data_34331 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Human telomeric G-quadruplex with 8-oxo-G substitution in the central G-quartet ; _BMRB_accession_number 34331 _BMRB_flat_file_name bmr34331.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" 165 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 2018-11-26 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-oxoG10 _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 ; TTGGGTTAGXGTTAGGGTTA GGGA ; 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 8OG 11 DG 12 DT 13 DT 14 DA 15 DG 16 DG 17 DG 18 DT 19 DT 20 DA 21 DG 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 278 . 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 7.50 0.0003 1 2 1 1 DT H1' H 6.08 0.0007 1 3 1 1 DT H3' H 4.46 0.0026 1 4 1 1 DT H71 H 1.51 0.0016 3 5 1 1 DT H72 H 1.51 0.0016 3 6 1 1 DT H73 H 1.51 0.0016 3 7 1 1 DT H2' H 1.97 0.0026 1 8 1 1 DT H2'' H 2.15 0.0189 1 9 2 2 DT H3 H 13.84 0.0019 1 10 2 2 DT H6 H 7.24 0.0008 1 11 2 2 DT H1' H 5.52 0.0015 1 12 2 2 DT H71 H 0.98 0.0015 3 13 2 2 DT H72 H 0.98 0.0015 3 14 2 2 DT H73 H 0.98 0.0015 3 15 2 2 DT H3' H 4.59 0.0003 1 16 2 2 DT H2' H 2.13 0.0050 1 17 2 2 DT H2'' H 2.19 0.0015 1 18 3 3 DG H4' H 4.20 0.0009 1 19 3 3 DG H8 H 8.02 0.0053 1 20 3 3 DG H1' H 5.83 0.0007 1 21 3 3 DG H2' H 2.60 0.0045 1 22 3 3 DG H2'' H 2.77 0.0032 1 23 3 3 DG H1 H 10.56 0.0010 1 24 4 4 DG H22 H 8.65 0.0022 1 25 4 4 DG H21 H 5.56 0.0017 1 26 4 4 DG H8 H 7.95 0.0032 1 27 4 4 DG H1' H 5.57 0.0012 1 28 4 4 DG H2' H 2.37 0.0005 1 29 4 4 DG H2'' H 2.55 0.0021 1 30 4 4 DG H1 H 11.31 0.0007 1 31 5 5 DG H3' H 4.21 0.0041 1 32 5 5 DG H22 H 9.96 0.0020 1 33 5 5 DG H21 H 6.01 0.0026 1 34 5 5 DG H1 H 11.36 0.0008 1 35 5 5 DG H8 H 7.74 0.0021 1 36 5 5 DG H1' H 5.40 0.0035 1 37 5 5 DG H2' H 1.86 0.0014 1 38 5 5 DG H2'' H 2.36 0.0037 1 39 6 6 DT H3' H 4.27 0.0008 1 40 6 6 DT H6 H 7.84 0.0004 1 41 6 6 DT H1' H 5.98 0.0021 1 42 6 6 DT H2' H 1.63 0.0004 1 43 6 6 DT H2'' H 2.75 0.0028 1 44 6 6 DT H71 H 1.85 0.0000 3 45 6 6 DT H72 H 1.85 0.0000 3 46 6 6 DT H73 H 1.85 0.0000 3 47 7 7 DT H3 H 12.39 0.0017 1 48 7 7 DT H6 H 7.59 0.0007 1 49 7 7 DT H1' H 5.96 0.0068 1 50 7 7 DT H3' H 4.44 0.0027 1 51 7 7 DT H2' H 1.79 0.0011 1 52 7 7 DT H2'' H 1.91 0.0033 1 53 7 7 DT H71 H 1.67 0.0058 3 54 7 7 DT H72 H 1.67 0.0058 3 55 7 7 DT H73 H 1.67 0.0058 3 56 8 8 DA H8 H 7.26 0.0020 1 57 8 8 DA H1' H 5.60 0.0013 1 58 8 8 DA H2 H 7.08 0.0136 1 59 8 8 DA H3' H 4.35 0.0005 1 60 8 8 DA H2' H 1.44 0.0014 1 61 8 8 DA H2'' H 2.29 0.0037 1 62 9 9 DG H3' H 4.61 0.0006 1 63 9 9 DG H2' H 2.73 0.0007 1 64 9 9 DG H2'' H 3.01 0.0013 1 65 9 9 DG H8 H 7.37 0.0025 1 66 9 9 DG H1' H 5.86 0.0020 1 67 9 9 DG H1 H 10.91 0.0010 1 68 10 10 8OG H2' H 2.75 0.0000 1 69 10 10 8OG H2'' H 2.45 0.0000 1 70 10 10 8OG H7 H 11.10 0.0011 1 71 10 10 8OG H1 H 11.20 0.0007 1 72 10 10 8OG H1' H 5.52 0.0013 1 73 11 11 DG H22 H 9.00 0.0019 1 74 11 11 DG H21 H 6.60 0.0001 1 75 11 11 DG H3' H 5.00 0.0016 