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. 2006 Dec 6;35(1):87–99. doi: 10.1093/nar/gkl1010

Figure 4.

Figure 4

The ATP-binding site. (a) Packing of the Clp1 NtD against the central domain. The central domain (green) is shown in a surface representation with the bound ATP shown in sticks. The NtD is shown as a ribbon representation (red). (b) Nucleotide binding loops. ATP is shown in stick representation with the associated magnesium ion shown as a blue sphere. The central domain of Clp1 is shown as a green ribbon whilst the P-loop, Switch I, Switch II and base-binding loops are shown in stick representation in light red, yellow, blue and grey, respectively. (c) A schematic diagram displaying the protein-ligand contacts observed at the Clp1-ATP-binding site. The ATP is shown in stick representation and Clp1 residues are represented by rectangles. The residues in Clp1 that make contacts with the ATP from the central domain are highlighted in green and those from the NtD are highlighted in red. Hydrogen bonding interactions were the donor and acceptor inter-atomic distance is less than 3.3 Å are indicated with black dashed lines.