3NXA

X-ray structure of the apo form of human S100A16

Summary for 3NXA

• Entry DOI: 10.2210/pdb3nxa/pdb
• Descriptor: Protein S100-A16 (2 entities in total)
• Functional Keywords: s100 family, calcium binding protein, apo, s100a16, ef-hand proteins, calcium binding proteins, s100 proteins, protein dynamics, metal binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleolus: Q96FQ6
• Total number of polymer chains: 4
• Total formula weight: 46048.14

Authors

Calderone, V. (deposition date: 2010-07-13, release date: 2010-11-03, Last modification date: 2024-04-03)

Primary citation

Babini, E.,Bertini, I.,Borsi, V.,Calderone, V.,Hu, X.,Luchinat, C.,Parigi, G.
Structural characterization of human S100A16, a low-affinity calcium binder.
J.Biol.Inorg.Chem., 16:243-256, 2011

PubMed Abstract: The homodimeric structure of human S100A16 in the apo state has been obtained both in the solid state and in solution, resulting in good agreement between the structures with the exception of two loop regions. The homodimeric solution structure of human S100A16 was also calculated in the calcium(II)-bound form. Differently from most S100 proteins, the conformational rearrangement upon calcium binding is minor. This characteristic is likely to be related to the weak binding affinity of the protein for the calcium(II) ions. In turn, this is ascribed to the lack of the glutamate residue at the end of the S100-specific N-domain binding site, which in most S100 proteins provides two important side chain oxygen atoms as calcium(II) ligands. Furthermore, the presence of hydrophobic interactions stronger than for other S100 proteins, present in the closed form of S100A16 between the third and fourth helices, likely make the closed structure of the second EF-hand particularly stable, so even upon calcium(II) binding such a conformation is not disrupted.

PubMed: 21046186
DOI: 10.1007/s00775-010-0721-3

Experimental method

X-RAY DIFFRACTION (2.1 Å)