Fig. 3
From: Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA
Structure of CTD2* in complex with ssDNA. a The asymmetric unit contains one protein (yellow) and one ssDNA (blue) molecule. A 2Fo–Fc electron density map contoured at 1σ is shown in cyan around the ssDNA. Zn2+ ion is colored purple. N and C indicate the N- and C-terminal ends of the protein, respectively. b An enlarged view shows interactions between the 5ʹ-TCCCA target sequence and the protein. Protein is colored yellow, 5ʹ-TCCCA is blue, and amino acid sidechains interacting with DNA are shown as sticks. c–f Enlarged views show interactions between T−3, C−2, C−1, C0, or A+1 and protein. C, N, and O atoms are colored yellow, blue, and red, respectively, for amino acid residues of the protein. Atoms in nucleotides are colored blue, navy blue, red, and orange for C, N, O, and P, respectively. Water molecules are shown as red spheres, and Zn2+ is shown as a purple sphere. Dotted lines indicate hydrogen bonds. In (c), the double arrow-headed line points to the neighboring backbone phosphorous atoms of C−1 and C−2. In (d), sidechains of F289 and Q318K are not shown. g Summary of the interactions between CTD2* and nucleotides in the 5ʹ-TCCCA target sequence
