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

General features for molecule PDB_01125 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01125 Molecule name [?]: GAAA TETRALOOP RECEPTOR COMPLEX WITH ASSOCIATED MANGANESE IONS. Source [?]: RCSB Protein Data Bank Source ID [?]: 2I7Z Reference [?]: J.H.DAVIS,T.R.FOSTER,M.TONELLI,S.E.BUTCHER. ROLE OF METAL IONS IN THE TETRALOOP-RECEPTOR COMPLEX AS ANALYZED BY NMR.. RNA V. 13 76 2007 ASTM RNARFU UK ISSN 1355-8382 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 [?]: NMR; ran through RNAview Number of molecules [?]: 2 Length [?]: 86 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00924, PDB_01124 Number of domains [?]: 2 Number of unpaired bases [?]: 14 Number of paired bases [?]: 72

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 36 Maximum length of a stem [?]: 13 Average length of a stem [?]: 9 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -9.2 Average estimated free energy [?]: -15.35 Minimum estimated free energy [?]: -21.5

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

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 2.5 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features