data_34332 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Human telomeric G-quadruplex with 8-oxo-G substitution in the outer G-quartet ; _BMRB_accession_number 34332 _BMRB_flat_file_name bmr34332.str _Entry_type original _Submission_date 2018-11-26 _Accession_date 2018-11-26 _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 Bielskute S. . . 2 Plavec J. . . 3 Podbevsek P. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 157 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-31 update BMRB 'update entry citation' 2019-01-25 original author 'original release' stop_ _Original_release_date 2018-11-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Impact of Oxidative Lesions on the Human Telomeric G-quadruplex ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30657306 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bielskute S. . . 2 Plavec J. . . 3 Podbevsek P. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 141 _Journal_issue 6 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2594 _Page_last 2603 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name hTel-oxoG21 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 7607.883 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; TTGGGTTAGGGTTAGGGTTA XGGA ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DG 4 DG 5 DG 6 DT 7 DT 8 DA 9 DG 10 DG 11 DG 12 DT 13 DT 14 DA 15 DG 16 DG 17 DG 18 DT 19 DT 20 DA 21 8OG 22 DG 23 DG 24 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_8OG _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE _BMRB_code 8OG _PDB_code 8OG _Standard_residue_derivative . _Molecular_mass 363.221 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? 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 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 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 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O8 O8 O . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H7 H7 H . 0 . ? H1 H1 H . 0 . ? H21 H21 H . 0 . ? H22 H22 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 OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? SING C8 N7 ? ? DOUB C8 O8 ? ? SING N7 C5 ? ? SING N7 H7 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 H1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING N3 C4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM DNA, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'potassium phosphate buffer' 20 mM 'natural abundance' KCl 70 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DDR2 _Field_strength 800 _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_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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' 70 . mM pH 7 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 4.8 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 DT H6 H 7.42 0.0001 1 2 1 1 DT H3' H 4.66 0.0038 1 3 1 1 DT H71 H 1.47 0.0019 3 4 1 1 DT H72 H 1.47 0.0019 3 5 1 1 DT H73 H 1.47 0.0019 3 6 1 1 DT H2' H 1.86 0.0056 1 7 1 1 DT H2'' H 2.29 0.0001 1 8 2 2 DT H6 H 7.38 0.0005 1 9 2 2 DT H71 H 1.46 0.0008 3 10 2 2 DT H72 H 1.46 0.0008 3 11 2 2 DT H73 H 1.46 0.0008 3 12 2 2 DT H2' H 1.96 0.0000 1 13 2 2 DT H2'' H 2.23 0.0000 1 14 3 3 DG H21 H 6.60 0.0000 1 15 3 3 DG H3' H 4.86 0.0000 1 16 3 3 DG H1 H 12.32 0.0183 1 17 3 3 DG H2' H 2.90 0.0047 1 18 3 3 DG H2'' H 3.15 0.0119 1 19 3 3 DG H8 H 7.42 0.0029 1 20 3 3 DG H1' H 6.11 0.0018 1 21 4 4 DG H1 H 11.84 0.0024 1 22 4 4 DG H3' H 5.02 0.0035 1 23 4 4 DG H2' H 2.64 0.0059 1 24 4 4 DG H8 H 8.02 0.0092 1 25 4 4 DG H1' H 5.81 0.0051 1 26 5 5 DG H2' H 2.62 0.0046 1 27 5 5 DG H1 H 11.08 0.0015 1 28 5 5 DG H3' H 5.06 0.0072 1 29 5 5 DG H8 H 7.83 0.0041 1 30 5 5 DG H1' H 6.43 0.0023 1 31 6 6 DT H2' H 2.48 0.0017 1 32 6 6 DT H2'' H 2.57 0.0047 1 33 6 6 DT H71 H 2.02 0.0069 3 34 6 6 DT H72 H 2.02 0.0069 3 35 6 6 DT H73 H 2.02 0.0069 3 36 6 6 DT H3' H 4.88 