data_3KNC # _entry.id 3KNC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3KNC pdb_00003knc 10.2210/pdb3knc/pdb NDB NA0360 ? ? RCSB RCSB056206 ? ? WWPDB D_1000056206 ? ? # 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 2010-12-08 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-02-01 4 'Structure model' 1 3 2017-11-01 5 'Structure model' 1 4 2021-10-13 6 'Structure model' 1 5 2024-02-21 # _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' Other 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Database references' 5 5 'Structure model' 'Derived calculations' 6 6 'Structure model' 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' pdbx_struct_conn_angle 4 5 'Structure model' struct_conn 5 5 'Structure model' struct_ref_seq 6 5 'Structure model' struct_ref_seq_dif 7 5 'Structure model' struct_site 8 6 'Structure model' chem_comp_atom 9 6 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.value' 7 5 'Structure model' '_struct_conn.pdbx_dist_value' 8 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 9 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 10 5 'Structure model' '_struct_ref_seq.db_align_beg' 11 5 'Structure model' '_struct_ref_seq.db_align_end' 12 5 'Structure model' '_struct_ref_seq_dif.details' 13 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3KNC _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-11-12 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ovaere, M.' 1 'Van Meervelt, L.' 2 # _citation.id primary _citation.title 'The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC).' _citation.journal_abbrev Chemistry _citation.journal_volume 17 _citation.page_first 7823 _citation.page_last 7830 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 0947-6539 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21618623 _citation.pdbx_database_id_DOI 10.1002/chem.201003594 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ovaere, M.' 1 ? primary 'Herdewijn, P.' 2 ? primary 'Van Meervelt, L.' 3 ? # 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(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'" 2887.177 1 ? ? ? CeNA 2 polymer syn "5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'" 2501.553 1 ? ? ? RNA 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 water nat water 18.015 47 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(XGR)(XCR)(XGR)(XTR)(XAR)(XGR)(XCR)(XGR)(XGR)' GCGTNGCGG A ? 2 polyribonucleotide no no CGCUACGC CGCUACGC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 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 XGR n 1 2 XCR n 1 3 XGR n 1 4 XTR n 1 5 XAR n 1 6 XGR n 1 7 XCR n 1 8 XGR n 1 9 XGR n 2 1 C n 2 2 G n 2 3 C n 2 4 U n 2 5 A n 2 6 C n 2 7 G n 2 8 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'The CeNA strand was synthesized.' 2 1 sample ? ? ? ? ? 'The RNA strand was synthesized.' # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 XAR 'DNA linking' . '[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C12 H16 N5 O5 P' 341.260 XCR 'DNA linking' n '[(1R,4S,6S)-4-(4-amino-2-oxopyrimidin-1(2H)-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate' ? 'C11 H16 N3 O6 P' 317.235 XGR 'DNA linking' n '[(1R,4S,6S)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate' ? 'C12 H16 N5 O6 P' 357.259 XTR 'DNA linking' n '[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate' ? 'C12 H17 N2 O7 P' 332.246 # 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 XGR 1 1 1 XGR XGR A . n A 1 2 XCR 2 2 2 XCR XCR A . n A 1 3 XGR 3 3 3 XGR XGR A . n A 1 4 XTR 4 4 4 XTR XTR A . n A 1 5 XAR 5 5 5 XAR XAR A . n A 1 6 XGR 6 6 6 XGR XGR A . n A 1 7 XCR 7 7 7 XCR XCR A . n A 1 8 XGR 8 8 8 XGR XGR A . n A 1 9 XGR 9 9 9 XGR XGR A . n B 2 1 C 1 1 1 C C B . n B 2 2 G 2 2 2 G G B . n B 2 3 C 3 3 3 C C B . n B 2 4 U 4 4 4 U U B . n B 2 5 A 5 5 5 A A B . n B 2 6 C 6 6 6 C C B . n B 2 7 G 7 7 7 G G B . n B 2 8 C 8 8 8 C 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 3 MG 1 100 100 MG MG A . D 3 MG 1 200 200 MG MG A . E 4 HOH 1 14 14 HOH HOH A . E 4 HOH 2 15 15 HOH HOH A . E 4 HOH 3 17 17 HOH