RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule PDB_01236 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01236 Molecule name [?]: STRUCTURE OF THE M-BOX RIBOSWITCH APTAMER DOMAIN Source [?]: RCSB Protein Data Bank Source ID [?]: 2QBZ Reference [?]: C.E.DANN III,C.A.WAKEMAN,C.L.SIELING,S.C.BAKER, I.IRNOV,W.C.WINKLER. STRUCTURE AND MECHANISM OF A METAL-SENSING REGULATORY RNA. CELL(CAMBRIDGE,MASS.) V. 130 878 2007 ASTM CELLB5 US ISSN 0092-8674 Type [?]: Synthetic RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SYNTHETIC Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.60 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 153 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 45 Number of paired bases [?]: 108

Click on any header below for additional features.

Stem features Number of stems [?]: 9 Number of base pairs in stems [?]: 54 Maximum length of a stem [?]: 10 Average length of a stem [?]: 6 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.2 Average estimated free energy [?]: -9.08 Minimum estimated free energy [?]: -15.4

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 7 Average number of free bases in hairpin loops [?]: 5.5 Minimum number of free bases in hairpin loop [?]: 4

Bulge loop features Number of bulge loops [?]: 3 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 1 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 3 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.83 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 5 Average number of free bases in multi-loops: 3.33 Minimum number of free bases in multi-loop: 1 Maximum multi-loop absolute asymmetry: 4 Average multi-loop absolute asymmetry: 2.67 Minimum multi-loop absolute asymmetry: 1 Maximum multi-loop relative asymmetry: 5 Average multi-loop relative asymmetry: 1.92 Minimum multi-loop relative asymmetry: 0.2 Maximum number of branches in multi-loops: 3 Average number of branches in multi-loops: 3 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 7 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 1

Pseudoknot features