Statistical analysis of structural characteristics of protein Ca2+-binding sites

Abstract

To better understand the biological significance of Ca(2+), we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca(2+)-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 +/- 2 vs. 7 +/- 1), fewer protein ligands (4 +/- 2 vs. 6 +/- 1), and more water ligands (2 +/- 2 vs. 1 +/- 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H(2)O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H(2)O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 +/- 1 vs. 3 +/- 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix-loop-helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca-O-C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca(2+)-binding proteins.

Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum

“…An earlier sequence alignment of CBD molecules showed that Asp927 in s3b is replaced by Ser896 in s3 (11). However, serine is rarely found to chelate with Ca 2ϩ (33). The crystal structure of s3 revealed that Asp897 is found in place to chelate with Ca 2ϩ atoms and Ser896 is pointed away from the ions.…”

“…These values vary from the few other available protein structures with square antiprismatic bound ions (see Table S4 in the supplemental material). Square antiprismatic coordination is relatively uncommon among macromolecules (33), and few are currently found in the Protein Data Bank. Ding et al described a Zn 2ϩ -bound RNase T 1 , at 1.8-Å resolution, in which six water molecules and a sole aspartate coordinate zinc (36).…”

Ca2+-binding Motif of βγ-Crystallins

“…The EF-hand loop between the E and the F helices coordinates Ca 2ϩ ion, usually with coordination numbers of 7 or 8 (6,(62)(63)(64). Non-EF-hand proteins utilize fewer protein ligands for coordinating Ca 2ϩ (65). Unlike ␤␥-crystallins in which the ion is exposed to the solvent with 1-4 water molecules in direct coordination with Ca 2ϩ , the EF-hand bound Ca 2ϩ is exposed to a single water molecule (Table 2).…”

Metals in proteins: cluster analysis studies

“…Kirberger et al [6] carried out a statistical analysis of calcium-binding proteins, identifying the main characteristics of the calcium binding sites, different coordination number and coordination distances.…”