HOH A . E 4 HOH 4 20 20 HOH HOH A . E 4 HOH 5 22 22 HOH HOH A . E 4 HOH 6 23 23 HOH HOH A . E 4 HOH 7 24 24 HOH HOH A . E 4 HOH 8 25 25 HOH HOH A . E 4 HOH 9 28 28 HOH HOH A . E 4 HOH 10 33 33 HOH HOH A . E 4 HOH 11 34 34 HOH HOH A . E 4 HOH 12 35 35 HOH HOH A . E 4 HOH 13 101 101 HOH HOH A . E 4 HOH 14 102 102 HOH HOH A . E 4 HOH 15 103 103 HOH HOH A . E 4 HOH 16 104 104 HOH HOH A . E 4 HOH 17 105 105 HOH HOH A . E 4 HOH 18 106 106 HOH HOH A . E 4 HOH 19 107 1 HOH HOH A . E 4 HOH 20 108 3 HOH HOH A . E 4 HOH 21 109 4 HOH HOH A . E 4 HOH 22 110 7 HOH HOH A . E 4 HOH 23 111 8 HOH HOH A . E 4 HOH 24 201 201 HOH HOH A . E 4 HOH 25 202 202 HOH HOH A . E 4 HOH 26 203 203 HOH HOH A . E 4 HOH 27 204 204 HOH HOH A . E 4 HOH 28 205 205 HOH HOH A . E 4 HOH 29 206 206 HOH HOH A . F 4 HOH 1 9 9 HOH HOH B . F 4 HOH 2 10 10 HOH HOH B . F 4 HOH 3 11 11 HOH HOH B . F 4 HOH 4 12 12 HOH HOH B . F 4 HOH 5 13 13 HOH HOH B . F 4 HOH 6 14 2 HOH HOH B . F 4 HOH 7 15 5 HOH HOH B . F 4 HOH 8 16 16 HOH HOH B . F 4 HOH 9 17 6 HOH HOH B . F 4 HOH 10 18 18 HOH HOH B . F 4 HOH 11 19 19 HOH HOH B . F 4 HOH 12 21 21 HOH HOH B . F 4 HOH 13 26 26 HOH HOH B . F 4 HOH 14 27 27 HOH HOH B . F 4 HOH 15 29 29 HOH HOH B . F 4 HOH 16 30 30 HOH HOH B . F 4 HOH 17 31 31 HOH HOH B . F 4 HOH 18 32 32 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A XGR 9 ? N1 ? A XGR 9 N1 2 1 Y 1 A XGR 9 ? C2 ? A XGR 9 C2 3 1 Y 1 A XGR 9 ? N2 ? A XGR 9 N2 4 1 Y 1 A XGR 9 ? N3 ? A XGR 9 N3 5 1 Y 1 A XGR 9 ? C4 ? A XGR 9 C4 6 1 Y 1 A XGR 9 ? C5 ? A XGR 9 C5 7 1 Y 1 A XGR 9 ? C6 ? A XGR 9 C6 8 1 Y 1 A XGR 9 ? O6 ? A XGR 9 O6 9 1 Y 1 A XGR 9 ? N7 ? A XGR 9 N7 10 1 Y 1 A XGR 9 ? C8 ? A XGR 9 C8 11 1 Y 1 A XGR 9 ? N9 ? A XGR 9 N9 12 1 Y 1 A XGR 9 ? "C1'" ? A XGR 9 "C1'" 13 1 Y 1 A XGR 9 ? "C2'" ? A XGR 9 "C2'" 14 1 Y 1 A XGR 9 ? "C3'" ? A XGR 9 "C3'" 15 1 Y 1 A XGR 9 ? "O3'" ? A XGR 9 "O3'" 16 1 Y 1 A XGR 9 ? "C4'" ? A XGR 9 "C4'" 17 1 Y 1 A XGR 9 ? "C5'" ? A XGR 9 "C5'" 18 1 Y 1 A XGR 9 ? "C6'" ? A XGR 9 "C6'" 19 1 Y 1 A XGR 9 ? "C7'" ? A XGR 9 "C7'" # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MOSFLM . ? package 'Andrew G.W. Leslie' andrew@mrc-lmb.cam.ac.uk 'data reduction' http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ ? ? 2 SCALA 3.3.9 2008/10/21 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 3 PHASER 2.1.4 'Thu Nov 13 11:40:59 2008' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 MAR345 CCD ? ? ? ? 'data collection' ? ? ? # _cell.length_a 41.919 _cell.length_b 41.919 _cell.length_c 68.444 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3KNC _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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.space_group_name_H-M 'P 32 2 1' _symmetry.entry_id 3KNC _symmetry.Int_Tables_number 154 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3KNC _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.22 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 61.82 _exptl_crystal.description 'The structure factor file contains Friedel pairs' _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH ? _exptl_crystal_grow.temp 289 _exptl_crystal_grow.pdbx_details '0.2M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 289K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'Magnesium formate' ? ? ? 1 2 2 'Magnesium formate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2008-09-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06DA' _diffrn_source.pdbx_wavelength_list 1.0000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06DA # _reflns.entry_id 3KNC _reflns.d_resolution_high 2.50 _reflns.d_resolution_low 36.3 _reflns.number_all 2460 _reflns.number_obs 2575 _reflns.pdbx_Rsym_value 0.048 _reflns.pdbx_redundancy 9.400 _reflns.percent_possible_obs 98.800 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 3KNC _refine.ls_d_res_high 2.50 _refine.ls_d_res_low 36.3 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 98.020 _refine.ls_number_reflns_obs 2574 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'The Friedel pairs were used in phasing' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.187 _refine.ls_R_factor_R_work 0.184 _refine.ls_wR_factor_R_work 0.184 _refine.ls_R_factor_R_free 0.232 _refine.ls_wR_factor_R_free 0.232 _refine.ls_percent_reflns_R_free 4.400 _refine.ls_number_reflns_R_free 114 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 61.046 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 4.490 _refine.aniso_B[2][2] 4.490 _refine.aniso_B[3][3] -6.730 _refine.aniso_B[1][2] 2.240 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.970 _refine.correlation_coeff_Fo_to_Fc_free 0.958 _refine.overall_SU_R_Cruickshank_DPI 0.310 _refine.overall_SU_R_free 0.237 _refine.pdbx_overall_ESU_R 0.310 _refine.pdbx_overall_ESU_R_Free 0.237 _refine.overall_SU_ML 0.190 _refine.overall_SU_B 9.838 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.762 _refine.B_iso_max 83.75 _refine.B_iso_min 37.01 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 341 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 390 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 36.3 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 396 0.018 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 617 2.247 2.972 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 63 0.120 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 199 0.010 0.017 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1 0.108 1.500 ? 'X-RAY DIFFRACTION' ? r_scbond_it 392 2.812 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 605 4.317 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.50 _refine_ls_shell.d_res_low 2.57 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 97.270 _refine_ls_shell.number_reflns_R_work 169 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.379 _refine_ls_shell.R_factor_R_free 0.733 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 9 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 178 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3KNC _struct.title 'Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3KNC _struct_keywords.text 'cyclohexene, sugar modification, RNA, RNA-CYCLOHEXENE-RNA HYBRID complex' _struct_keywords.pdbx_keywords 'RNA/CYCLOHEXENE-RNA HYBRID' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 PDB 3KNC 3KNC 1 GCGTAGCGG 1 ? 2 PDB 3KNC 3KNC 2 CGCUACGC 1 ? # 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 3KNC A 1 ? 9 ? 3KNC 1 ? 9 ? 1 9 2 2 3KNC B 1 ? 8 ? 3KNC 1 ? 8 ? 1 8 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3KNC XGR A 1 ? PDB 3KNC C 2 'engineered mutation' 1 1 1 3KNC XCR A 2 ? PDB 3KNC G 3 'engineered mutation' 2 2 1 3KNC XGR A 3 ? PDB 3KNC DT 4 'engineered mutation' 3 3 1 3KNC XTR A 4 ? PDB 3KNC A 5 'engineered mutation' 4 4 1 3KNC XAR A 5 ? PDB 3KNC G 6 'engineered mutation' 5 5 1 3KNC XGR A 6 ? PDB 3KNC C 7 'engineered mutation' 6 6 1 3KNC XCR A 7 ? PDB 3KNC G 8 'engineered mutation' 7 7 1 3KNC XGR A 8 ? PDB 3KNC G 9 'engineered mutation' 8 8 1 3KNC XGR A 9 ? PDB 3KNC G 10 'engineered mutation' 9 9 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1280 ? 1 MORE -34.1 ? 1 'SSA (A^2)' 11444 ? # _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 _struct_biol.details 'Biological unit is the same as asymmetric unit' # 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 XTR 4 "O3'" ? ? ? 1_555 A XAR 5 P ? ? A XTR 4 A XAR 5 1_555 ? ? ? ? ? ? ? 1.572 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 101 1_555 ? ? ? ? ? ? ? 2.136 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 102 1_555 ? ? ? ? ? ? ? 2.134 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 103 1_555 ? ? ? ? ? ? ? 2.130 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 104 1_555 ? ? ? ? ? ? ? 2.146 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 105 1_555 ? ? ? ? ? ? ? 2.137 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 100 A HOH 106 1_555 ? ? ? ? ? ? ? 2.141 ? ? metalc7 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 201 1_555 ? ? ? ? ? ? ? 2.160 ? ? metalc8 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 202 1_555 ? ? ? ? ? ? ? 2.172 ? ? metalc9 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 203 1_555 ? ? ? ? ? ? ? 2.176 ? ? metalc10 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 204 1_555 ? ? ? ? ? ? ? 2.160 ? ? metalc11 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 205 1_555 ? ? ? ? ? ? ? 2.164 ? ? metalc12 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 200 A HOH 206 1_555 ? ? ? ? ? ? ? 2.163 ? ? hydrog1 hydrog ? ? A XGR 1 N1 ? ? ? 1_555 B C 8 N3 ? ? A XGR 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A XGR 1 N2 ? ? ? 1_555 B C 8 O2 ? ? A XGR 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A XGR 1 O6 ? ? ? 1_555 B C 8 N4 ? ? A XGR 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A XCR 2 N3 ? ? ? 1_555 B G 7 N1 ? ? A XCR 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A XCR 2 N4 ? ? ? 1_555 B G 7 O6 ? ? A XCR 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A XCR 2 O2 ? ? ? 1_555 B G 7 N2 ? ? A XCR 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A XGR 3 N1 ? ? ? 1_555 B C 6 N3 ? ? A XGR 3 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A XGR 3 N2 ? ? ? 1_555 B C 6 O2 ? ? A XGR 3 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A XGR 3 O6 ? ? ? 1_555 B C 6 N4 ? ? A XGR 3 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A XTR 4 N3 ? ? ? 1_555 B A 5 N1 ? ? A XTR 4 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A XTR 4 O4 ? ? ? 1_555 B A 5 N6 ? ? A XTR 4 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A XGR 6 N1 ? ? ? 1_555 B C 3 N3 ? ? A XGR 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A XGR 6 N2 ? ? ? 1_555 B C 3 O2 ? ? A XGR 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A XGR 6 O6 ? ? ? 1_555 B C 3 N4 ? ? A XGR 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A XCR 7 N3 ? ? ? 1_555 B G 2 N1 ? ? A XCR 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A XCR 7 N4 ? ? ? 1_555 B G 2 O6 ? ? A XCR 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A XCR 7 O2 ? ? ? 1_555 B G 2 N2 ? ? A XCR 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A XGR 8 N1 ? ? ? 1_555 B C 1 N3 ? ? A XGR 8 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A XGR 8 N2 ? ? ? 1_555 B C 1 O2 ? ? A XGR 8 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A XGR 8 O6 ? ? ? 1_555 B C 1 N4 ? ? A XGR 8 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 101 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 102 ? 1_555 176.6 ? 2 O ? E HOH . ? A HOH 101 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 103 ? 1_555 92.0 ? 3 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 103 ? 1_555 86.0 ? 4 O ? E HOH . ? A HOH 101 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 104 ? 1_555 92.6 ? 5 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 104 ? 1_555 90.0 ? 6 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 104 ? 1_555 90.3 ? 7 O ? E HOH . ? A HOH 101 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 105 ? 1_555 90.9 ? 8 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 105 ? 1_555 86.5 ? 9 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 105 ? 1_555 90.9 ? 10 O ? E HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 105 ? 1_555 176.2 ? 11 O ? E HOH . ? A HOH 101 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 86.1 ? 12 O ? E HOH . ? A HOH 102 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 96.1 ? 13 O ? E HOH . ? A HOH 103 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 177.4 ? 14 O ? E HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 88.1 ? 15 O ? E HOH . ? A HOH 105 ? 1_555 MG ? C MG . ? A MG 100 ? 1_555 O ? E HOH . ? A HOH 106 ? 1_555 90.8 ? 16 O ? E HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 202 ? 1_555 179.4 ? 17 O ? E HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 89.5 ? 18 O ? E HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 90.0 ? 19 O ? E HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 90.8 ? 20 O ? E HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 88.8 ? 21 O ? E HOH . ? A HOH 203 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 88.5 ? 22 O ? E HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 89.1 ? 