Bond valence sum analysis of metal-ligand bond lengths in metalloenzymes and model complexes. 2. Refined distances and other enzymes

Abstract

The bond valence sum (BVS) method is further applied to metalloenzyme active sites. When a particular coordination model is assumed, the BVS method allows for oxidation states of metal ions in metalloproteins to be determined from metal-ligand bond distances measured using extended X-ray absorption fine structure (EXAFS) analysis. Thus, the BVS can be used to determine the compatibility between a given coordination model and a particular oxidation state. A new procedure for calculating ro values on which BVS's are based is presented. This procedure allows for calculation of ro values on heteroleptic complexes and was used to determine a new set of ro distances using complexes that more closely model the active sites of interest. In particular, the new distances allow for calculations involving vanadium, molybdenum, and nickel. New calculations using EXAFS data on CO dehydrogenase, NiFe hydrogenase, manganese catalase, sulfite oxidase, MoFe nitrogenase, and VFe nitrogenase are presented. The interplay between oxidation state and coordination geometry can be quantitatively assessed using the BVS method.Determining the structures of metal ion binding sites is critical in understanding the mechanism of action of metalloenzymes. Extended X-ray absorption fine structure (EXAFS) provides a means for determining the metal-ligand bond lengths for a given metal ion in a protein. l-3 X-ray absorption near-edge spectroscopy (XANES) can also provide some information on the oxidation stateof the metal Recently, we reportedon theapplication of the bond valence sum (BVS) method to the analysis of metalligand bond lengths determined by EXAFS in metalloenzymes.5 In particular, when a structural model is deduced from EXAFS and other spectroscopic methods, the BVS can be used to confirm the compatibility of that model with a given oxidation state of the metal ion. Conversely, if the oxidation state is known, BVS can be used to test structural models. We have demonstrated that this method is effective in a variety of mononuclear and polynuclear metal ions in a wide range of oxidation states for a series of metalloenzymes.Bond valences (s) are calculated according to eq 1, where B *Abstract published in Advance ACS Abstracts, August 15, 1993. Koningsberger, D. C., Prins, R., Eds.; X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS, and XANES; John Wiley and Sons: New York, 1988. Stavrapoulos, P.; Muetterties, M. C.; Carrib, M.; Holm, R. H. J. Am. Chem. SOC. 1991, 113, 8485. Bastian, N . R.; Diekert, G.; Niederhoffer, E. C.; Teo, B.-K.; Walsh, C. T.; Orme-Johnson, W. H. J. Am. Chem. SOC. 1988, 110, 5581. Tan, G. 0.; Ensign, S. A.; Ciurli, S.; Scott, M. J.; Hedman, B.; Holm, R. H.; Ludden, P. W.; Korzun, 2. R.; Stephens, P. J.; Hodgson, K. 0. Proc. Narl. Acad. Sci. U.S.A. 1992, 89, 4427. Baidya, N.; Olmstead, M.; Mascharak, P. K. Inorg. Chem. 1991, 30, 929. Baidya, N.; Olmstead, M. M.; Mascharak, P. K. J . Am. Chem. SOC. 1992, 114, 9666. The Bioinorganic Chemistry ofNickel; Lancaster, L. R., Jr., Ed.; VCH Publishers...

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

“…Table 1 summarizes the optimized R 0 parameters for iron(II) and iron(III), estimated using both homoleptic and heteroleptic metal-binding sites within the first coordination sphere, and compares them with several previous studies (Brese & O’Keeffe, 1991; Liu & Thorp, 1993; Kanowitz & Palenik, 1998). While most of the R 0 parameters derived here for iron agree within ±0.1 Å with previously reported values, we found that the Fe—N R 0 parameters reported previously appear to agree well only with the corresponding high-spin (HS) species.…”

“…The few reports including heteroleptic sites do employ optimization techniques, nonetheless they are based on a small selection of manually chosen structures (Liu & Thorp, 1993). The method we adopted allows the simultaneous refinement of multiple R 0 parameters based on a large set of varied structures, including heteroleptic binding sites.…”

“…Iron has been established to be in the low-spin ferric form [LS iron(III)] in the oxidized form of hemoglobin (oxyhemoglobin) by X-ray photoelectron spectroscopy and X-ray absorption near-edge structure (XANES) studies at the Fe K edge (Pin et al , 1982; Bianconi et al , 1985). However, applying the literature reference R 0 parameter for iron(III) (1.815–1.86 Å ; Liu & Thorp, 1993; Brese & O’Keeffe, 1991) to the metal geometry observed in protein crystal structures of oxyhemoglobin results in a BVS of 3.90–4.41 (Table 3). In contrast, using the R 0 parameter in the low-spin state for Fe III —N derived here (1.70 Å) leads to a BVS of 2.86 [ i.e.…”

“…Our numerical procedure is conceptually similar to the approach adopted in a previous study (Liu & Thorp, 1993), where a damped least-squares method was used to fit three R 0 parameters simultaneously to a number of similar binding sites. In our case, the data set for each iron type is much more varied, with binding sites that contain different numbers and types of ligands.…”

Structural and Kinetic Characterization of an Archaeal β-Class Carbonic Anhydrase

“…fits 3 to 6, Table 2). Bond valence sum (BVS) analysis is an empirical method for correlating the sum of the strength of the metalligand bonds, as measured by the bond length, to the oxidation state of the metal (40,57). BVS confirms that the Zn site has a coordination number of 4 (the BVS value should be approximately equal to the oxidation state of the metal, i.e., 2).…”