Fig. 4: Cryo-EM structure of the intermediate state 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 state R-2 (blue) and state T8sec (gray) 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 Coordination of Mg2+ at sites B and A* in the active site of RT by the two different dATP conformers (dATP-g and dATP-i) that are observed in the intermediate state of the RT-T/P-dATP complex. The map around the Mg2+ ions at sites B and A* is shown as a grey mesh and is contoured at 8.5σ (Map sharpened at B-factor −60 Å2). Coordination distances (in Å) are indicated next to dashed lines. c Density around dATP-g in state R-2 of the RT-T/P-dATP complex (blue mesh, left panel) and around dATP-g and dATP-i in state T8sec of the RT-T/P-dATP complex (gray mesh, middle panel). Overlay of the R-2 and T8sec state maps contoured at 13σ and 8.5σ, respectively, is shown in the right panel. Maps sharpened at B-factors −60 Å2 and −100 Å2 for states R-2 and T8sec, respectively.
