Keywords

EF-hand, Calcium, Lanthanide, Vector Geometry Mapping, Ca2+, Metal Binding, Coordination Chemistry

Reference

DOI: 10.1007/s007750100214

Abstract

A comprehensive survey of X-ray structures of Ca²⁺ and lanthanide (Ln³⁺)-binding proteins and coordination complexes identifies common structural features in metal-binding sites.

  • 515 Ca²⁺-containing protein structures were considered, with a final data set of 44 proteins and 60 Ca²⁺ sites (323 ligands).
  • 18 lanthanide-containing proteins narrowed to 8 structures and 11 binding sites.
  • Structural features analyzed: coordination number, ligand identity, carboxylate denticity, and secondary structure origins.
  • Three Ca²⁺ site types were classified:
    1. Class I: Ligands from a continuous short sequence.
    2. Class II: One ligand from a remote sequence region.
    3. Class III: Ligands scattered across distant sequence positions.
  • EF-hand motifs are under-represented relative to biological prevalence but chemically well-represented in the dataset.

Notes

1. General Features of Ca²⁺ and Lanthanide Binding

  • Turn/loop regions primarily provide Ca²⁺ ligands; helix and sheet regions are better for bidentate carboxylate ligation.
  • Average Ca²⁺ coordination number: 6.0; 7 in EF-hand motifs.
  • Lanthanide coordination numbers:
    • Intrinsic protein sites: ~7.2.
    • Adventitious sites: ~4.4 (possibly due to missing water molecules in structures).
  • Ligand types: Mostly oxygen donors, favoring hard acid/base interactions typical for Ca²⁺ and Ln³⁺.

2. Ca²⁺ Binding Site Classification

  • Class I: Continuous amino acid sequence regions form compact binding motifs.
  • Class II: Mix of local and distant residues; one ligand is remote.
  • Class III: Ligands scattered across protein sequence, forming a more composite site.
  • EF-hand motifs, despite biological abundance, are underrepresented in crystal structures analyzed (possible selection bias).

3. Coordination Chemistry and Structural Observations

  • Coordination number variability:
    • Ca²⁺: Prefers 6–7 coordination, often pentagonal bipyramidal geometry.
    • Lanthanide ions: Typically higher coordination (up to 8–9), but observed lower coordination (4.4) may be artifact (missing waters).
  • Ligand denticity: Carboxylate residues (Asp/Glu) may bind monodentate or bidentate, depending on geometry.
  • Secondary structure contributions: Loops dominate, but helices and sheets contribute when bidentate ligands are involved.

4. Comparison of Ca²⁺ and Lanthanide Binding

  • Lanthanide-binding sites often show reduced hydrogen bonding among ligating residues, possibly as an adjustment for the higher charge (+3) of lanthanides compared to Ca²⁺ (+2).
  • Despite charge difference, overall topology of binding sites is similar, supporting functional analogy between lanthanides and calcium in some biochemical contexts (e.g., as probes).
  • Structural differences do not always predict affinity, suggesting that electrostatics and induced conformational changes play major roles in modulating metal-binding strength.

5. Functional and Experimental Implications

  • Vector geometry mapping could be employed to better understand spatial arrangement of ligands.
  • Long-range electrostatic effects and protein dynamics significantly influence metal binding but are hard to capture from static X-ray structures.
  • Lanthanides as calcium mimics: Understanding differences/similarities in binding geometry helps in designing lanthanide-based probes for calcium-binding proteins.
  • Structural determinants of metal selectivity between Ca²⁺ and Ln³⁺ involve geometry, ligand flexibility, and charge distribution.

6. RD’s Reflections

  • This paper provides a rich structural landscape of Ca²⁺ and lanthanide sites — useful reference for EF-hand-related work.
  • RD finds the classification into three classes of Ca²⁺ sites very useful for dissecting complex metal-binding motifs.
  • The comparison between EF-hand and non-canonical sites helps contextualize RD’s own observations of diverse Ca²⁺ binding modes.
  • Noticing hydrogen bond adjustments in lanthanide sites sparks ideas for engineering altered Ca²⁺ affinity or specificity by tuning charge and H-bond networks.
  • Possible to combine this knowledge with EFβ-scaffold concepts to interpret how flexibility and rigidity balance metal binding.

Take-home Messages

  • Ca²⁺ binding sites show diversity in sequence and structure, yet often share loop-based ligation and coordination numbers around 6–7.
  • Three structural classes (Class I, II, III) explain different modes of metal coordination within protein scaffolds.
  • Lanthanide ions bind similarly to Ca²⁺ but often with fewer hydrogen bonds, reflecting charge adaptation.
  • EF-hands, though biologically abundant, are structurally underrepresented in the dataset but chemically typical for Ca²⁺ binding.
  • Understanding metal-binding site diversity aids in protein design, metal ion selectivity engineering, and the use of lanthanides as Ca²⁺ probes.