Fig. 4: Differences between open and closed MDDEF bound with ligands.
From: Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase
a Superposition of open (MDDEF-MVAPP-AMPPCP-Mg2+, magenta) and closed (MDDEF-MVAPP-ADPBeF3-Mg2+, blue) conformations of MDDEF. A gray surface represents the envelope of the apo-MDDEF. The greatest distance between the β10-α4 loops is 9.4 Å (left white arrow) determined by measuring the distance between K187 Cα carbons in the open and closed structures. The greatest distance between the phosphate-binding loops is 10.6 Å (right white arrow) determined by measuring the distance between A101 Cα carbons in open and closed structures. b Distances of Cα atoms between open and closed conformations. The structural models of open and closed MDDEF were Cα-aligned to apo-MDDEF with r.m.s. deviation values of 0.35 and 0.40 Å, respectively. The distances between corresponding Cα atoms in both structures is plotted as a function of residue number. The regions of helix α1 (α1, 66–81), the phosphate-binding loop (97–104) and the β10-α4 loop (183–190) are highlighted in cyan, gray, and pink, respectively. Source data are provided as a Source Data file.