1 76 11 11 DG H2' H 2.05 0.0025 1 77 11 11 DG H2'' H 2.97 0.0012 1 78 11 11 DG H8 H 7.67 0.0009 1 79 11 11 DG H1' H 5.79 0.0006 1 80 11 11 DG H1 H 10.65 0.0009 1 81 12 12 DT H71 H 1.70 0.0016 3 82 12 12 DT H72 H 1.70 0.0016 3 83 12 12 DT H73 H 1.70 0.0016 3 84 12 12 DT H3' H 4.48 0.0013 1 85 12 12 DT H2' H 2.12 0.0016 1 86 12 12 DT H2'' H 2.32 0.0028 1 87 12 12 DT H1' H 5.93 0.0016 1 88 12 12 DT H6 H 7.52 0.0008 1 89 13 13 DT H3' H 4.49 0.0012 1 90 13 13 DT H2' H 0.99 0.0027 1 91 13 13 DT H2'' H 1.83 0.0012 1 92 13 13 DT H71 H 1.19 0.0024 3 93 13 13 DT H72 H 1.19 0.0024 3 94 13 13 DT H73 H 1.19 0.0024 3 95 13 13 DT H6 H 6.74 0.0061 1 96 13 13 DT H1' H 5.54 0.0010 1 97 14 14 DA H2' H 2.53 0.0006 1 98 14 14 DA H2'' H 2.69 0.0037 1 99 14 14 DA H2 H 7.91 0.0053 1 100 14 14 DA H3' H 4.00 0.0017 1 101 14 14 DA H8 H 8.14 0.0052 1 102 14 14 DA H1' H 5.05 0.0023 1 103 15 15 DG H2' H 2.70 0.0010 1 104 15 15 DG H2'' H 2.88 0.0032 1 105 15 15 DG H3' H 4.28 0.0004 1 106 15 15 DG H1 H 11.53 0.0011 1 107 15 15 DG H8 H 7.86 0.0004 1 108 15 15 DG H1' H 6.03 0.0005 1 109 16 16 DG H3' H 4.51 0.0012 1 110 16 16 DG H2' H 2.25 0.0021 1 111 16 16 DG H2'' H 2.43 0.0019 1 112 16 16 DG H8 H 7.25 0.0014 1 113 16 16 DG H1' H 5.86 0.0003 1 114 16 16 DG H1 H 10.82 0.0019 1 115 17 17 DG H3' H 4.75 0.0028 1 116 17 17 DG H1' H 6.01 0.0009 1 117 17 17 DG H2' H 2.37 0.0033 1 118 17 17 DG H2'' H 2.42 0.0017 1 119 17 17 DG H8 H 7.51 0.0003 1 120 17 17 DG H1 H 10.48 0.0022 1 121 18 18 DT H3' H 4.12 0.0055 1 122 18 18 DT H2' H 2.34 0.0025 1 123 18 18 DT H2'' H 2.40 0.0026 1 124 18 18 DT H71 H 1.80 0.0016 3 125 18 18 DT H72 H 1.80 0.0016 3 126 18 18 DT H73 H 1.80 0.0016 3 127 18 18 DT H6 H 7.53 0.0009 1 128 18 18 DT H1' H 6.18 0.0007 1 129 19 19 DT H3' H 4.58 0.0011 1 130 19 19 DT H2' H 1.81 0.0022 1 131 19 19 DT H2'' H 2.17 0.0020 1 132 19 19 DT H6 H 7.36 0.0012 1 133 19 19 DT H1' H 5.78 0.0003 1 134 19 19 DT H71 H 1.76 0.0008 3 135 19 19 DT H72 H 1.76 0.0008 3 136 19 19 DT H73 H 1.76 0.0008 3 137 20 20 DA H3' H 4.93 0.0002 1 138 20 20 DA H2' H 2.59 0.0016 1 139 20 20 DA H2'' H 2.80 0.0081 1 140 20 20 DA H2 H 8.08 0.0132 1 141 20 20 DA H8 H 8.23 0.0092 1 142 20 20 DA H1' H 6.33 0.0007 1 143 21 21 DG H2' H 2.43 0.0055 1 144 21 21 DG H2'' H 2.74 0.0041 1 145 21 21 DG H8 H 7.90 0.0011 1 146 21 21 DG H1' H 5.87 0.0009 1 147 21 21 DG H22 H 9.13 0.0025 1 148 21 21 DG H21 H 6.22 0.0028 1 149 21 21 DG H1 H 11.43 0.0012 1 150 22 22 DG H2' H 2.46 0.0018 1 151 22 22 DG H2'' H 2.74 0.0007 1 152 22 22 DG H8 H 7.71 0.0022 1 153 22 22 DG H1' H 5.51 0.0025 1 154 22 22 DG H1 H 11.13 0.0020 1 155 23 23 DG H3' H 4.37 0.0001 1 156 23 23 DG H2' H 2.44 0.0032 1 157 23 23 DG H2'' H 2.58 0.0032 1 158 23 23 DG H8 H 7.70 0.0034 1 159 23 23 DG H1' H 5.99 0.0012 1 160 23 23 DG H1 H 10.74 0.0005 1 161 24 24 DA H2' H 1.97 0.0007 1 162 24 24 DA H2'' H 2.78 0.0011 1 163 24 24 DA H3' H 4.48 0.0009 1 164 24 24 DA H8 H 7.65 0.0002 1 165 24 24 DA H1' H 6.05 0.0005 1 stop_ save_