Figure 4. Superimposition of the known APOBEC structures around the Zn active site.

A3A (green, PDB: 2M65), A3C (red, PDB: 3VOW), A3FCD2 (purple, PDB: 4J4J and 4IOU), A3GCD2 (yellow, PDB: 3IQS and 3IR2), A3BCD2 (pink, modelled structure). (A) A view of the superimposition of loop-1, loop-3 and loop-7 around the Zn active site. The conserved Tyr¹³⁰ in A3A can adopt a conformation different from its equivalent tyrosine residues in other APOBECs (in sticks), which is probably permitted by the different loop-1 conformation in A3A (green). The loop-1 conformations in other APOBECs should prevent their tyrosine residues to assume the conformation of Tyr¹³⁰ in A3A. (B) A closer view of the active site for the non-A3A APOBECs, showing the conserved tyrosine residue as a partial ‘lid’ on the edge of the mC at the active site pocket. (C) A closer view of the active site for A3A and the modelled A3BCD2, showing the different conformation for loop-1, and for the conserved tyrosine residue (Tyr¹³⁰ for A3A, Tyr³¹³ for A3BCD2) next to the mC at the active site. Tyr³¹³ of A3BCD2 is closer to the mC, causing some clashes with the methyl group.