data_25531 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; N2-dG-IQ modified DNA at the G1 position of the NarI recognition sequence ; _BMRB_accession_number 25531 _BMRB_flat_file_name bmr25531.str _Entry_type original _Submission_date 2015-03-11 _Accession_date 2015-03-11 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Stavros Kallie . . 2 Hawkins Edward . . 3 Rizzo Carmelo . . 4 Stone Michael . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 156 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-03-29 original BMRB . stop_ _Original_release_date 2016-03-29 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26083477 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Stavros Kallie . . 2 Hawkins Edward . . 3 Rizzo Carmelo . . 4 Stone Michael . . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_volume 28 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1455 _Page_last 1468 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'N2-dG IQ at G1 in NarI sequence' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3')" $DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') "DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')" $DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') _Molecular_mass 3251.149 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CTCXGCGCCATC ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DT 3 DC 4 IQG 5 DG 6 DC 7 DG 8 DC 9 DC 10 DA 11 DT 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') _Molecular_mass 3728.459 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ; GATGGCGCCGAG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DG 2 14 DA 3 15 DT 4 16 DG 5 17 DG 6 18 DC 7 19 DG 8 20 DC 9 21 DC 10 22 DG 11 23 DA 12 24 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_IQG _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common "N-(2-amino-3-methyl-3H-imidazo[4,5-f]quinolin-5-yl)-2'-deoxyguanosine 5'-(dihydrogen phosphate)" _BMRB_code IQG _PDB_code IQG _Standard_residue_derivative . _Molecular_mass 543.429 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? C23 C23 C . 0 . ? C22 C22 C . 0 . ? N21 N21 N . 0 . ? C20 C20 C . 0 . ? C19 C19 C . 0 . ? C18 C18 C . 0 . ? C17 C17 C . 0 . ? C16 C16 C . 0 . ? N15 N15 N . 0 . ? C14 C14 C . 0 . ? N14 N14 N . 0 . ? N13 N13 N . 0 . ? C13 C13 C . 0 . ? C12 C12 C . 0 . ? C11 C11 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C3' C3' C . 0 . ? C2' C2' C . 0 . ? O3' O3' O . 0 . ? HO2' HO2' H . 0 . ? H5'2 H5'2 H . 0 . ? H5'1 H5'1 H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H20 H20 H . 0 . ? H19 H19 H . 0 . ? H18 H18 H . 0 . ? H14 H14 H . 0 . ? H14' H14' H . 0 . ? H13 H13 H . 0 . ? H13' H13' H . 0 . ? H12 H12 H . 0 . ? H11 H11 H . 0 . ? H3' H3' H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H3 H3 H . 0 . ? OP3 OP3 O . 