0.041135 0.023749 0.000000 0.000000 0.047499 0.000000 0.000000 0.000000 0.008078 0.00000 0.00000 0.00000 Minasov, G. Matulic-Adamic, J. Wilds, C.J. Haeberli, P. Usman, N. Beigelman, L. Egli, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 24.310 24.310 123.790 C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking Ca 2 40.078 CALCIUM ION non-polymer C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C11 H15 O7 P 290.206 D-RIBOFURANOSYL-BENZENE-5'-MONOPHOSPHATE RNA 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 S C N 10 N O N 11 R C N 12 N O N 13 R C N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N N N 20 N C N 21 N C 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 H N 36 N CA N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 R C N 48 N O N 49 R C Y 50 N N Y 51 N C Y 52 N N Y 53 N C N 54 N C N 55 N O N 56 N N N 57 N C N 58 N N N 59 N N Y 60 N C 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 71 N H N 72 N H N 73 N H N 74 N H N 75 N O N 76 N H N 77 N H N 78 N P N 79 N O N 80 N O N 81 N O N 82 N C N 83 R C N 84 N O N 85 S C Y 86 N C Y 87 N C Y 88 N C Y 89 N C Y 90 N C Y 91 N C N 92 R C N 93 N O N 94 S C N 95 N O N 96 N O N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing 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 sing N 27 N doub N 28 N sing N 29 N doub N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub 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 Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing N 66 N sing Y 67 N doub N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing Y 95 N doub Y 96 N sing Y 97 N sing N 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing UK RNA RNARFU 2122 1355-8382 6 1516 1528 10.1017/S1355838200001114 11105752 Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines. 2000 10.2210/pdb1g2j/pdb pdb_00001g2j 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD 2000-03-15 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.0000 1.0 5ID-B APS 1.0000 SYNCHROTRON APS BEAMLINE 5ID-B 2523.602 5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3' 1 syn polymer 40.078 CALCIUM ION 2 syn non-polymer 18.015 water 37 nat water no yes CCC(PYY)GGGG CCCNGGGG A polyribonucleotide n n n n n n n n 1 2.09 41.21 VAPOR DIFFUSION, HANGING DROP 6.5 Oligonucleotide, Calcium Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K 277.0 Oligonucleotide 1 Calcium Acetate 1 Sodium Cacodylate 1 PEG 8000 1 15.048 1 19 A 1 A 7 -3.413 A_C1:G7_A 1 -11.386 0.210 -0.295 -0.150 4.968 1 19 A 2 A 6 5.896 A_C2:G6_A 2 -10.992 0.304 0.050 0.015 4.991 1 19 A 3 A 5 -1.767 A_C3:G5_A 3 -5.811 0.517 0.073 -0.187 15.048 1 19 A 1 A 7 -3.413 A_C1:G7_A 4 -11.386 0.210 -0.295 -0.150 4.968 1 19 A 2 A 6 5.896 A_C2:G6_A 5 -10.992 0.304 0.050 0.015 4.991 1 19 A 3 A 5 -1.767 A_C3:G5_A 6 -5.811 0.517 0.073 -0.187 2.870 33.758 A A 1 2 14.920 A A 7 6 3.483 8.564 -0.039 -2.010 AA_C1C2:G6G7_AA 1 -2.938 5.118 32.555 -4.835 -0.404 2.629 33.750 A A 2 3 14.565 A A 6 5 3.234 8.372 -0.291 -2.083 AA_C2C3:G5G6_AA 2 0.738 -1.285 32.716 -4.824 0.610 2.870 33.758 A A 1 2 14.920 A A 7 6 3.483 8.564 -0.039 -2.010 AA_C1C2:G6G7_AA 3 -2.938 5.118 32.555 -4.835 -0.404 2.629 33.750 A A 2 3 14.565 A A 6 5 3.234 8.372 -0.291 -2.083 AA_C2C3:G5G6_AA 4 0.738 -1.285 32.716 -4.824 0.610 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2000-12-06 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id NDB Y NDB 2000-10-20 REL REL CA CALCIUM ION HOH water RNA tetramer duplex Other in silico model CA 9 2 CA CA 9 A CA 14 2 CA CA 14 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A HOH 45 3 HOH HOH 45 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A C 1 n 1 C 1 A C 2 n 2 C 2 A C 3 n 3 C 3 A PYL 4 n 4 PYY 4 A G 5 n 5 G 5 A G 6 n 6 G 6 A G 7 n 7 G 7 A G 8 n 8 G 8 A author_defined_assembly 2 dimeric A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A G 8 A O3' G 8 1_555 88.9 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A G 8 A O2' G 8 1_555 113.7 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 A G 8 A O2' G 8 1_555 71.2 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A HOH 10 D O HOH 1_555 166.9 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 10 D O HOH 1_555 82.0 A G 8 A O2' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 10 D O HOH 1_555 72.2 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A HOH 11 D O HOH 1_555 92.7 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 11 D O HOH 1_555 145.9 A G 8 A O2' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 11 D O HOH 1_555 137.0 A HOH 10 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 11 D O HOH 1_555 89.7 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 100.8 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 137.9 A G 8 A O2' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 67.4 A HOH 10 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 92.3 A HOH 11 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 75.0 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 84.9 