1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0003-1889-1713 Garavis, M. 0000-0002-8068-4566 El Khoury, R. 0000-0002-4458-1623 Damha, M.J. 0000-0001-8796-1282 Gonzalez, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C9 H13 F N3 O7 P 325.188 n 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 R C N 10 N O N 11 S C N 12 R C N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N F N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C N 47 N N N 48 N C N 49 N O N 50 N N N 51 N C N 52 N O N 53 N C N 54 N C N 55 N C N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 1 N sing N 2 N sing N 3 N sing N 4 N doub N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing UK Commun Chem 2399-3669 6 31 31 10.1038/s42004-023-00831-7 36797370 i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. 2023 0000-0002-8068-4566 0000-0001-8796-1282 0000-0003-1889-1713 0000-0002-4458-1623 10.2210/pdb7zyx/pdb pdb_00007zyx 10.13018/BMR34735 1795.099 DNA (5'-D(*TP*(CFL)P*(CFL)P*(CFL)P*(CFL)P*(CFL))-3') 2 syn polymer no yes (DT)(CFL)(CFL)(CFL)(CFL)(CFL) TCCCCC A,B polydeoxyribonucleotide n n n n n n 15.096 2 12 A 1 B 7 -177.958 A_DT1:DT7_B 1 17.327 -1.737 0.348 1.094 -12.030 2 15 A 2 B 8 179.385 A_CFL2:CFL8_B 2 6.974 2.060 0.174 1.656 2.798 2 15 A 6 B 12 178.595 A_CFL6:CFL12_B 3 -7.854 2.056 0.059 1.778 1.040 2 15 A 3 B 9 177.806 A_CFL3:CFL9_B 4 6.526 2.107 0.009 1.873 -4.913 2 15 A 5 B 11 178.286 A_CFL5:CFL11_B 5 19.096 2.048 0.149 1.860 12.960 2 15 A 4 B 10 177.855 A_CFL4:CFL10_B 6 -11.078 1.995 -0.101 1.488 2.586 -148.759 A A 1 2 0.252 B B 7 8 2.586 -0.486 -0.103 -0.062 AA_DT1CFL2:CFL8DT7_BB 1 2.607 1.354 -148.750 0.034 -0.045 0.276 178.927 A A 2 6 -61.156 B B 8 12 0.311 -122.205 2.188 -2.160 AA_CFL2CFL6:CFL12CFL8_BB 2 -126.964 63.538 146.995 -1.051 -1.125 -0.165 178.826 A A 6 3 -49.665 B B 12 9 -0.057 -99.004 -1.548 2.619 AA_CFL6CFL3:CFL9CFL12_BB 3 -148.565 74.526 73.840 1.279 0.820 0.125 -179.095 A A 3 5 -59.484 B B 9 11 -0.099 118.652 -2.691 2.705 AA_CFL3CFL5:CFL11CFL9_BB 4 133.895 67.126 -68.940 -1.357 -1.341 0.394 177.306 A A 5 4 -53.165 B B 11 10 0.290 -105.395 -2.005 2.219 AA_CFL5CFL4:CFL10CFL11_BB 5 -142.081 71.671 59.070 1.228 0.843 chem_comp_atom chem_comp_bond database_2 repository Initial release Data collection Database references 1 0 2023-03-01 1 1 2024-06-19 _database_2.pdbx_DOI Spain Spanish Ministry of Science, Innovation, and Universities PID2020-116620GB-I00 European Union H2020 Marie Curie Actions of the European Commission 799693 mgaravis@iqfr.csic.es 0000-0003-1889-1713 Miguel Garavis principal investigator/group leader cgonzalez@iqfr.csic.es 0000-0001-8796-1282 Carlos Gonzalez principal investigator/group leader masad.damha@mcgill.ca 0000-0002-4458-1623 Masad Damha J principal investigator/group leader Dimeric i-motif from 2'Farabinocytidine-modified TC5 N PDBE Y PDBE 2022-05-25 REL REL REL 9606 Homo sapiens sample 1 6 N back calculated data agree with experimental NOESY spectrum 45 10 isotropic 1 2D 1H-1H NOESY isotropic 2 2D 1H-1H TOCSY isotropic 2 2D DQF-COSY isotropic 2 2D 1H-19F HOESY 10 mM natural abundance 10 mM Conditions_1 5.0 pH 1 atm 278 K