0 . ? HO3' HO3' H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N14 C14 ? ? DOUB C14 N15 ? ? SING C14 N13 ? ? SING C13 N13 ? ? SING O3' C3' ? ? SING N15 C16 ? ? DOUB OP1 P ? ? SING N13 C12 ? ? SING C3' C4' ? ? SING C3' C2' ? ? SING C5' C4' ? ? SING C5' O5' ? ? SING C4' O4' ? ? SING O5' P ? ? SING C16 C12 ? ? DOUB C16 C17 ? ? SING P OP2 ? ? DOUB C12 C11 ? ? SING C2' C1' ? ? SING C18 C17 ? ? DOUB C18 C19 ? ? SING O4' C1' ? ? SING C17 C22 ? ? SING C11 C23 ? ? SING C1' N9 ? ? SING C19 C20 ? ? DOUB C22 C23 ? ? SING C22 N21 ? ? SING C23 N2 ? ? SING N9 C4 ? ? SING N9 C8 ? ? SING N3 C4 ? ? DOUB N3 C2 ? ? DOUB C20 N21 ? ? DOUB C4 C5 ? ? SING N2 C2 ? ? DOUB C8 N7 ? ? SING C2 N1 ? ? SING C5 N7 ? ? SING C5 C6 ? ? SING N1 C6 ? ? DOUB C6 O6 ? ? SING OP2 HO2' ? ? SING C5' H5'2 ? ? SING C5' H5'1 ? ? SING C4' H4' ? ? SING C1' H1' ? ? SING C8 H8 ? ? SING N1 H1 ? ? SING N2 H2 ? ? SING C20 H20 ? ? SING C19 H19 ? ? SING C18 H18 ? ? SING N14 H14 ? ? SING N14 H14' ? ? SING C13 H13 ? ? SING C13 H13' ? ? SING C13 H12 ? ? SING C11 H11 ? ? SING C3' H3' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING O3' H3 ? ? SING P OP3 ? ? SING OP3 HO3' ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') . . . . . . $DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 430 mM 'natural abundance' $DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 430 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'chemical shift calculation' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Gladys _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.1 . M pH 7 . pH pressure 1 . atm temperature 288 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio water H 1 protons ppm 4.868 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3')" _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DC H1' H 5.798 . . 2 1 1 DC H2' H 2.201 . . 3 1 1 DC H2'' H 2.528 . . 4 1 1 DC H3' H 4.585 . . 5 1 1 DC H5 H 5.882 . . 6 1 1 DC H6 H 7.853 . . 7 2 2 DT H1' H 6.112 . . 8 2 2 DT H2' H 2.345 . . 9 2 2 DT H2'' H 2.303 . . 10 2 2 DT H3' H 4.947 . . 11 2 2 DT H4' H 4.139 . . 12 2 2 DT H5' H 4.317 . . 13 2 2 DT H5'' H 4.253 . . 14 2 2 DT H6 H 7.575 . . 15 2 2 DT H71 H 1.626 . . 16 2 2 DT H72 H 1.626 . . 17 2 2 DT H73 H 1.626 . . 18 3 3 DC H1' H 5.698 . . 19 3 3 DC H2' H 2.008 . . 20 3 3 DC H2'' H 2.066 . . 21 3 3 DC H3' H 4.946 . . 22 3 3 DC H5 H 5.526 . . 23 3 3 DC H6 H 7.332 . . 24 4 4 IQG H4a H 8.569 . . 25 4 4 IQG H1' H 5.857 . . 26 4 4 IQG H7a H 8.112 . . 27 4 4 IQG H2'1 H 2.719 . . 28 4 4 IQG H2'2 H 2.916 . . 29 4 4 IQG H8a H 6.877 . . 30 4 4 IQG H2' H 2.669 . . 31 4 4 IQG H2'' H 2.770 . . 32 4 4 IQG H9a H 7.744 . . 33 4 4 IQG H3' H 4.939 . . 34 4 4 IQG H3'a H 5.122 . . 35 4 4 IQG M15 H 3.223 . . 36 4 4 IQG H8 H 7.990 . . 37 4 4 IQG H8b H 8.302 . . 38 5 5 DG H1' H 5.751 . . 39 5 5 DG H2' H 2.456 . . 40 5 5 DG H2'' H 2.609 . . 41 5 5 DG H3' H 4.921 . . 42 5 5 DG H8 H 7.771 . . 43 6 6 DC H1' H 5.692 . . 44 6 6 DC H2' H 1.695 . . 45 6 6 DC H2'' H 2.265 . . 46 6 6 DC H3' H 4.702 . . 47 6 6 DC H5 H 5.060 . . 48 6 6 DC H6 H 7.039 . . 49 7 7 DG H1' H 5.915 . . 50 7 7 DG H2' H 2.607 . . 51 7 7 DG H2'' H 2.614 . . 