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1. Cluster information

Table1. RMSD between presentative RNA and other RNA in a cluster

Sequence identity cut-off Representative Class members and RMSD(Å) to representative RNA
0.95 3FO4 3GER(0.13), 2XNZ(0.16), 3GOT(0.18), 2XO1(0.20), 3FO6(0.20), 2EET(0.20), 2G9C(0.22), 4FEJ(0.23), 3GOG(0.24), 4FE5(0.24), 4FEO(0.25), 2B57(0.25), 3GES(0.26), 4FEL(0.26), 2EEU(0.27), 2EEW(0.28), 2EES(0.31), 2XO0(0.32), 3GAO(0.33), 2EEV(0.36), 2XNW(0.37), 3G4M(0.41), 5C7U(0.82)

2. Pocket information

Table2. Pocket of 3FO4

General information
PDB_ID PubMed Nts Re(Å) [1] Class Organism Method Description
3FO4 19523903 68 1.9 riboswitch N/A X-ray Diffraction Crystal structure of guanine riboswitch C74U mutant bound to 6-chloroguanine
RNA-Ligand interaction information
Ligand Site [2] Sequence [3] H-bond interaction [4] Non-bonded Contact [5]
6GU 21-22, 47, 51-52, 73-75 AU, U, UA, AUU amino, N amino purine
ACT 32-33, 38-39, 66-67 GA, GC, AU ether bond, oxygen ion acetate
NCO 21-24, 26-27, 30-32, 37-39, 41-42, 45-47, 50-51, 53-58, 65-69, 71-73 AUAA, CG, UGG, GGC, CG, AGU, CU, CCGGGC, AAUGU, CGA amino amino
Pocket information
P_ID [6] V (Å3) [7] A (Å2) [8] Si [9] R (Å) [10] Rc (Å) [11] Shape (rpd1, rpd2) [12] Secondary structural elements [13]
3FO4_1 300 261 0.56 3.44 (-43.3, -32.7, -29.3) rod-like (0.33, 0.89) internal loop, multibranched loop
3FO4_2 686 417 0.51 4.93 (-43.1, -31.8, -29.1) sphere-like (0.65, 0.86) internal loop
3FO4_3 858 530 0.45 4.85 (-43.1, -32.6, -25.2) sphere-like (0.54, 0.91) internal loop, multibranched loop

3. Sequence Preview

Ligand(6GU) binding sites GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCA
Ligand(ACT) binding sites GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCA
Ligand(NCO) binding sites GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCA
Transcriptional regulatory motif GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCA
Functional RNA sequences (ISE) GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCA