
covale ? ?
hydrog ? ?
#
loop_
_pdbx_struct_mod_residue.id
_pdbx_struct_mod_residue.label_asym_id
_pdbx_struct_mod_residue.label_comp_id
_pdbx_struct_mod_residue.label_seq_id
_pdbx_struct_mod_residue.auth_asym_id
_pdbx_struct_mod_residue.auth_comp_id
_pdbx_struct_mod_residue.auth_seq_id
_pdbx_struct_mod_residue.PDB_ins_code
_pdbx_struct_mod_residue.parent_comp_id
_pdbx_struct_mod_residue.details
1 A 3ME 6 A 3ME 6 ? U ?
2 B 3ME 6 B 3ME 16 ? U ?
#
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
3ME P P N N 1
3ME OP1 O N N 2
3ME OP2 O N N 3
3ME "O5'" O N N 4
3ME "C5'" C N N 5
3ME "C4'" C N R 6
3ME "O4'" O N N 7
3ME "C1'" C N R 8
3ME N1 N N N 9
3ME C6 C N N 10
3ME C2 C N N 11
3ME O2 O N N 12
3ME N3 N N N 13
3ME C4 C N N 14
3ME O4 O N N 15
3ME C5 C N N 16
3ME C5A C N N 17
3ME "C2'" C N R 18
3ME "O2'" O N N 19
3ME "CB'" C N N 20
3ME "CC'" C N N 21
3ME "OD'" O N N 22
3ME "CE'" C N N 23
3ME "CF'" C N N 24
3ME "NG'" N N N 25
3ME "CI'" C N N 26
3ME "CJ'" C N N 27
3ME "C3'" C N R 28
3ME "O3'" O N N 29
3ME HO2 H N N 30
3ME "H5'1" H N N 31
3ME "H5'2" H N N 32
3ME "H4'" H N N 33
3ME "H1'" H N N 34
3ME HC6 H N N 35
3ME HN3 H N N 36
3ME H5A1 H N N 37
3ME H5A2 H N N 38
3ME H5A3 H N N 39
3ME "H2'" H N N 40
3ME "HB'1" H N N 41
3ME "HB'2" H N N 42
3ME "HC'1" H N N 43
3ME "HC'2" H N N 44
3ME "HE'1" H N N 45
3ME "HE'2" H N N 46
3ME "HF'1" H N N 47
3ME "HF'2" H N N 48
3ME "HI'1" H N N 49
3ME "HI'2" H N N 50
3ME "HI'3" H N N 51
3ME "HJ'1" H N N 52
3ME "HJ'2" H N N 53
3ME "HJ'3" H N N 54
3ME "H3'" H N N 55
3ME "HO3'" H N N 56
3ME OXT O N N 57
3ME HXT H N N 58
DA OP3 O N N 59
DA P P N N 60
DA OP1 O N N 61
DA OP2 O N N 62
DA "O5'" O N N 63
DA "C5'" C N N 64
DA "C4'" C N R 65
DA "O4'" O N N 66
DA "C3'" C N S 67
DA "O3'" O N N 68
DA "C2'" C N N 69
DA "C1'" C N R 70
DA N9 N Y N 71
DA C8 C Y N 72
DA N7 N Y N 73
DA C5 C Y N 74
DA C6 C Y N 75
DA N6 N N N 76
DA N1 N Y N 77
DA C2 C Y N 78
DA N3 N Y N 79
DA C4 C Y N 80
DA HOP3 H N N 81
DA HOP2 H N N 82
DA "H5'" H N N 83
DA "H5''" H N N 84
DA "H4'" H N N 85
DA "H3'" H N N 86
DA "HO3'" H N N 87
DA "H2'" H N N 88
DA "H2''" H N N 89
DA "H1'" H N N 90
DA H8 H N N 91
DA H61 H N N 92
DA H62 H N N 93
DA H2 H N N 94
DC OP3 O N N 95
DC P P N N 96
DC OP1 O N N 97
DC OP2 O N N 98
DC "O5'" O N N 99
DC "C5'" C N N 100
DC "C4'" C N R 101
DC "O4'" O N N 102
DC "C3'" C N S 103
DC "O3'" O N N 104
DC "C2'" C N N 105
DC "C1'" C N R 106
DC N1 N N N 107
DC C2 C N N 108
DC O2 O N N 109
DC N3 N N N 110
DC C4 C N N 111
DC N4 N N N 112
DC C5 C N N 113
DC C6 C N N 114
DC HOP3 H N N 115