23 O ? E HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 91.3 ? 24 O ? E HOH . ? A HOH 203 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 92.6 ? 25 O ? E HOH . ? A HOH 204 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 178.9 ? 26 O ? E HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 93.2 ? 27 O ? E HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 87.2 ? 28 O ? E HOH . ? A HOH 203 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 176.4 ? 29 O ? E HOH . ? A HOH 204 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 89.0 ? 30 O ? E HOH . ? A HOH 205 ? 1_555 MG ? D MG . ? A MG 200 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 89.9 ? # 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 MG 100 ? 6 'BINDING SITE FOR RESIDUE MG A 100' AC2 Software A MG 200 ? 12 'BINDING SITE FOR RESIDUE MG A 200' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH E . ? HOH A 101 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 102 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 103 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 104 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 105 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH A 106 . ? 1_555 ? 7 AC2 12 HOH E . ? HOH A 201 . ? 1_555 ? 8 AC2 12 HOH E . ? HOH A 201 . ? 5_555 ? 9 AC2 12 HOH E . ? HOH A 202 . ? 1_555 ? 10 AC2 12 HOH E . ? HOH A 202 . ? 5_555 ? 11 AC2 12 HOH E . ? HOH A 203 . ? 1_555 ? 12 AC2 12 HOH E . ? HOH A 203 . ? 5_555 ? 13 AC2 12 HOH E . ? HOH A 204 . ? 5_555 ? 14 AC2 12 HOH E . ? HOH A 204 . ? 1_555 ? 15 AC2 12 HOH E . ? HOH A 205 . ? 5_555 ? 16 AC2 12 HOH E . ? HOH A 205 . ? 1_555 ? 17 AC2 12 HOH E . ? HOH A 206 . ? 5_555 ? 18 AC2 12 HOH E . ? HOH A 206 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C5'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 U _pdbx_validate_rmsd_bond.auth_seq_id_1 4 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C4'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 U _pdbx_validate_rmsd_bond.auth_seq_id_2 4 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.465 _pdbx_validate_rmsd_bond.bond_target_value 1.508 _pdbx_validate_rmsd_bond.bond_deviation -0.043 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # 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 XGR 1 A XGR 1 ? DG ? 2 A XCR 2 A XCR 2 ? DC ? 3 A XGR 3 A XGR 3 ? DG ? 4 A XTR 4 A XTR 4 ? DT ? 5 A XGR 6 A XGR 6 ? DG ? 6 A XCR 7 A XCR 7 ? DC ? 7 A XGR 8 A XGR 8 ? DG ? 8 A XGR 9 A XGR 9 ? DG ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id MG _pdbx_struct_special_symmetry.auth_seq_id 200 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id MG _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_phasing_MR.entry_id 3KNC _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor 31.370 _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.500 _pdbx_phasing_MR.d_res_low_rotation 24.900 _pdbx_phasing_MR.d_res_high_translation 2.500 _pdbx_phasing_MR.d_res_low_translation 24.900 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DT OP3 O N N 73 DT P P N N 74 DT OP1 O N N 75 DT OP2 O N N 76 DT "O5'" O N N 77 DT "C5'" C N N 78 DT "C4'" C N R 79 DT "O4'" O N N 80 DT "C3'" C N S 81 DT "O3'" O N N 82 DT "C2'" C N N 83 DT "C1'" C N R 84 DT N1 N N N 85 DT C2 C N N 86 DT O2 O N N 87 DT N3 N N N 88 DT C4 C N N 89 DT O4 O N N 90 DT C5 C N N 91 DT C7 C N N 92 DT C6 C N N 93 DT HOP3 H N N 94 DT HOP2 H N N 95 DT "H5'" H N N 96 DT "H5''" H N N 97 DT "H4'" H N N 98 DT "H3'" H N N 99 DT "HO3'" H N N 100 DT "H2'" H N N 101 DT "H2''" H N N 102 DT "H1'" H N N 103 DT H3 H N N 104 DT H71 H N N 105 DT H72 H N N 106 DT H73 H N N 107 DT H6 H N N 108 G OP3 O N N 109 G P P N N 110 G OP1 O N N 111 G OP2 O N N 112 G "O5'" O N N 113 G "C5'" C N N 114 G "C4'" C N R 115 G "O4'" O N N 116 G "C3'" C N S 117 G "O3'" O N N 118 G "C2'" C N R 119 G "O2'" O N N 120 G "C1'" C N R 121 G N9 N Y N 122 G C8 C Y N 123 G N7 N Y N 124 G C5 C Y N 125 G C6 C N N 126 G O6 O N N 127 G N1 N N N 128 G C2 C N N 129 G N2 N N N 130 G N3 N N N 131 G C4 C Y N 132 G HOP3 H N N 133 G HOP2 H N N 134 G "H5'" H N N 135 G "H5''" H N N 136 G "H4'" H N N 137 G "H3'" H N N 138 G "HO3'" H N N 139 G "H2'" H N N 140 G "HO2'" H N N 141 G "H1'" H N N 142 G H8 H N N 143 G H1 H N N 144 G H21 H N N 145 G H22 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 MG MG MG N N 150 U OP3 O N N 151 U P P N N 152 U OP1 O N N 153 U OP2 O N N 154 U "O5'" O N N 155 U "C5'" C N N 156 U "C4'" C N R 157 U "O4'" O N N 158 U "C3'" C N S 159 U "O3'" O N N 160 U "C2'" C N R 161 U "O2'" O N N 162 U "C1'" C N R 163 U N1 N N N 164 U C2 C N N 165 U O2 O N N 166 U N3 N N N 167 U C4 C N N 168 U O4 O N N 169 U C5 C N N 170 U C6 C N N 171 U HOP3 H N N 172 U HOP2 H N N 173 U "H5'" H N N 174 U "H5''" H N N 175 U "H4'" H N N 176 U "H3'" H N N 177 U "HO3'" H N N 178 U "H2'" H N N 179 U "HO2'" H N N 180 U "H1'" H N N 181 U H3 H N N 182 U H5 H N N 183 U H6 H N N 184 XAR O3P O N N 185 XAR O1P O N N 186 XAR P P N N 187 XAR O2P O N N 188 XAR "O5'" O N N 189 XAR "C5'" C N N 190 XAR "C4'" C N R 191 XAR "C3'" C N S 192 XAR "O3'" O N N 193 XAR "C2'" C N N 194 XAR "C1'" C N S 195 XAR "C7'" C N N 196 XAR "C6'" C N N 197 XAR N9 N Y N 198 XAR C8 C Y N 199 XAR N7 N Y N 200 XAR C5 C Y N 201 XAR C4 C Y N 202 XAR N3 N Y N 203 XAR C6 C Y N 204 XAR N6 N N N 205 XAR N1 N Y N 206 XAR C2 C Y N 207 XAR HOP3 H N N 208 XAR HOP2 H N N 209 XAR "H5'1" H N N 210 XAR "H5'2" H N N 211 XAR "H4'" H N N 212 XAR "H3'" H N N 213 XAR H3T H N N 214 XAR "H2'1" H N N 215 XAR "H2'2" H N N 216 XAR "H1'" H N N 217 XAR "H7'" H N N 218 XAR "H6'" H N N 219 XAR H8 H N N 220 XAR HN61 H N N 221 XAR HN62 H N N 222 XAR H2 H N N 223 XCR P P N N 224 XCR N1 N N N 225 XCR C2 C N N 226 XCR O2 O N N 227 XCR N3 N N N 228 XCR C4 C N N 229 XCR N4 N N N 230 XCR C5 C N N 231 XCR C6 C N N 232 XCR "C1'" C N S 233 XCR "C2'" C N N 234 XCR "C3'" C N S 235 XCR "O3'" O N N 236 XCR "C4'" C N R 237 XCR "C5'" C N N 238 XCR "O5'" O N N 239 XCR "C6'" C N N 240 XCR "C7'" C N N 241 XCR OP1 O N N 242 XCR OP2 O N N 243 XCR OP3 O N N 244 XCR HN4 H N N 245 XCR HN4A H N N 246 XCR H5 H N N 247 XCR H6 H N N 248 XCR "H1'" H N N 249 XCR "H2'" H N N 250 XCR "H2'A" H N N 251 XCR "H3'" H N N 252 XCR "HO3'" H N N 253 XCR "H4'" H N N 254 XCR "H5'" H N N 255 XCR "H5'A" H N N 256 XCR "H6'" H N N 257 XCR "H7'" H N N 258 XCR HOP1 H N N 259 XCR HOP3 H N N 260 XGR P P N N 261 XGR N1 N N N 262 XGR C2 C N N 263 XGR N2 N N N 264 XGR N3 N N N 265 XGR C4 C Y N 266 XGR C5 C Y N 267 XGR C6 C N N 268 XGR O6 O N N 269 XGR N7 N Y N 270 XGR C8 C Y N 271 XGR N9 N Y N 272 XGR "C1'" C N S 273 XGR "C2'" C N N 274 XGR "C3'" C N S 275 XGR "O3'" O N N 276 XGR "C4'" C N R 277 XGR "C5'" C N N 278 XGR "O5'" O N N 279 XGR "C6'" C N N 280 XGR "C7'" C N N 281 XGR OP1 O N N 282 XGR OP2 O N N 283 XGR OP3 O N N 284 XGR HN1 H N N 285 XGR HN2 H N N 286 XGR HN2A H N N 287 XGR H8 H N N 288 XGR "H1'" H N N 289 XGR "H2'" H N N 290 XGR "H2'A" H N N 291 XGR "H3'" H N N 292 XGR "HO3'" H N N 293 XGR "H4'" H N N 294 XGR "H5'" H N N 295 XGR "H5'A" H N N 296 XGR "H6'" H N N 297 XGR "H7'" H N N 298 XGR HOP1 H N N 299 XGR HOP3 H N N 300 XTR OP3 O N N 301 XTR "C4'" C N R 302 XTR "C7'" C N N 303 XTR "C6'" C N N 304 XTR "C1'" C N S 305 XTR O4 O N N 306 XTR C4 C N N 307 XTR C5 C N N 308 XTR C5M C N N 309 XTR C6 C N N 310 XTR N3 N N N 311 XTR C2 C N N 312 XTR O2 O N N 313 XTR N1 N N N 314 XTR "C2'" C N N 315 XTR "C3'" C N S 316 XTR P P N N 317 XTR OP1 O N N 318 XTR OP2 O N N 319 XTR "O5'" O N N 320 XTR "C5'" C N N 321 XTR "O3'" O N N 322 XTR HOP3 H N N 323 XTR "H4'" H N N 324 XTR "H7'" H N N 325 XTR "H6'" H N N 326 XTR "H1'" H N N 327 XTR H5M H N N 328 XTR H5MA H N N 329 XTR H5MB H N N 330 XTR H6 H N N 331 XTR HN3 H N N 332 XTR "H2'" H N N 333 XTR "H2'A" H N N 334 XTR "H3'" H N N 335 XTR "H5'" H N N 336 XTR "H5'A" H N N 337 XTR "HO3'" H N N 338 XTR HOP2 H N N 339 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DT OP3 P sing N N 76 DT OP3 HOP3 sing N N 77 DT P OP1 doub N N 78 DT P OP2 sing N N 79 DT P "O5'" sing N N 80 DT OP2 HOP2 sing N N 81 DT "O5'" "C5'" sing N N 82 DT "C5'" "C4'" sing N N 83 DT "C5'" "H5'" sing N N 84 DT "C5'" "H5''" sing N N 85 DT "C4'" "O4'" sing N N 86 DT "C4'" "C3'" sing N N 87 DT "C4'" "H4'" sing N N 88 DT "O4'" "C1'" sing N N 89 DT "C3'" "O3'" sing N N 90 DT "C3'" "C2'" sing N N 91 DT "C3'" "H3'" sing N N 92 DT "O3'" "HO3'" sing N N 93 DT "C2'" "C1'" sing N N 94 DT "C2'" "H2'" sing N N 95 DT "C2'" "H2''" sing N N 96 DT "C1'" N1 sing N N 97 DT "C1'" "H1'" sing N N 98 DT N1 C2 sing N N 99 DT N1 C6 sing N N 100 DT C2 O2 doub N N 101 DT C2 N3 sing N N 102 DT N3 C4 sing N N 103 DT N3 H3 sing N N 104 DT C4 O4 doub N N 105 DT C4 C5 sing N N 106 DT C5 C7 sing N N 107 DT C5 C6 doub N N 108 DT C7 H71 sing N N 109 DT C7 H72 sing N N 110 DT C7 H73 sing N N 111 DT C6 H6 sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 U OP3 P sing N N 155 U OP3 HOP3 sing N N 156 U P OP1 doub N N 157 U P OP2 sing N N 158 U P "O5'" sing N N 159 U OP2 HOP2 sing N N 160 U "O5'" "C5'" sing N N 161 U "C5'" "C4'" sing N N 162 U "C5'" "H5'" sing N N 163 U "C5'" "H5''" sing N N 164 U "C4'" "O4'" sing N N 165 U "C4'" "C3'" sing N N 166 U "C4'" "H4'" sing N N 167 U "O4'" "C1'" sing N N 168 U "C3'" "O3'" sing N N 169 U "C3'" "C2'" sing N N 170 U "C3'" "H3'" sing N N 171 U "O3'" "HO3'" sing N N 172 U "C2'" "O2'" sing N N 173 U "C2'" "C1'" sing N N 174 U "C2'" "H2'" sing N N 175 U "O2'" "HO2'" sing N N 176 U "C1'" N1 sing N N 177 U "C1'" "H1'" sing N N 178 U N1 C2 sing N N 179 U N1 C6 sing N N 180 U C2 O2 doub N N 181 U C2 N3 sing N N 182 U N3 C4 sing N N 183 U N3 H3 sing N N 184 U C4 O4 doub N N 185 U C4 C5 sing N N 186 U C5 C6 doub N N 187 U C5 H5 sing N N 188 U C6 H6 sing N N 189 XAR O3P P sing N N 190 XAR O3P HOP3 sing N N 191 XAR O1P P doub N N 192 XAR P O2P sing N N 193 XAR P "O5'" sing N N 194 XAR O2P HOP2 sing N N 195 XAR "O5'" "C5'" sing N N 196 XAR "C5'" "C4'" sing N N 197 XAR "C5'" "H5'1" sing N N 198 XAR "C5'" "H5'2" sing N N 199 XAR "C4'" "C6'" sing N N 200 XAR "C4'" "C3'" sing N N 201 XAR "C4'" "H4'" sing N N 202 XAR "C3'" "O3'" sing N N 203 XAR "C3'" "C2'" sing N N 204 XAR "C3'" "H3'" sing N N 205 XAR "O3'" H3T sing N N 206 XAR "C2'" "C1'" sing N N 207 XAR "C2'" "H2'1" sing N N 208 XAR "C2'" "H2'2" sing N N 209 XAR "C1'" "C7'" sing N N 210 XAR "C1'" N9 sing N N 211 XAR "C1'" "H1'" sing N N 212 XAR "C7'" "C6'" doub N N 213 XAR "C7'" "H7'" sing N N 214 XAR "C6'" "H6'" sing N N 215 XAR N9 C8 sing Y N 216 XAR N9 C4 sing Y N 217 XAR C8 N7 doub Y N 218 XAR C8 H8 sing N N 219 XAR N7 C5 sing Y N 220 XAR C5 C4 doub Y N 221 XAR C5 C6 sing Y N 222 XAR C4 N3 sing Y N 223 XAR N3 C2 doub Y N 224 XAR C6 N1 doub Y N 225 XAR C6 N6 sing N N 226 XAR N6 HN61 sing N N 227 XAR N6 HN62 sing N N 228 XAR N1 C2 sing Y N 229 XAR C2 H2 sing N N 230 XCR OP2 P doub N N 231 XCR "O5'" P sing N N 232 XCR OP3 P sing N N 233 XCR P OP1 sing N N 234 XCR C2 N1 sing N N 235 XCR N1 C6 sing N N 236 XCR N1 "C1'" sing N N 237 XCR N3 C2 sing N N 238 XCR O2 C2 doub N N 239 XCR N3 C4 doub N N 240 XCR N4 C4 sing N N 241 XCR C4 C5 sing N N 242 XCR N4 HN4 sing N N 243 XCR N4 HN4A sing N N 244 XCR C5 C6 doub N N 245 XCR C5 H5 sing N N 246 XCR C6 H6 sing N N 247 XCR "C1'" "C7'" sing N N 248 XCR "C1'" "C2'" sing N N 249 XCR "C1'" "H1'" sing N N 250 XCR "C2'" "C3'" sing N N 251 XCR "C2'" "H2'" sing N N 252 XCR "C2'" "H2'A" sing N N 253 XCR "C3'" "C4'" sing N N 254 XCR "C3'" "O3'" sing N N 255 XCR "C3'" "H3'" sing N N 256 XCR "O3'" "HO3'" sing N N 257 XCR "C6'" "C4'" sing N N 258 XCR "C4'" "C5'" sing N N 259 XCR "C4'" "H4'" sing N N 260 XCR "O5'" "C5'" sing N N 261 XCR "C5'" "H5'" sing N N 262 XCR "C5'" "H5'A" sing N N 263 XCR "C7'" "C6'" doub N N 264 XCR "C6'" "H6'" sing N N 265 XCR "C7'" "H7'" sing N N 266 XCR OP1 HOP1 sing N N 267 XCR OP3 HOP3 sing N N 268 XGR "O5'" P sing N N 269 XGR OP2 P doub N N 270 XGR OP3 P sing N N 271 XGR P OP1 sing N N 272 XGR C2 N1 sing N N 273 XGR N1 C6 sing N N 274 XGR N1 HN1 sing N N 275 XGR N2 C2 sing N N 276 XGR C2 N3 doub N N 277 XGR N2 HN2 sing N N 278 XGR N2 HN2A sing N N 279 XGR N3 C4 sing N N 280 XGR C4 C5 doub Y N 281 XGR C4 N9 sing Y N 282 XGR C6 C5 sing N N 283 XGR C5 N7 sing Y N 284 XGR O6 C6 doub N N 285 XGR N7 C8 doub Y N 286 XGR N9 C8 sing Y N 287 XGR C8 H8 sing N N 288 XGR N9 "C1'" sing