Computational protocol: NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

Similar protocols

Protocol publication

[…] A subset of three residues (G8, A12 and G13) was extracted from the X-ray structure of the hairpin ribozyme determined with vanadate [pdb entry code 1M5O; ()]. Residues A12 and G13 in this subset were modified using Coot () to match the base type of their equivalents in the VS ribozyme (G620 and A621). The bases of residues G8 and G12 of this modified model were then aligned on the model of the active conformation of SLI of the VS ribozyme (). A hybrid SLI model was generated in which residues G620, A621, G638 of SLI were replaced by their equivalents in the modified hairpin model. Using Coot, residue A756 of the SLVI structure was moved by hand to allow stacking with A621. Finally, the model of the SLI/SLVI complex was energy minimized with Amber (). […]

Pipeline specifications

Software tools Coot, AMBER
Application Protein structure analysis
Chemicals Magnesium