DC HOP2 H N N 116
DC "H5'" H N N 117
DC "H5''" H N N 118
DC "H4'" H N N 119
DC "H3'" H N N 120
DC "HO3'" H N N 121
DC "H2'" H N N 122
DC "H2''" H N N 123
DC "H1'" H N N 124
DC H41 H N N 125
DC H42 H N N 126
DC H5 H N N 127
DC H6 H N N 128
DG OP3 O N N 129
DG P P N N 130
DG OP1 O N N 131
DG OP2 O N N 132
DG "O5'" O N N 133
DG "C5'" C N N 134
DG "C4'" C N R 135
DG "O4'" O N N 136
DG "C3'" C N S 137
DG "O3'" O N N 138
DG "C2'" C N N 139
DG "C1'" C N R 140
DG N9 N Y N 141
DG C8 C Y N 142
DG N7 N Y N 143
DG C5 C Y N 144
DG C6 C N N 145
DG O6 O N N 146
DG N1 N N N 147
DG C2 C N N 148
DG N2 N N N 149
DG N3 N N N 150
DG C4 C Y N 151
DG HOP3 H N N 152
DG HOP2 H N N 153
DG "H5'" H N N 154
DG "H5''" H N N 155
DG "H4'" H N N 156
DG "H3'" H N N 157
DG "HO3'" H N N 158
DG "H2'" H N N 159
DG "H2''" H N N 160
DG "H1'" H N N 161
DG H8 H N N 162
DG H1 H N N 163
DG H21 H N N 164
DG H22 H N N 165
DT OP3 O N N 166
DT P P N N 167
DT OP1 O N N 168
DT OP2 O N N 169
DT "O5'" O N N 170
DT "C5'" C N N 171
DT "C4'" C N R 172
DT "O4'" O N N 173
DT "C3'" C N S 174
DT "O3'" O N N 175
DT "C2'" C N N 176
DT "C1'" C N R 177
DT N1 N N N 178
DT C2 C N N 179
DT O2 O N N 180
DT N3 N N N 181
DT C4 C N N 182
DT O4 O N N 183
DT C5 C N N 184
DT C7 C N N 185
DT C6 C N N 186
DT HOP3 H N N 187
DT HOP2 H N N 188
DT "H5'" H N N 189
DT "H5''" H N N 190
DT "H4'" H N N 191
DT "H3'" H N N 192
DT "HO3'" H N N 193
DT "H2'" H N N 194
DT "H2''" H N N 195
DT "H1'" H N N 196
DT H3 H N N 197
DT H71 H N N 198
DT H72 H N N 199
DT H73 H N N 200
DT H6 H N N 201
HOH O O N N 202
HOH H1 H N N 203
HOH H2 H N N 204
#
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
3ME P OP1 doub N N 1
3ME P OP2 sing N N 2
3ME P "O5'" sing N N 3
3ME OP2 HO2 sing N N 4
3ME "O5'" "C5'" sing N N 5
3ME "C5'" "C4'" sing N N 6
3ME "C5'" "H5'1" sing N N 7
3ME "C5'" "H5'2" sing N N 8
3ME "C4'" "O4'" sing N N 9
3ME "C4'" "C3'" sing N N 10
3ME "C4'" "H4'" sing N N 11
3ME "O4'" "C1'" sing N N 12
3ME "C1'" N1 sing N N 13
3ME "C1'" "C2'" sing N N 14
3ME "C1'" "H1'" sing N N 15
3ME N1 C6 sing N N 16
3ME N1 C2 sing N N 17
3ME C6 C5 doub N N 18
3ME C6 HC6 sing N N 19
3ME C2 O2 doub N N 20
3ME C2 N3 sing N N 21
3ME N3 C4 sing N N 22
3ME N3 HN3 sing N N 23
3ME C4 O4 doub N N 24
3ME C4 C5 sing N N 25
3ME C5 C5A sing N N 26
3ME C5A H5A1 sing N N 27
3ME C5A H5A2 sing N N 28
3ME C5A H5A3 sing N N 29
3ME "C2'" "O2'" sing N N 30
3ME "C2'" "C3'" sing N N 31
3ME "C2'" "H2'" sing N N 32
3ME "O2'" "CB'" sing N N 33
3ME "CB'" "CC'" sing N N 34
3ME "CB'" "HB'1" sing N N 35
3ME "CB'" "HB'2" sing N N 36