52 7 7 DG H3' H 4.972 . . 53 7 7 DG H8 H 7.961 . . 54 8 8 DC H1' H 5.729 . . 55 8 8 DC H2' H 2.132 . . 56 8 8 DC H2'' H 2.184 . . 57 8 8 DC H3' H 4.825 . . 58 8 8 DC H5 H 5.180 . . 59 8 8 DC H6 H 7.375 . . 60 9 9 DC H1' H 5.296 . . 61 9 9 DC H2' H 2.204 . . 62 9 9 DC H2'' H 2.115 . . 63 9 9 DC H3' H 4.724 . . 64 9 9 DC H5 H 5.451 . . 65 9 9 DC H6 H 7.384 . . 66 10 10 DA H1' H 6.229 . . 67 10 10 DA H2 H 7.781 . . 68 10 10 DA H2' H 2.663 . . 69 10 10 DA H2'' H 2.884 . . 70 10 10 DA H3' H 4.989 . . 71 10 10 DA H8 H 8.266 . . 72 11 11 DT H1' H 5.928 . . 73 11 11 DT H2' H 2.206 . . 74 11 11 DT H2'' H 2.092 . . 75 11 11 DT H3' H 4.822 . . 76 11 11 DT H6 H 7.136 . . 77 11 11 DT H71 H 1.411 . . 78 11 11 DT H72 H 1.411 . . 79 11 11 DT H73 H 1.411 . . 80 12 12 DC H1' H 6.204 . . 81 12 12 DC H2' H 2.181 . . 82 12 12 DC H2'' H 2.213 . . 83 12 12 DC H3' H 4.501 . . 84 12 12 DC H5 H 5.677 . . 85 12 12 DC H6 H 7.522 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3')" _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 13 1 DG H1' H 5.619 . . 2 13 1 DG H2' H 2.586 . . 3 13 1 DG H2'' H 2.601 . . 4 13 1 DG H3' H 4.674 . . 5 13 1 DG H8 H 7.811 . . 6 14 2 DA H1' H 6.273 . . 7 14 2 DA H2 H 8.002 . . 8 14 2 DA H2' H 2.774 . . 9 14 2 DA H2'' H 2.866 . . 10 14 2 DA H3' H 5.034 . . 11 14 2 DA H8 H 8.251 . . 12 15 3 DT H1' H 5.614 . . 13 15 3 DT H2' H 2.096 . . 14 15 3 DT H2'' H 1.953 . . 15 15 3 DT H3' H 4.754 . . 16 15 3 DT H6 H 7.010 . . 17 15 3 DT H71 H 1.243 . . 18 15 3 DT H72 H 1.243 . . 19 15 3 DT H73 H 1.243 . . 20 16 4 DG H1' H 5.534 . . 21 16 4 DG H2' H 2.585 . . 22 16 4 DG H2'' H 2.697 . . 23 16 4 DG H3' H 4.917 . . 24 16 4 DG H8 H 7.705 . . 25 17 5 DG H1' H 5.786 . . 26 17 5 DG H2' H 2.454 . . 27 17 5 DG H2'' H 2.572 . . 28 17 5 DG H3' H 4.958 . . 29 17 5 DG H8 H 7.611 . . 30 18 6 DC H1' H 6.015 . . 31 18 6 DC H2' H 2.308 . . 32 18 6 DC H2'' H 2.213 . . 33 18 6 DC H3' H 4.848 . . 34 18 6 DC H5 H 5.514 . . 35 18 6 DC H6 H 7.602 . . 36 19 7 DG H1' H 5.641 . . 37 19 7 DG H2' H 2.344 . . 38 19 7 DG H2'' H 2.605 . . 39 19 7 DG H3' H 4.754 . . 40 19 7 DG H8 H 7.524 . . 41 20 8 DC H1' H 5.873 . . 42 20 8 DC H2' H 2.203 . . 43 20 8 DC H2'' H 2.242 . . 44 20 8 DC H3' H 4.833 . . 45 20 8 DC H5 H 5.158 . . 46 20 8 DC H6 H 7.079 . . 47 21 9 DC H1' H 6.066 . . 48 21 9 DC H2' H 2.275 . . 49 21 9 DC H2'' H 2.197 . . 50 21 9 DC H3' H 4.892 . . 51 21 9 DC H4' H 4.584 . . 52 21 9 DC H5 H 5.677 . . 53 21 9 DC H5' H 4.203 . . 54 21 9 DC H5'' H 4.283 . . 55 21 9 DC H6 H 7.711 . . 56 22 10 DG H1' H 5.236 . . 57 22 10 DG H2' H 2.347 . . 58 22 10 DG H2'' H 2.492 . . 59 22 10 DG H3' H 4.881 . . 60 22 10 DG H8 H 7.614 . . 61 23 11 DA H1' H 5.997 . . 62 23 11 DA H2 H 7.827 . . 63 23 11 DA H2' H 2.711 . . 64 23 11 DA H2'' H 2.728 . . 65 23 11 DA H3' H 4.960 . . 66 23 11 DA H8 H 7.989 . . 67 24 12 DG H1' H 5.924 . . 68 24 12 DG H2' H 2.201 . . 69 24 12 DG H2'' H 2.345 . . 70 24 12 DG H3' H 4.576 . . 71 24 12 DG H8 H 7.540 . . stop_ save_