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 76.6 A G 8 A O2' G 8 1_555 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 141.9 A HOH 10 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 83.8 A HOH 11 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 69.7 A HOH 12 D O HOH 1_555 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 144.5 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 A G 8 A OP1 G 8 8_675 82.5 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 1_555 91.4 A G 8 A OP1 G 8 8_675 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 1_555 173.2 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 8_675 173.4 A G 8 A OP1 G 8 8_675 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 8_675 91.7 A HOH 15 D O HOH 1_555 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 8_675 94.5 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 1_555 92.5 A G 8 A OP1 G 8 8_675 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 1_555 91.4 A HOH 15 D O HOH 1_555 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 1_555 85.9 A HOH 15 D O HOH 8_675 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 1_555 90.7 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 91.2 A G 8 A OP1 G 8 8_675 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 92.6 A HOH 15 D O HOH 1_555 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 90.5 A HOH 15 D O HOH 8_675 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 86.0 A HOH 16 D O HOH 1_555 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 174.9 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 0.5000000000 0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 12_565 x,x-y+1,-z+1/6 crystal symmetry operation -12.1550000000 21.0530775660 20.6316666667 1 A CA 14 C CA 1 A G 7 0.051 SIDE CHAIN -17.632 -3.890 0.000 -17.632 0.000 35.264 Used residual target 0.2690000 0.2170000 1.97 20.0 185 1736 1736 95.3 random 1 Isotropic THROUGHOUT 0.0 0.0 MOLECULAR REPLACEMENT RNA tetramer duplex G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, Acta Cryst. D, 52, 57-64 (1996). 1.97 20.0 45 214 2 167 0 0.009 1.40 29.47 1.94 1.97 20.0 1G2J 1904 1904 0.0 -3.0 0.0460000 1 20.5 13.6 99.1 0.2430000 1.97 2.04 17.3 186 11.5 99.5 phasing AMoRE refinement CNS 0.9 data reduction DENZO data scaling SCALEPACK RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE 1 N N 2 N N 2 N N 3 N N covale 1.606 both A C 3 A O3' C 3 1_555 A PYY 4 A P PYY 4 1_555 covale 1.603 both A PYY 4 A O3' PYY 4 1_555 A G 5 A P G 5 1_555 metalc 2.580 A PYY 4 A O1P PYY 4 1_565 A CA 9 B CA CA 1_555 metalc 2.284 A G 8 A O3' G 8 1_555 A CA 9 B CA CA 1_555 metalc 2.543 A G 8 A O2' G 8 1_555 A CA 9 B CA CA 1_555 metalc 2.366 A G 8 A OP1 G 8 1_555 A CA 14 C CA CA 1_555 metalc 2.361 A G 8 A OP1 G 8 8_675 A CA 14 C CA CA 1_555 metalc 2.419 A CA 9 B CA CA 1_555 A HOH 10 D O HOH 1_555 metalc 2.332 A CA 9 B CA CA 1_555 A HOH 11 D O HOH 1_555 metalc 2.593 A CA 9 B CA CA 1_555 A HOH 12 D O HOH 1_555 metalc 2.463 A CA 9 B CA CA 1_555 A HOH 13 D O HOH 1_555 metalc 2.653 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 1_555 metalc 2.647 A CA 14 C CA CA 1_555 A HOH 15 D O HOH 8_675 metalc 2.272 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 1_555 metalc 2.274 A CA 14 C CA CA 1_555 A HOH 16 D O HOH 8_675 hydrog WATSON-CRICK A C 1 A N3 C 1 1_555 A G 7 A N1 G 7 12_565 hydrog WATSON-CRICK A C 1 A N4 C 1 1_555 A G 7 A O6 G 7 12_565 hydrog WATSON-CRICK A C 1 A O2 C 1 1_555 A G 7 A N2 G 7 12_565 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 A G 6 A N1 G 6 12_565 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 A G 6 A O6 G 6 12_565 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 A G 6 A N2 G 6 12_565 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 5 A N1 G 5 12_565 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 5 A O6 G 5 12_565 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 5 A N2 G 5 12_565 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 3 A N3 C 3 12_565 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 3 A O2 C 3 12_565 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 3 A N4 C 3 12_565 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 A C 2 A N3 C 2 12_565 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 A C 2 A O2 C 2 12_565 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 A C 2 A N4 C 2 12_565 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 A C 1 A N3 C 1 12_565 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 A C 1 A O2 C 1 12_565 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 A C 1 A N4 C 1 12_565 RNA RNA duplex, phenyl-ribonucleotide, RNA 1G2J PDB 1 1G2J 1 8 1G2J 1 8 1G2J A 1 1 8 BINDING SITE FOR RESIDUE CA A 9 A CA 9 Software 6 BINDING SITE FOR RESIDUE CA A 14 A CA 14 Software 6 A PYY 4 A PYY 4 6 1_565 A G 8 A G 8 6 1_555 A HOH 10 D HOH 6 1_555 A HOH 11 D HOH 6 1_555 A HOH 12 D HOH 6 1_555 A HOH 13 D HOH 6 1_555 A G 8 A G 8 6 1_555 A G 8 A G 8 6 8_675 A HOH 15 D HOH 6 8_675 A HOH 15 D HOH 6 1_555 A HOH 16 D HOH 6 8_675 A HOH 16 D HOH 6 1_555 178 P 61 2 2