3ME "CC'" "OD'" sing N N 37
3ME "CC'" "HC'1" sing N N 38
3ME "CC'" "HC'2" sing N N 39
3ME "OD'" "CE'" sing N N 40
3ME "CE'" "CF'" sing N N 41
3ME "CE'" "HE'1" sing N N 42
3ME "CE'" "HE'2" sing N N 43
3ME "CF'" "NG'" sing N N 44
3ME "CF'" "HF'1" sing N N 45
3ME "CF'" "HF'2" sing N N 46
3ME "NG'" "CI'" sing N N 47
3ME "NG'" "CJ'" sing N N 48
3ME "CI'" "HI'1" sing N N 49
3ME "CI'" "HI'2" sing N N 50
3ME "CI'" "HI'3" sing N N 51
3ME "CJ'" "HJ'1" sing N N 52
3ME "CJ'" "HJ'2" sing N N 53
3ME "CJ'" "HJ'3" sing N N 54
3ME "C3'" "O3'" sing N N 55
3ME "C3'" "H3'" sing N N 56
3ME "O3'" "HO3'" sing N N 57
3ME P OXT sing N N 58
3ME OXT HXT sing N N 59
DA OP3 P sing N N 60
DA OP3 HOP3 sing N N 61
DA P OP1 doub N N 62
DA P OP2 sing N N 63
DA P "O5'" sing N N 64
DA OP2 HOP2 sing N N 65
DA "O5'" "C5'" sing N N 66
DA "C5'" "C4'" sing N N 67
DA "C5'" "H5'" sing N N 68
DA "C5'" "H5''" sing N N 69
DA "C4'" "O4'" sing N N 70
DA "C4'" "C3'" sing N N 71
DA "C4'" "H4'" sing N N 72
DA "O4'" "C1'" sing N N 73
DA "C3'" "O3'" sing N N 74
DA "C3'" "C2'" sing N N 75
DA "C3'" "H3'" sing N N 76
DA "O3'" "HO3'" sing N N 77
DA "C2'" "C1'" sing N N 78
DA "C2'" "H2'" sing N N 79
DA "C2'" "H2''" sing N N 80
DA "C1'" N9 sing N N 81
DA "C1'" "H1'" sing N N 82
DA N9 C8 sing Y N 83
DA N9 C4 sing Y N 84
DA C8 N7 doub Y N 85
DA C8 H8 sing N N 86
DA N7 C5 sing Y N 87
DA C5 C6 sing Y N 88
DA C5 C4 doub Y N 89
DA C6 N6 sing N N 90
DA C6 N1 doub Y N 91
DA N6 H61 sing N N 92
DA N6 H62 sing N N 93
DA N1 C2 sing Y N 94
DA C2 N3 doub Y N 95
DA C2 H2 sing N N 96
DA N3 C4 sing Y N 97
DC OP3 P sing N N 98
DC OP3 HOP3 sing N N 99
DC P OP1 doub N N 100
DC P OP2 sing N N 101
DC P "O5'" sing N N 102
DC OP2 HOP2 sing N N 103
DC "O5'" "C5'" sing N N 104
DC "C5'" "C4'" sing N N 105
DC "C5'" "H5'" sing N N 106
DC "C5'" "H5''" sing N N 107
DC "C4'" "O4'" sing N N 108
DC "C4'" "C3'" sing N N 109
DC "C4'" "H4'" sing N N 110
DC "O4'" "C1'" sing N N 111
DC "C3'" "O3'" sing N N 112
DC "C3'" "C2'" sing N N 113
DC "C3'" "H3'" sing N N 114
DC "O3'" "HO3'" sing N N 115
DC "C2'" "C1'" sing N N 116
DC "C2'" "H2'" sing N N 117
DC "C2'" "H2''" sing N N 118
DC "C1'" N1 sing N N 119
DC "C1'" "H1'" sing N N 120
DC N1 C2 sing N N 121
DC N1 C6 sing N N 122
DC C2 O2 doub N N 123
DC C2 N3 sing N N 124
DC N3 C4 doub N N 125
DC C4 N4 sing N N 126
DC C4 C5 sing N N 127
DC N4 H41 sing N N 128
DC N4 H42 sing N N 129
DC C5 C6 doub N N 130
DC C5 H5 sing N N 131
DC C6 H6 sing N N 132
DG OP3 P sing N N 133
DG OP3 HOP3 sing N N 134
DG P OP1 doub N N 135
DG P OP2 sing N N 136
