Folding of the Trigger loop (TL) restructures an amino acid content of the active centre. The active centre of the Thermus thermophilus RNAP elongation complex with bound substrate is shown (there is complete conservation of sequence in TL and active site residues between T. thermophilus and T. aquaticus (used in this study) RNAPs). Unfolded TL (magenta) and folded TL (green; PDB 2PPB and 2O5J, respectively ) in the active centre are shown as ribbons. The amino acids of the TL that face the nucleotide triphosphate (NTP; orange) bound in the i+1 site upon TL folding, and that were analysed in our study, are shown as coloured sticks (Q1235 grey, M1238 yellow, R1239 blue, F1241 green, H1242 cyan, T1243 red) in both folded and unfolded states of TL. The NTP in i+1 site is orange, RNA is red and template DNA in grey. Mg2+ ions of the active centre are shown as spheres.