6egm | pdb_00006egm

Crystal Structure of a de novo Three-stranded Coiled Coil Peptide Containing D-Leu in a d-site Position of a Tris-thiolate Binding Site

spinqualitylabelsall models 6egm, resolution 1.84Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6egm is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.84Å Ligands: DLE, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed A challenging objective of De Novo metalloprotein design is to control of the second coordination sphere of an active site to fine tune metal properties.The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question.Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as Hg(II), Pb(II) and As(III) result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies showed Cd(II) formed 3-, 4- or 5-coordinate Cd(II)S(3)(OH(2))x (where x=0-2) when the second coordination sphere was perturbed.Unfortunately, there has been little crystallographic examination of these proteins to explain the observations.Herein,we compare the high-resolution x-ray structures of apo- and mercurated proteins to explain the modifications that lead to metal coordination number and geometry variation.It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating Cd(II)S(3)(OH(2)).Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal binding plane that displaces water, forming Cd(II)S(3).D-Leu, above the Cys site, reorients the side chain towards the Cys layer diminishing the space for water accommodation yielding Cd(II)S(3), while D-Leu below opens more space, allowing for equal Cd(II)S(3)(OH(2)) and Cd(II)S(3)(OH(2))(2).These studies provide insights on how to control desired metal geometries in metalloproteins using coded and non-coded amino acids. How Second Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation.,Pecoraro VL, Ruckthong L, Stuckey JA Chemistry. 2019 Mar 12. doi: 10.1002/chem.201806040. PMID:30861211 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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