Fig 5. Overall monomer structure of H. pylori Csd1_125–312.

(A) Schematic representation of secondary structures of Csd1_125–312 and topology diagram of Csd1_125–312. Secondary structures have been defined by the STRIDE program [42]. α-Helices, β-strands, 3₁₀-helices, and loops are shown as cylinders (colored in light pink), arrows (blue-green), flat cylinders (yellow), and solid lines (grey), respectively. Loop 1 (β1-β2 loop; cyan), Loop 2 (β4-β5 loop; red), Loop 3 (β8-β9 loop; skyblue), and Loop 4 (β9-β10 loop; purple) form the substrate-binding groove of the Csd1 LytM domain. Dotted lines indicate disordered regions. (B) Ribbon diagram of Csd1_125–312 monomer structure (chain C of Csd1-Csd2 dimer I), colored as in the topology diagram in Fig 5A. Close-up views on the right represent the surface representation of the substrate-binding groove formed by four loops of the LytM domain (top) and canonical Zn²⁺-coordination with three protein ligands and two water molecules (bottom). Dark grey and red spheres represent a Zn²⁺ ion and water molecules, respectively. Side chains of the Zn²⁺-coordinating residues (His169, Asp173, and His252) are shown in stick models. Black dotted lines denote penta-coordination of the Zn²⁺ ion. The electron density for the Zn²⁺-bound active site in 2mF_o − DF_c map (grey colored mesh) are shown at the 1.0 σ level.