PDBsum entry 1ig5

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protein metals links
Metal binding protein PDB id
Protein chain
75 a.a. *
Waters ×50
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Bovine calbindin d9k binding mg2+
Structure: Vitamin d-dependent calcium-binding protein, intestinal. Chain: a. Synonym: calbindin d9k. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: synthetic gene. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.196     R-free:   0.285
Authors: E.M.Andersson,L.A.Svensson
Key ref: M.Andersson et al. (1997). Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k. Protein Sci, 6, 1139-1147. PubMed id: 9194174 DOI: 10.1002/pro.5560060602
17-Apr-01     Release date:   25-Apr-01    
Supersedes: 5icb
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02633  (S100G_BOVIN) -  Protein S100-G
79 a.a.
75 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     apical plasma membrane   2 terms 
  Biochemical function     vitamin D binding     3 terms  


DOI no: 10.1002/pro.5560060602 Protein Sci 6:1139-1147 (1997)
PubMed id: 9194174  
Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k.
M.Andersson, A.Malmendal, S.Linse, I.Ivarsson, S.Forsén, L.A.Svensson.
The three-dimensional structures of the magnesium- and manganese-bound forms of calbindin D9k were determined to 1.6 A and 1.9 A resolution, respectively, using X-ray crystallography. These two structures are nearly identical but deviate significantly from both the calcium bound form and the metal ion-free (apo) form. The largest structural differences are seen in the C-terminal EF-hand, and involve changes in both metal ion coordination and helix packing. The N-terminal calcium binding site is not occupied by any metal ion in the magnesium and manganese structures, and shows little structural deviation from the apo and calcium bound forms. 1H-NMR and UV spectroscopic studies at physiological ion concentrations show that the C-terminal site of the protein is significantly populated by magnesium at resting cell calcium levels, and that there is a negative allosteric interaction between magnesium and calcium binding. Calcium binding was found to occur with positive cooperativity at physiological magnesium concentration.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262274 Z.Grabarek (2011).
Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins.
  Biochim Biophys Acta, 1813, 913-921.  
  20054830 H.Huang, H.Ishida, and H.J.Vogel (2010).
The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells.
  Protein Sci, 19, 475-485.
PDB code: 2ksz
20141114 T.Atanasijevic, X.A.Zhang, S.J.Lippard, and A.Jasanoff (2010).
MRI sensing based on the displacement of paramagnetic ions from chelated complexes.
  Inorg Chem, 49, 2589-2591.  
19008222 C.Li, J.Chan, F.Haeseleer, K.Mikoshiba, K.Palczewski, M.Ikura, and J.B.Ames (2009).
Structural Insights into Ca2+-dependent Regulation of Inositol 1,4,5-Trisphosphate Receptors by CaBP1.
  J Biol Chem, 284, 2472-2481.  
19005224 T.Jursa, and D.R.Smith (2009).
Ceruloplasmin alters the tissue disposition and neurotoxicity of manganese, but not its loading onto transferrin.
  Toxicol Sci, 107, 182-193.  
18359862 M.C.Bauer, H.Nilsson, E.Thulin, B.Frohm, J.Malm, and S.Linse (2008).
Zn2+ binding to human calbindin D(28k) and the role of histidine residues.
  Protein Sci, 17, 760-767.  
  18690045 M.C.Lin, and D.M.Papazian (2007).
Differences between ion binding to eag and HERG voltage sensors contribute to differential regulation of activation and deactivation gating.
  Channels (Austin), 1, 429-437.  
11867433 M.S.Cates, M.L.Teodoro, and G.N.Phillips (2002).
Molecular mechanisms of calcium and magnesium binding to parvalbumin.
  Biophys J, 82, 1133-1146.  
11948788 W.Yang, H.W.Lee, H.Hellinga, and J.J.Yang (2002).
Structural analysis, identification, and design of calcium-binding sites in proteins.
  Proteins, 47, 344-356.  
11733025 F.Yumoto, M.Nara, H.Kagi, W.Iwasaki, T.Ojima, K.Nishita, K.Nagata, and M.Tanokura (2001).
Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups.
  Eur J Biochem, 268, 6284-6290.  
11316872 M.Håkansson, A.Svensson, J.Fast, and S.Linse (2001).
An extended hydrophobic core induces EF-hand swapping.
  Protein Sci, 10, 927-933.
PDB code: 1ht9
11258955 S.B.Tikunova, D.J.Black, J.D.Johnson, and J.P.Davis (2001).
Modifying Mg2+ binding and exchange with the N-terminal of calmodulin.
  Biochemistry, 40, 3348-3353.  
11056042 A.H.Juffer, and H.J.Vogel (2000).
pK(a) calculations of calbindin D(9k): effects of Ca(2+) binding, protein dielectric constant, and ionic strength.
  Proteins, 41, 554-567.  
10757979 J.L.Enmon, Beer, and M.Overduin (2000).
Solution structure of Eps15's third EH domain reveals coincident Phe-Trp and Asn-Pro-Phe binding sites.
  Biochemistry, 39, 4309-4319.
PDB code: 1c07
11087403 T.Ozawa, M.Fukuda, M.Nara, A.Nakamura, Y.Komine, K.Kohama, and Y.Umezawa (2000).
How can Ca2+ selectively activate recoverin in the presence of Mg2+? Surface plasmon resonance and FT-IR spectroscopic studies.
  Biochemistry, 39, 14495-14503.  
  11055995 W.R.Silverman, C.Y.Tang, A.F.Mock, K.B.Huh, and D.M.Papazian (2000).
Mg(2+) modulates voltage-dependent activation in ether-à-go-go potassium channels by binding between transmembrane segments S2 and S3.
  J Gen Physiol, 116, 663-678.  
  10548066 J.P.Declercq, C.Evrard, V.Lamzin, and J.Parello (1999).
Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core.
  Protein Sci, 8, 2194-2204.
PDB code: 2pvb
9485409 A.Malmendal, G.Carlstrom, C.Hambraeus, T.Drakenberg, S.Forsen, and M.Akke (1998).
Sequence and context dependence of EF-hand loop dynamics. An 15N relaxation study of a calcium-binding site mutant of calbindin D9k.
  Biochemistry, 37, 2586-2595.  
9667926 J.Evenäs, A.Malmendal, and S.Forsén (1998).
  Curr Opin Chem Biol, 2, 293-302.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.