Fig. 3: Cryo-EM structure of reactant state R-2 of the RT-T/P-dATP complex.
From: Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription
a Overlay of the active sites of states R-1 (yellow) and R-2 (blue) of the RT-T/P-dATP complex. The protein backbone is shown in the cartoon representation; selected key residues are shown in the ball-and-stick representation. b Two Mg2+ sites, B and A*, are observed at state R-2. The map displayed as blue mesh (sharpening at B-factor = −80 Å2 and contoured at 11σ). Coordination distances (in Å) are indicated next to dashed lines. c Unsharpened density map for state R-2, contoured at 10σ (blue mesh) showing density around site A* Mg2+ (yellow sphere); and d unsharpened density map, contoured at 10σ (teal mesh) for RT-T/P-dATP in the absence of MgCl2 showing no density at the A* position (dashed circle). A mobile small density was observed at site B (labeled as Me: metal), but its identity could not be determined. e Two views of the surface representation of RT-T/P-dATP in state R-2 colored according to electrostatic potential, from red (−5 kT/e, negatively charged) to blue (+5 kT/e, positively charged), showing Mg2+ A* positioned in a negatively charged pocket. Mg2+ ion site A* is colored as a yellow sphere.