DG P "O5'" sing N N 137
DG OP2 HOP2 sing N N 138
DG "O5'" "C5'" sing N N 139
DG "C5'" "C4'" sing N N 140
DG "C5'" "H5'" sing N N 141
DG "C5'" "H5''" sing N N 142
DG "C4'" "O4'" sing N N 143
DG "C4'" "C3'" sing N N 144
DG "C4'" "H4'" sing N N 145
DG "O4'" "C1'" sing N N 146
DG "C3'" "O3'" sing N N 147
DG "C3'" "C2'" sing N N 148
DG "C3'" "H3'" sing N N 149
DG "O3'" "HO3'" sing N N 150
DG "C2'" "C1'" sing N N 151
DG "C2'" "H2'" sing N N 152
DG "C2'" "H2''" sing N N 153
DG "C1'" N9 sing N N 154
DG "C1'" "H1'" sing N N 155
DG N9 C8 sing Y N 156
DG N9 C4 sing Y N 157
DG C8 N7 doub Y N 158
DG C8 H8 sing N N 159
DG N7 C5 sing Y N 160
DG C5 C6 sing N N 161
DG C5 C4 doub Y N 162
DG C6 O6 doub N N 163
DG C6 N1 sing N N 164
DG N1 C2 sing N N 165
DG N1 H1 sing N N 166
DG C2 N2 sing N N 167
DG C2 N3 doub N N 168
DG N2 H21 sing N N 169
DG N2 H22 sing N N 170
DG N3 C4 sing N N 171
DT OP3 P sing N N 172
DT OP3 HOP3 sing N N 173
DT P OP1 doub N N 174
DT P OP2 sing N N 175
DT P "O5'" sing N N 176
DT OP2 HOP2 sing N N 177
DT "O5'" "C5'" sing N N 178
DT "C5'" "C4'" sing N N 179
DT "C5'" "H5'" sing N N 180
DT "C5'" "H5''" sing N N 181
DT "C4'" "O4'" sing N N 182
DT "C4'" "C3'" sing N N 183
DT "C4'" "H4'" sing N N 184
DT "O4'" "C1'" sing N N 185
DT "C3'" "O3'" sing N N 186
DT "C3'" "C2'" sing N N 187
DT "C3'" "H3'" sing N N 188
DT "O3'" "HO3'" sing N N 189
DT "C2'" "C1'" sing N N 190
DT "C2'" "H2'" sing N N 191
DT "C2'" "H2''" sing N N 192
DT "C1'" N1 sing N N 193
DT "C1'" "H1'" sing N N 194
DT N1 C2 sing N N 195
DT N1 C6 sing N N 196
DT C2 O2 doub N N 197
DT C2 N3 sing N N 198
DT N3 C4 sing N N 199
DT N3 H3 sing N N 200
DT C4 O4 doub N N 201
DT C4 C5 sing N N 202
DT C5 C7 sing N N 203
DT C5 C6 doub N N 204
DT C7 H71 sing N N 205
DT C7 H72 sing N N 206
DT C7 H73 sing N N 207
DT C6 H6 sing N N 208
HOH O H1 sing N N 209
HOH O H2 sing N N 210
#
_ndb_struct_conf_na.entry_id 1NZG
_ndb_struct_conf_na.feature 'a-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 DG 1 1_555 B DC 10 1_555 -0.243 -0.168 0.271 0.799 -7.020 -2.274 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1
1 A DC 2 1_555 B DG 9 1_555 0.155 -0.095 -0.009 7.658 -14.705 0.675 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1
1 A DG 3 1_555 B DC 8 1_555 -0.373 -0.186 0.001 -8.232 -15.199 1.268 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1
1 A DT 4 1_555 B DA 7 1_555 -0.157 -0.136 -0.147 -3.162 -17.057 0.288 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1
1 A DA 5 1_555 B 3ME 6 1_555 0.257 0.007 0.114 -2.856 -12.201 -5.065 5 A_DA5:3ME16_B A 5 ? B 16 ? 20 1
