1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Horowitz, E.D. Lilavivat, S. Holladay, B.W. Germann, M.W. Hud, N.V. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C13 H11 N3 209.247 PROFLAVIN non-polymer US J.Am.Chem.Soc. JACSAT 0004 0002-7863 131 5831 5838 10.1021/ja810068e 19309071 Solution structure and thermodynamics of 2',5' RNA intercalation. 2009 10.2210/pdb2kd4/pdb pdb_00002kd4 2556.593 5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2' 2 syn polymer 209.247 PROFLAVIN 2 syn non-polymer no no GCCGCGGC GCCGCGGC A,B polyribonucleotide n n n n n n n n -23.280 1 19 A 1 B 8 3.603 A_G1:C8_B 1 -29.530 -0.240 -0.546 0.023 15.650 1 19 A 2 B 7 -6.304 A_C2:G7_B 2 -39.027 0.359 0.406 -0.210 15.018 1 19 A 3 B 6 2.153 A_C3:G6_B 3 -8.216 0.880 -0.198 -0.276 7.428 1 19 A 4 B 5 0.727 A_G4:C5_B 4 -13.834 -1.083 0.560 -0.463 -3.789 1 19 A 5 B 4 1.215 A_C5:G4_B 5 -13.446 1.049 0.501 -0.424 -13.600 1 19 A 6 B 3 -1.714 A_G6:C3_B 6 -12.364 -0.958 0.166 -0.413 -15.672 1 19 A 7 B 2 -1.036 A_G7:C2_B 7 -30.999 -0.206 -0.102 -0.074 12.867 1 19 A 8 B 1 1.480 A_C8:G1_B 8 -26.131 0.152 -0.262 -0.029 -0.195 -163.946 A A 1 2 -87.043 B B 8 7 -1.209 162.562 3.746 -0.499 AA_G1C2:G7C8_BB 1 13.000 6.961 -36.680 0.761 1.851 3.743 39.958 A A 2 3 0.091 B B 7 6 4.093 0.061 0.421 -1.821 AA_C2C3:G6G7_BB 2 -13.222 19.691 37.792 -2.674 -2.493 6.065 24.776 A A 3 4 -29.639 B B 6 5 6.681 -11.950 -0.083 -1.167 AA_C3G4:C5G6_BB 3 -7.874 19.528 20.278 5.069 -4.936 3.399 49.803 A A 4 5 -0.671 B B 5 4 3.397 -0.565 0.069 -0.188 AA_G4C5:G4C5_BB 4 0.222 -0.263 49.800 -0.180 -0.065 6.574 23.037 A A 5 6 -17.545 B B 4 3 6.619 -6.875 -0.135 -1.180 AA_C5G6:C3G4_BB 5 3.496 -8.922 21.724 2.057 2.887 2.887 43.478 A A 6 7 17.677 B B 3 2 3.686 12.693 0.164 -1.822 AA_G6G7:C2C3_BB 6 14.100 -19.636 39.303 -3.763 1.227 -0.154 -166.211 A A 7 8 -86.610 B B 2 1 -1.268 164.474 -3.411 -0.634 AA_G7C8:G1C2_BB 7 -10.038 -5.286 -49.960 0.773 -1.690 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list pdbx_validate_polymer_linkage struct_conn struct_site repository Initial release Version format compliance Advisory Data collection Database references Derived calculations 1 0 2009-04-07 1 1 2011-07-13 1 2 2022-03-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BMRB Y RCSB 2009-01-02 REL REL PRL PROFLAVIN Synthetic 2',5' RNA sample 14 14 378 258 378 258 structures with the lowest energy 10 1 1H-1H NOESY 31P-1H HETCOR 1H-1H TOCSY 31P-decoupled 1H-1H COSY 1H-1H NOESY with WATERGATE water suppression 2 mM 4 mM 60 mM 200 mM 260 6.5 1 atm 282 K 130 1 atm 282 K 300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed simulated annealing 1 lowest energy 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O 99.9% D2O Bruker Biospin collection XwinNMR Bruker Biospin data analysis XwinNMR Bruker Biospin processing XwinNMR Goddard chemical shift assignment Sparky Goddard data analysis Sparky Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm structure solution Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm refinement Amber 600 Bruker DRX Bruker DRX 500 Bruker DRX Bruker DRX PRL 17 2 PRL PRL 17 A PRL 17 2 PRL PRL 17 B G 1 n 1 G 1 A C 2 n 2 C 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A C 5 n 5 C 5 A G 6 n 6 G 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A G 1 n 1 G 1 B C 2 n 2 C 2 B C 3 n 3 C 3 B G 4 n 4 G 4 B C 5 n 5 C 5 B G 6 n 6 G 6 B G 7 n 7 G 7 B C 8 n 8 C 8 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A G 1 0.077 SIDE CHAIN 1 A C 2 0.120 SIDE CHAIN 1 A G 4 0.127 SIDE CHAIN 1 A G 6 0.149 SIDE CHAIN 1 A G 7 0.089 SIDE CHAIN 1 B G 1 0.065 SIDE CHAIN 1 B C 2 0.117 SIDE CHAIN 1 B G 4 0.115 SIDE CHAIN 1 B G 6 0.115 SIDE CHAIN 1 B G 7 0.129 SIDE CHAIN 1 7.28 0.80 106.10 113.38 A A A O4' C4' C3' G G G 1 1 1 N 1 5.49 0.90 109.80 115.29 A A A C5' C4' O4' G G G 1 1 1 N 1 3.19 0.50 113.10 116.29 