Phosphoryl transfer only occurs on closing of the open lid.  This causes an exclusion of water molecules that brings the substrates in proximity to each other, lowering the energy barrier for the nucleophilic attack by the α-phosphoryl of AMP on the γ-phosphoryl group of ATP resulting in formation of ADP by transfer of the γ-phosphoryl group to AMP.  In the crystal structure of the ADK enzyme from E. coli with inhibitor Ap5A, the Arg88 residue binds the Ap5A at the α-phosphate group.  It has been shown that the mutation R88G results in 99% loss of catalytic activity of this enzyme, suggesting that this residue is intimately involved in the phosphoryl transfer.  Another highly conserved residue is Arg119, which lies in the adenosine binding region of the ADK, and acts to sandwich the adenine in the active site.  It has been suggested that the promiscuity of these enzymes in accepting other NTPs is due to this relatively inconsequential interactions of the base in the ATP binding pocket.  A network of positive, conserved residues (Lys13, Arg123, Arg156, and Arg167 in ADK from E. coli') stabilize the buildup of negative charge on phosphoryl group during the transfer.  Two distal aspartate residues bind to the arginine network, causing the enzyme to fold and reduces its flexibility.  A magnesium cofactor is also required, essential for increasing the electrophilicity of the phosphate on AMP, though this magnesium ion is only held in the active pocket by electrostatic interactions and dissociates easily.