Volume 90, Issue 6, Pages (March 2006)

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Volume 90, Issue 6, Pages 2109-2119 (March 2006) Dehydration of Ribonucleotides Catalyzed by Ribonucleotide Reductase: The Role of the Enzyme Nuno M.F.S.A. Cerqueira, Pedro Alexandrino Fernandes, Leif A. Eriksson, Maria João Ramos Biophysical Journal Volume 90, Issue 6, Pages 2109-2119 (March 2006) DOI: 10.1529/biophysj.104.054627 Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 1 (a) The E-S model obtained from the x-ray structure of the active site for R12 dimer of RNR with the bound substrate. The reactive region is colored red, the active site region is colored yellow and the surrounding region is colored blue. The blue background is indicative of a 10Å layer of water molecules. (b) The division of the system in three theoretical levels for geometry optimizations. The high level layer is colored by element type, the medium level layer is colored green and the low level layer is colored blue. (c) The gas phase model. As geometry is optimized with the ribose ring and the active site residues disconnected from the protein, they can adopt the most favorable positions to the reaction without steric strain. Biophysical Journal 2006 90, 2109-2119DOI: (10.1529/biophysj.104.054627) Copyright © 2006 The Biophysical Society Terms and Conditions

Figure 2 Reactants (top), transition state (center), and products (bottom) for the reaction studied here. The reactive region is depicted in ball-and-stick representation, the active site region is depicted in stick representation, and the surrounding region is depicted in wire model and ribbons. Relevant atomic charges and spin densities are included in atomic units. Biophysical Journal 2006 90, 2109-2119DOI: (10.1529/biophysj.104.054627) Copyright © 2006 The Biophysical Society Terms and Conditions

Scheme 1 Catalytic mechanism for class I ribonucleotide reductase. Biophysical Journal 2006 90, 2109-2119DOI: (10.1529/biophysj.104.054627) Copyright © 2006 The Biophysical Society Terms and Conditions

Scheme 2 Chemical structures of the stationary points along the reaction pathway. Biophysical Journal 2006 90, 2109-2119DOI: (10.1529/biophysj.104.054627) Copyright © 2006 The Biophysical Society Terms and Conditions