molecular dynamics 1 closest to the average 10 mM NaPi, 90% H2O/10% D2O TC5_sample 90% H2O/10% D2O solution Lee W, Tonelli M, Markley JL. chemical shift assignment NMRFAM-SPARKY Bruker Biospin collection TopSpin Guntert, Mumenthaler and Wuthrich structure calculation CYANA Lee W, Tonelli M, Markley JL. peak picking NMRFAM-SPARKY Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman refinement Amber 600 Bruker AVANCE NEO 600 Bruker AVANCE III HD DT 1 n 1 DT 1 A CFL 2 n 2 CFL 2 A CFL 3 n 3 CFL 3 A CFL 4 n 4 CFL 4 A CFL 5 n 5 CFL 5 A CFL 6 n 6 CFL 6 A DT 7 n 1 DT 7 B CFL 8 n 2 CFL 8 B CFL 9 n 3 CFL 9 B CFL 10 n 4 CFL 10 B CFL 11 n 5 CFL 11 B CFL 12 n 6 CFL 12 B author_and_software_defined_assembly PISA 2 dimeric NMR Distance Restraints native gel electrophoresis 4490 38 780 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 5 B B O1P HO3' CFL CFL 9 12 1.33 6 B B O1P HO3' CFL CFL 9 12 1.28 7 B B O1P HO3' CFL CFL 9 12 1.28 8 B B O1P HO3' CFL CFL 9 12 1.29 2 -4.07 0.60 122.90 118.83 A A A C6 C5 C7 DT DT DT 1 1 1 N 3 2.13 0.30 108.30 110.43 A A A O4' C1' N1 DT DT DT 1 1 1 N 4 -3.80 0.60 122.90 119.10 A A A C6 C5 C7 DT DT DT 1 1 1 N 4 -3.64 0.60 122.90 119.26 B B B C6 C5 C7 DT DT DT 7 7 7 N 5 -3.65 0.60 122.90 119.25 B B B C6 C5 C7 DT DT DT 7 7 7 N 7 2.31 0.30 108.30 110.61 B B B O4' C1' N1 DT DT DT 7 7 7 N 8 -3.61 0.60 122.90 119.29 A A A C6 C5 C7 DT DT DT 1 1 1 N 8 -4.70 0.60 122.90 118.20 B B B C6 C5 C7 DT DT DT 7 7 7 N N Dimeric i-motif from 2'Farabinocytidine-modified TC5 1 N N 1 N N covale 1.611 both A DT 1 A O3' DT 1 1_555 A CFL 2 A P CFL 2 1_555 covale 1.608 one A CFL 2 A O3' CFL 2 1_555 A CFL 3 A P CFL 3 1_555 covale 1.614 one A CFL 3 A O3' CFL 3 1_555 A CFL 4 A P CFL 4 1_555 covale 1.613 one A CFL 4 A O3' CFL 4 1_555 A CFL 5 A P CFL 5 1_555 covale 1.617 one A CFL 5 A O3' CFL 5 1_555 A CFL 6 A P CFL 6 1_555 covale 1.619 both B DT 7 B O3' DT 1 1_555 B CFL 8 B P CFL 2 1_555 covale 1.615 one B CFL 8 B O3' CFL 2 1_555 B CFL 9 B P CFL 3 1_555 covale 1.621 one B CFL 9 B O3' CFL 3 1_555 B CFL 10 B P CFL 4 1_555 covale 1.618 one B CFL 10 B O3' CFL 4 1_555 B CFL 11 B P CFL 5 1_555 covale 1.619 one B CFL 11 B O3' CFL 5 1_555 B CFL 12 B P CFL 6 1_555 hydrog TYPE_12_PAIR A DT 1 A N3 DT 1 1_555 B DT 7 B O4 DT 1 1_555 hydrog TYPE_12_PAIR A DT 1 A O4 DT 1 1_555 B DT 7 B N3 DT 1 1_555 hydrog TYPE_15_PAIR A CFL 2 A N4 CFL 2 1_555 B CFL 8 B O2 CFL 2 1_555 hydrog TYPE_15_PAIR A CFL 2 A O2 CFL 2 1_555 B CFL 8 B N4 CFL 2 1_555 hydrog TYPE_15_PAIR A CFL 3 A N4 CFL 3 1_555 B CFL 9 B O2 CFL 3 1_555 hydrog TYPE_15_PAIR A CFL 3 A O2 CFL 3 1_555 B CFL 9 B N4 CFL 3 1_555 hydrog TYPE_15_PAIR A CFL 4 A N4 CFL 4 1_555 B CFL 10 B O2 CFL 4 1_555 hydrog TYPE_15_PAIR A CFL 4 A O2 CFL 4 1_555 B CFL 10 B N4 CFL 4 1_555 hydrog TYPE_15_PAIR A CFL 5 A N4 CFL 5 1_555 B CFL 11 B O2 CFL 5 1_555 hydrog TYPE_15_PAIR A CFL 5 A O2 CFL 5 1_555 B CFL 11 B N4 CFL 5 1_555 hydrog TYPE_15_PAIR A CFL 6 A N4 CFL 6 1_555 B CFL 12 B O2 CFL 6 1_555 hydrog TYPE_15_PAIR A CFL 6 A O2 CFL 6 1_555 B CFL 12 B N4 CFL 6 1_555 DNA i-motif, FANA, 2'Farabinocytidine, DNA 7ZYX PDB 1 1 7ZYX 1 6 7ZYX 1 6 7ZYX A 1 1 6 7 12 7ZYX 7 12 7ZYX B 1 1 6