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Figure 2
Overall structure of MtMetRS–Met-AMP and the architecture of the active site. (a) Ribbon model of MtMetRS. The individual domains are differently coloured, with the catalytic domain in cyan, the CP domain in magenta, the KMSKS domain in green and the anticodon domain in blue. The docking of the intermediate product Met-AMP in the active site is shown as a stick model in orange. The π-helix α13 connecting the KMSKS domain and the anticodon domain is shown in grey. Secondary-structure features of the structure are labelled. (b) A magnified view of the MtMetRS structure showing the details of the active site. Residues making up the substrate-binding pockets are shown as stick models and labelled. The methionine pocket is highlighted in yellow and the AMP pocket is highlighted in blue. Met-AMP is shown as a stick model and coloured orange. Ordered waters mediating the interaction between MtMetRS and Met-AMP are shown as red spheres. Hydrogen bonds between MtMetRS and Met-AMP are indicated by dashed lines. (c) A magnified view of the structure of the active site with a superimposed polder OMIT map for Met-AMP. The map is contoured at ±3σ with green and red densities. (d) A two-dimensional diagram of the active site of MtMetRS occupied by Met-AMP. The colour scheme is the same as that in (b). Hydrogen bonds are shown as dashed lines and the bond lengths are indicated.

IUCrJ
Volume 5| Part 4| July 2018| Pages 478-490
ISSN: 2052-2525
https://doi.org/10.1107/S2052252518008217