0.0041 1 37 6 6 DT H6 H 7.74 0.0042 1 38 6 6 DT H1' H 6.41 0.0033 1 39 7 7 DT H2'' H 2.31 0.0095 1 40 7 7 DT H2' H 1.92 0.0177 1 41 7 7 DT H71 H 2.01 0.0056 3 42 7 7 DT H72 H 2.01 0.0056 3 43 7 7 DT H73 H 2.01 0.0056 3 44 7 7 DT H3' H 4.83 0.0017 1 45 7 7 DT H6 H 7.57 0.0062 1 46 7 7 DT H1' H 6.15 0.0084 1 47 8 8 DA H2 H 8.26 0.0114 1 48 8 8 DA H3' H 5.14 0.0021 1 49 8 8 DA H2' H 2.89 0.0016 1 50 8 8 DA H2'' H 3.06 0.0011 1 51 8 8 DA H8 H 8.47 0.0033 1 52 8 8 DA H1' H 6.50 0.0072 1 53 9 9 DG H1 H 12.22 0.0031 1 54 9 9 DG H3' H 5.02 0.0021 1 55 9 9 DG H2'' H 3.47 0.0048 1 56 9 9 DG H2' H 3.01 0.0016 1 57 9 9 DG H8 H 7.39 0.0051 1 58 9 9 DG H1' H 5.98 0.0028 1 59 10 10 DG H1 H 12.29 0.0061 1 60 10 10 DG H3' H 5.07 0.0027 1 61 10 10 DG H2' H 2.58 0.0033 1 62 10 10 DG H2'' H 2.68 0.0019 1 63 10 10 DG H8 H 8.08 0.0135 1 64 10 10 DG H1' H 5.53 0.0068 1 65 11 11 DG H1 H 11.23 0.0011 1 66 11 11 DG H3' H 5.04 0.0035 1 67 11 11 DG H2' H 2.52 0.0055 1 68 11 11 DG H2'' H 2.65 0.0021 1 69 11 11 DG H8 H 7.93 0.0045 1 70 11 11 DG H1' H 6.28 0.0026 1 71 12 12 DT H3' H 4.68 0.0014 1 72 12 12 DT H2'' H 2.47 0.0070 1 73 12 12 DT H2' H 2.40 0.0036 1 74 12 12 DT H71 H 1.88 0.0069 3 75 12 12 DT H72 H 1.88 0.0069 3 76 12 12 DT H73 H 1.88 0.0069 3 77 12 12 DT H6 H 7.56 0.0046 1 78 12 12 DT H1' H 6.24 0.0020 1 79 13 13 DT H5' H 2.80 0.0041 1 80 13 13 DT H5'' H 3.50 0.0072 1 81 13 13 DT H3' H 4.49 0.0074 1 82 13 13 DT H4' H 3.93 0.0030 1 83 13 13 DT H6 H 6.60 0.0030 1 84 13 13 DT H1' H 5.32 0.0050 1 85 13 13 DT H2' H 1.29 0.0026 1 86 13 13 DT H2'' H 2.08 0.0055 1 87 13 13 DT H71 H 1.35 0.0031 3 88 13 13 DT H72 H 1.35 0.0031 3 89 13 13 DT H73 H 1.35 0.0031 3 90 14 14 DA H2 H 7.40 0.0065 1 91 14 14 DA H3' H 4.67 0.0000 1 92 14 14 DA H2' H 2.29 0.0036 1 93 14 14 DA H2'' H 2.53 0.0022 1 94 14 14 DA H8 H 7.78 0.0077 1 95 14 14 DA H1' H 6.32 0.0056 1 96 15 15 DG H1 H 11.29 0.0007 1 97 15 15 DG H2' H 2.94 0.0036 1 98 15 15 DG H2'' H 3.45 0.0054 1 99 15 15 DG H8 H 7.33 0.0035 1 100 15 15 DG H1' H 6.10 0.0048 1 101 16 16 DG H1 H 11.21 0.0039 1 102 16 16 DG H3' H 4.99 0.0026 1 103 16 16 DG H2' H 2.41 0.0027 1 104 16 16 DG H2'' H 2.51 0.0055 1 105 16 16 DG H8 H 7.31 0.0048 1 106 16 16 DG H1' H 5.76 0.0026 1 107 17 17 DG H1 H 11.93 0.0041 1 108 17 17 DG H3' H 5.18 0.0027 1 109 17 17 DG H2' H 2.55 0.0026 1 110 17 17 DG H2'' H 2.68 0.0026 1 111 17 17 DG H8 H 7.63 0.0045 1 112 17 17 DG H1' H 5.88 0.0070 1 113 18 18 DT H3' H 4.94 0.0051 1 114 18 18 DT H2' H 2.33 0.0049 1 115 18 18 DT H2'' H 2.54 0.0043 1 116 18 18 DT H71 H 2.06 0.0028 3 117 18 18 DT H72 H 2.06 0.0028 3 118 18 18 DT H73 H 2.06 0.0028 3 119 18 18 DT H6 H 7.97 0.0024 1 120 18 18 DT H1' H 6.36 0.0030 1 121 19 19 DT H3' H 4.69 0.0006 1 122 19 19 DT H2'' H 1.87 0.0029 1 123 19 19 DT H71 H 1.51 0.0045 3 124 19 19 DT H72 H 1.51 0.0045 3 125 19 19 DT H73 H 1.51 0.0045 3 126 19 19 DT H2' H 0.95 0.0004 1 127 19 19 DT H6 H 7.14 0.0009 1 128 19 19 DT H1' H 5.76 0.0021 1 129 20 20 DA H2 H 8.26 0.0001 1 130 20 20 DA H3' H 5.00 0.0053 1 131 20 20 DA H2' H 2.68 0.0040 1 132 20 20 DA H2'' H 2.85 0.0023 1 133 20 20 DA H1' H 6.06 0.0065 1 134 20 20 DA H8 H 8.07 0.0017 1 135 21 21 8OG H3' H 4.97 0.0052 1 136 21 21 8OG H2' H 2.80 0.0046 1 137 21 21 8OG H2'' H 3.51 0.0049 1 138 21 21 8OG H1 H 11.39 0.0044 1 139 21 21 8OG H1' H 6.01 0.0033 1 140 22 22 DG H3' H 5.05 0.0028 1 141 22 22 DG H2' H 2.29 0.0013 1 142 22 22 DG H2'' H 2.69 0.0024 1 143 22 22 DG H1 H 11.62 0.0018 1 144 22 22 DG H8 H 8.20 0.0034 1 145 22 22 DG H1' H 5.72 0.0048 1 146 23 23 DG H3' H 4.93 0.0009 1 147 23 23 DG H2' H 2.15 0.0013 1 148 23 23 DG H2'' H 2.55 0.0020 1 149 23 23 DG H8 H 7.48 0.0035 1 150 23 23 DG H1' H 5.90 0.0035 1 151 23 23 DG H1 H 10.60 0.0044 1 152 24 24 DA H2 H 7.48 0.0097 1 153 24 24 DA H3' H 4.67 0.0000 1 154 24 24 DA H2' H 2.40 0.0034 1 155 24 24 DA H2'' H 2.65 0.0016 1 156 24 24 DA H8 H 7.82 0.0039 1 157 24 24 DA H1' H 6.10 0.0066 1 stop_ save_