1 A 3ME 6 1_555 B DA 5 1_555 -0.005 -0.112 0.227 5.327 -13.532 6.126 6 A_3ME6:DA15_B A 6 ? B 15 ? 20 1
1 A DA 7 1_555 B DT 4 1_555 0.083 -0.159 0.076 5.597 -11.520 2.212 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1
1 A DC 8 1_555 B DG 3 1_555 0.229 -0.189 -0.318 10.890 -15.325 2.842 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1
1 A DG 9 1_555 B DC 2 1_555 -0.014 -0.171 -0.050 -5.636 -9.259 2.209 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1
1 A DC 10 1_555 B DG 1 1_555 0.251 -0.085 0.002 -1.864 5.410 0.141 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.351 -1.572 3.102 3.640 0.421 39.090 -2.388 -0.110 3.104 0.627
-5.426 39.254 1 AA_DG1DC2:DG19DC20_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 0.258 -2.046 3.566 0.274 10.238 25.204 -6.858 -0.482 2.556 22.322
-0.598 27.174 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 DT 4 1_555 B DA 7 1_555 -1.109 -1.356 3.059 -1.384 6.094 37.321 -2.805 1.549 2.848 9.442
2.144 37.822 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ?
1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B 3ME 6 1_555 0.590 -1.560 3.193 1.461 20.125 25.883 -5.649 -0.839 1.621 38.366
-2.785 32.713 4 AA_DT4DA5:3ME16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ?
1 A DA 5 1_555 B 3ME 6 1_555 A 3ME 6 1_555 B DA 5 1_555 0.871 -1.327 3.101 0.246 5.477 32.036 -3.250 -1.518 2.848 9.834
-0.442 32.489 5 AA_DA53ME6:DA153ME16_BB A 5 ? B 16 ? A 6 ? B 15 ?
1 A 3ME 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.327 -1.405 3.090 0.546 12.833 30.508 -4.344 0.655 2.321 23.142
-0.985 33.042 6 AA_3ME6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ?
1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.250 -1.601 3.245 3.269 4.655 31.577 -3.703 0.112 2.994 8.468
-5.947 32.072 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ?
1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.308 -1.836 3.621 -1.628 11.956 29.154 -5.621 0.262 2.691 22.572
3.073 31.503 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ?
1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.282 -1.753 3.320 1.360 2.334 34.270 -3.330 -0.265 3.205 3.954
-2.304 34.373 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ?
#
_atom_sites.entry_id 1NZG
_atom_sites.fract_transf_matrix[1][1] 0.039588
_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] 0.022671
_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] 0.021964
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
loop_
_atom_type.symbol
C
N
O
P
#
loop_