Computational modeling of the dizinc–ferroxidase complex of human H ferritin: direct comparison of the density functional theory calculated and experimental structures

Abstract

Density functional theory optimizations of structures of dizinc(II) complexes with a six-residue model of the ferroxidase center of human H ferritin have been performed and the results compared with the crystallographically determined structure of the complex as presented in Protein Data Bank file 2CEI. The model employs the full structures of Glu27, Glu62, His65, Glu107, Gln141, and Ala144, and the structural effect of Tyr34 is also examined. The mean absolute deviation from experiment of atomic positions in the best calculated structures is less than 0.3 A. The experimental structure is reproduced well enough to determine the coordination environment of the metal ions. Each zinc(II) center is pentacoordinate with a single water ligand, and the two centers are bridged by a hydroxide ion. Ala144 interacts weakly and repulsively with the rest of the complex. Tyr34 displays a weak attraction through a hydrogen bond to Glu107 that affects the orientation of that group.