N N 289 XGR "C1'" "C7'" sing N N 290 XGR "C1'" "C2'" sing N N 291 XGR "C1'" "H1'" sing N N 292 XGR "C2'" "C3'" sing N N 293 XGR "C2'" "H2'" sing N N 294 XGR "C2'" "H2'A" sing N N 295 XGR "C3'" "C4'" sing N N 296 XGR "C3'" "O3'" sing N N 297 XGR "C3'" "H3'" sing N N 298 XGR "O3'" "HO3'" sing N N 299 XGR "C6'" "C4'" sing N N 300 XGR "C4'" "C5'" sing N N 301 XGR "C4'" "H4'" sing N N 302 XGR "O5'" "C5'" sing N N 303 XGR "C5'" "H5'" sing N N 304 XGR "C5'" "H5'A" sing N N 305 XGR "C7'" "C6'" doub N N 306 XGR "C6'" "H6'" sing N N 307 XGR "C7'" "H7'" sing N N 308 XGR OP1 HOP1 sing N N 309 XGR OP3 HOP3 sing N N 310 XTR OP3 HOP3 sing N N 311 XTR "C4'" "C6'" sing N N 312 XTR "C4'" "H4'" sing N N 313 XTR "C7'" "C6'" doub N N 314 XTR "C7'" "H7'" sing N N 315 XTR "C6'" "H6'" sing N N 316 XTR "C1'" "C7'" sing N N 317 XTR "C1'" N1 sing N N 318 XTR "C1'" "H1'" sing N N 319 XTR C4 O4 doub N N 320 XTR C5 C4 sing N N 321 XTR C5 C5M sing N N 322 XTR C5M H5M sing N N 323 XTR C5M H5MA sing N N 324 XTR C5M H5MB sing N N 325 XTR C6 C5 doub N N 326 XTR C6 H6 sing N N 327 XTR N3 C4 sing N N 328 XTR N3 HN3 sing N N 329 XTR C2 N3 sing N N 330 XTR O2 C2 doub N N 331 XTR N1 C6 sing N N 332 XTR N1 C2 sing N N 333 XTR "C2'" "C1'" sing N N 334 XTR "C2'" "C3'" sing N N 335 XTR "C2'" "H2'" sing N N 336 XTR "C2'" "H2'A" sing N N 337 XTR "C3'" "C4'" sing N N 338 XTR "C3'" "H3'" sing N N 339 XTR P OP3 sing N N 340 XTR P OP1 doub N N 341 XTR OP2 P sing N N 342 XTR "O5'" P sing N N 343 XTR "C5'" "C4'" sing N N 344 XTR "C5'" "O5'" sing N N 345 XTR "C5'" "H5'" sing N N 346 XTR "C5'" "H5'A" sing N N 347 XTR "O3'" "C3'" sing N N 348 XTR "O3'" "HO3'" sing N N 349 XTR OP2 HOP2 sing N N 350 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3KNC 'double helix' 3KNC 'a-form double helix' 3KNC '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 XGR 1 1_555 B C 8 1_555 0.061 -0.125 0.545 1.753 -12.277 1.052 1 A_XGR1:C8_B A 1 ? B 8 ? 19 1 1 A XCR 2 1_555 B G 7 1_555 0.005 -0.244 0.521 -5.102 -12.505 1.030 2 A_XCR2:G7_B A 2 ? B 7 ? 19 1 1 A XGR 3 1_555 B C 6 1_555 -0.165 0.080 0.317 -9.561 -14.167 5.729 3 A_XGR3:C6_B A 3 ? B 6 ? 19 1 1 A XTR 4 1_555 B A 5 1_555 0.375 -0.121 0.439 -8.304 -13.046 -2.908 4 A_XTR4:A5_B A 4 ? B 5 ? 20 1 1 A XGR 6 1_555 B C 3 1_555 -0.063 -0.279 -0.065 -2.720 -11.560 -5.217 5 A_XGR6:C3_B A 6 ? B 3 ? 19 1 1 A XCR 7 1_555 B G 2 1_555 -0.466 -0.086 0.191 -3.273 -10.283 0.859 6 A_XCR7:G2_B A 7 ? B 2 ? 19 1 1 A XGR 8 1_555 B C 1 1_555 -0.473 0.018 -0.252 -9.236 -15.039 5.307 7 A_XGR8:C1_B A 8 ? B 1 ? 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 XGR 1 1_555 B C 8 1_555 A XCR 2 1_555 B G 7 1_555 -0.159 -2.349 3.270 -1.344 3.054 35.098 -4.319 0.069 3.065 5.050 2.222 35.251 1 AA_XGR1XCR2:G7C8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A XCR 2 1_555 B G 7 1_555 A XGR 3 1_555 B C 6 1_555 -0.151 -1.941 3.125 2.134 8.686 30.917 -4.865 0.607 2.487 15.881 -3.901 32.155 2 AA_XCR2XGR3:C6G7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A XGR 3 1_555 B C 6 1_555 A XTR 4 1_555 B A 5 1_555 -0.415 -1.691 3.143 1.632 6.416 35.729 -3.532 0.874 2.787 10.348 -2.631 36.317 3 AA_XGR3XTR4:A5C6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A XTR 4 1_555 B A 5 1_555 A XGR 6 1_555 B C 3 1_555 0.181 -3.741 5.819 3.937 28.602 59.744 -5.281 0.086 3.873 27.077 -3.727 65.770 4 AA_XTR4XGR6:C3A5_BB A 4 ? B 5 ? A 6 ? B 3 ? 1 A XGR 6 1_555 B C 3 1_555 A XCR 7 1_555 B G 2 1_555 0.957 -2.249 3.382 1.749 5.223 28.518 -5.613 -1.531 2.983 10.479 -3.508 29.035 5 AA_XGR6XCR7:G2C3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A XCR 7 1_555 B G 2 1_555 A XGR 8 1_555 B C 1 1_555 -0.250 -2.222 3.246 1.636 13.860 29.913 -5.921 0.678 2.029 25.197 -2.974 32.941 6 AA_XCR7XGR8:C1G2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _atom_sites.entry_id 3KNC _atom_sites.fract_transf_matrix[1][1] 0.023856 _atom_sites.fract_transf_matrix[1][2] 0.013773 _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] 0.027546 _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] 0.014610 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P # loop_