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The N-terminal zinc binding site (consisting of C4, C22, H28 and C32) and the C-terminal zinc binding site (C157, C160, H198 and C201) of DraIII (Fig. 3C) deviate from the CXXC/CXXC configuration.
The exclusion lists are composed of the most common solvent molecules and other non-ligand hetero compounds often found in PDB files, as well as some less common solvents and molecules that were found to have very simple binding sites (e.g., a binding site consisting of just 1 2 residues).
The 1H NMR shift induced by adding a potassium ion (counter anion: SCN−) in (CD3 2CO suggested that the cation moiety of the chiral guests was located at the binding site consisting of the –O C C O– units and the ring-oxygens of the saccharide moieties.
In addition to the +3 binding site, this cube contained the pY residue binding site consisting mainly of R609 and K591 [23] and a hydrophobic binding site consisting of 5 residues—W623, Q635, V637, Y640 and Y657.
Although these molecules present in the crystallization medium are probably not the functional CA3427 ligands, we used them to identify the putative binding site consisting of the residues less than 5 Å apart from the co-crystallized molecules (Fig. 2A, Tables 2 and 3).
Comparison of RNA sequences bound by L22 has allowed for the establishment of a consensus L22 binding site consisting of a stem-loop structure with a G-C base pair at the base of the loop and a 5 7 nucleotide loop with a U residue at the 3' end [25].
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The first binding site consists of a positively charged pocket created by a cluster of unpaired backbone amides at the N-terminus of the P-helix and the side chain of Arg192 [8].
A dimer binding site consists of two binding sites in opposite orientation.
Additionally, most of the protein surface, including the binding site, consists of hydrophilic residues, indicating that hydrophobic interactions are unlikely to be energetically favorable.
The binding site consists of a pair of palindromic sequences that are located between positions 59 (there is one nucleotide overlap with one of the TAS containing repeats) and 91.
The new binding site consists of seven residues: Val415, Leu478, and Phe482 form the bottom of the pocket whilst Tyr417, Tyr421, Tyr481, and Tyr485 form the sides of the pocket.
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