A A A N7 C8 N9 G G G 1 1 1 N 1 7.10 0.80 106.10 113.20 A A A O4' C4' C3' C C C 2 2 2 N 1 6.12 0.80 101.50 107.62 A A A C3' C2' C1' C C C 2 2 2 N 1 -5.40 0.80 108.20 102.80 A A A O4' C1' N1 C C C 2 2 2 N 1 3.76 0.60 118.90 122.66 A A A N1 C2 O2 C C C 2 2 2 N 1 -4.32 0.70 121.90 117.58 A A A N3 C2 O2 C C C 5 5 5 N 1 -2.55 0.40 106.40 103.85 A A A C8 N9 C4 G G G 6 6 6 N 1 13.65 1.90 111.70 125.35 A A A O5' C5' C4' G G G 7 7 7 N 1 -10.38 1.40 115.20 104.82 A A A C5' C4' C3' G G G 7 7 7 N 1 -5.68 0.80 108.20 102.52 A A A O4' C1' N9 G G G 7 7 7 N 1 5.00 0.80 106.10 111.10 A A A O4' C4' C3' C C C 8 8 8 N 1 6.01 0.90 109.80 115.81 A A A C5' C4' O4' C C C 8 8 8 N 1 5.44 0.80 101.50 106.94 A A A C3' C2' C1' C C C 8 8 8 N 1 -7.59 1.20 120.80 113.21 A A A C6 N1 C1' C C C 8 8 8 N 1 8.06 1.10 118.80 126.86 A A A C2 N1 C1' C C C 8 8 8 N 1 6.88 0.80 106.10 112.98 B B B O4' C4' C3' G G G 1 1 1 N 1 5.97 0.90 109.80 115.77 B B B C5' C4' O4' G G G 1 1 1 N 1 6.88 0.80 106.10 112.98 B B B O4' C4' C3' C C C 2 2 2 N 1 5.41 0.80 101.50 106.91 B B B C3' C2' C1' C C C 2 2 2 N 1 -5.46 0.80 108.20 102.74 B B B O4' C1' N1 C C C 2 2 2 N 1 -4.20 0.70 121.90 117.70 B B B N3 C2 O2 C C C 2 2 2 N 1 5.00 0.80 101.50 106.50 B B B C3' C2' C1' G G G 6 6 6 N 1 -6.03 0.80 108.20 102.17 B B B O4' C1' N9 G G G 7 7 7 N 1 6.53 0.90 109.80 116.33 B B B C5' C4' O4' C C C 8 8 8 N 1 4.85 0.80 101.50 106.35 B B B C3' C2' C1' C C C 8 8 8 N 1 -7.79 1.20 120.80 113.01 B B B C6 N1 C1' C C C 8 8 8 N 1 8.03 1.10 118.80 126.83 B B B C2 N1 C1' C C C 8 8 8 N lowest energy, model 1 Solution structure and thermodynamics of 2',5' RNA intercalation 1 N N 1 N N 2 N N 2 N N covale 1.609 one A G 1 A O2' G 1 1_555 A C 2 A P C 2 1_555 covale 1.595 one A C 2 A O2' C 2 1_555 A C 3 A P C 3 1_555 covale 1.625 one A C 3 A O2' C 3 1_555 A G 4 A P G 4 1_555 covale 1.600 one A G 4 A O2' G 4 1_555 A C 5 A P C 5 1_555 covale 1.611 one A C 5 A O2' C 5 1_555 A G 6 A P G 6 1_555 covale 1.619 one A G 6 A O2' G 6 1_555 A G 7 A P G 7 1_555 covale 1.595 one A G 7 A O2' G 7 1_555 A C 8 A P C 8 1_555 covale 1.608 one B G 1 B O2' G 1 1_555 B C 2 B P C 2 1_555 covale 1.609 one B C 2 B O2' C 2 1_555 B C 3 B P C 3 1_555 covale 1.613 one B C 3 B O2' C 3 1_555 B G 4 B P G 4 1_555 covale 1.595 one B G 4 B O2' G 4 1_555 B C 5 B P C 5 1_555 covale 1.605 one B C 5 B O2' C 5 1_555 B G 6 B P G 6 1_555 covale 1.600 one B G 6 B O2' G 6 1_555 B G 7 B P G 7 1_555 covale 1.601 one B G 7 B O2' G 7 1_555 B C 8 B P C 8 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 7 B N2 G 7 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 6 B N1 G 6 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 6 B O6 G 6 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 6 B N2 G 6 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B C 5 B N3 C 5 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B C 5 B O2 C 5 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B C 5 B N4 C 5 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 B G 4 B N1 G 4 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 B G 4 B O6 G 4 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 B G 4 B N2 G 4 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 2 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 2 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 2 B N4 C 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 1 B N2 G 1 1_555 RNA proflavine, intercalation, 2', 5' RNA, RNA, nearest-neighbor exclusion 2KD4 PDB 1 1 2KD4 GCCGCGGC 1 8 2KD4 1 8 2KD4 A 1 1 8 1 8 2KD4 1 8 2KD4 B 1 1 8 BINDING SITE FOR RESIDUE PRL B 17 B PRL 17 Software 5 BINDING SITE FOR RESIDUE PRL A 17 A PRL 17 Software 5 A G 4 A G 4 5 1_555 A C 5 A C 5 5 1_555 A G 6 A G 6 5 1_555 B C 3 B C 3 5 1_555 B G 4 B G 4 5 1_555 A C 2 A C 2 5 1_555 A C 3 A C 3 5 1_555 A G 4 A G 4 5 1_555 B C 5 B C 5 5 1_555 B G 6 B G 6 5 1_555