The structure of HBV-RT4/DNA-RNA/dATP and the active site Mg
network in comparison with that from the HIV-RT/DNA-RNA/dATP crystal structure.
a The HBV-RT4/DNA-RNA/dATP structure model is shown in cartoon with each domain in different color (N-terminal: orange; fingers: purple; thumb: red; palm: green; dsDNA: silver). The substrate dATP and the residues involved in direct interaction with it are in stick and ball representation. The corresponding part from the template HIV-RT/DNA-RNA/dATP (PDB code: 4PQU; chain A, residue 1 to residue 320) is shown in gray surface representation, structurally aligned to the HBV-RT4/DNA-RNA/dATP model; b The active site configuration of the HBV-RT4/DNA-RNA/dATP model. The non-bonded interactions are explicitly represented as black dashed lines as the two H-bonds (Hb1 and Hb2), and the ionic bonds formed between the Mg2+ ions (in red ball representation without labeling) and the chelating oxygen atoms. The water oxygen atoms participating in the chelation are labeled as from W1 to W4; c The active site configuration of the HIV-RT/DNA-RNA/dATP crystal structure, only one water molecule (labeled as W) is involved in the Mg2+ network. The D110 has no counterpart in the HBV-RT model. The hydrogen atoms are hided in the representations for clearance