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PDBsum entry 1ncy

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protein ligands metals links
Calcium-binding protein PDB id
1ncy
Jmol
Contents
Protein chain
162 a.a. *
Ligands
SO4
Metals
_MN ×2
Waters ×105
* Residue conservation analysis
PDB id:
1ncy
Name: Calcium-binding protein
Title: Troponin-c, complex with manganese
Structure: Troponin c. Chain: a
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: skeletal. Tissue: skeletal muscle
Resolution:
2.10Å     R-factor:   0.130    
Authors: M.Sundaralingam,S.T.Rao
Key ref:
S.T.Rao et al. (1996). X-ray structures of Mn, Cd and Tb metal complexes of troponin C. Acta Crystallogr D Biol Crystallogr, 52, 916-922. PubMed id: 15299599 DOI: 10.1107/S0907444996006166
Date:
02-Jun-96     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02588  (TNNC2_CHICK) -  Troponin C, skeletal muscle
Seq:
Struc:
163 a.a.
162 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     troponin complex   1 term 
  Biological process     skeletal muscle contraction   1 term 
  Biochemical function     actin binding     3 terms  

 

 
DOI no: 10.1107/S0907444996006166 Acta Crystallogr D Biol Crystallogr 52:916-922 (1996)
PubMed id: 15299599  
 
 
X-ray structures of Mn, Cd and Tb metal complexes of troponin C.
S.T.Rao, K.A.Satyshur, M.L.Greaser, M.Sundaralingam.
 
  ABSTRACT  
 
The crystal structures of three metal complexes of troponin C (TnC) have been determined and refined where the two occupied structural Ca(2+) sites in the C domain have been substituted by Mn(2+), Cd(2+) and Tb(3+). The X-ray intensity data were collected to 2.1, 1.8 and 1.8 A resolution, respectively, on the three metal complexes, which are isomorphous with Ca-TnC. The three complexes have r.m.s. deviations of 0.27, 0.25 and 0.35 A, respectively, for all protein atoms, from Ca-TnC. Irrespective of the charge on the metal (+2 or +3), the occupied sites 3 and 4 exhibit a distorted pentagonal bipyramidal coordination, like Ca-TnC, with seven ligands, six from the 12-residue binding loop and the seventh from a water molecule. Mn(2+) at site 4 seems to display a longer distance to one of the carboxyl bidentate ligands representing an intermediate coordination simulating the six-coordinate Mg(2+). The carboxyl O atoms of the bidentate Glu12 are displaced on the side of the equatorial plane passing through the remaining three ligands with one O atom closer to the plane (Delta of 0.11 to 0.76 A) than the other (Delta of 0.93 to 1.38 A). The two axial ligands are an aspartic carboxyl O atom and a water molecule. The metal is displaced (0.18 to 0.56 A) towards the water facing the water channel.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo figure superposing the seven ligands for site 3 of Cd-TnC on a (a) regular pentagonal biprism and (b) a regular octahedron. For the polyhedra, a metal-to-ligand distance of 2.4 A was used.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 916-922) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19529883 X.C.Su, and G.Otting (2010).
Paramagnetic labelling of proteins and oligonucleotides for NMR.
  J Biomol NMR, 46, 101-112.  
18576649 J.J.Yang, J.Yang, L.Wei, O.Zurkiya, W.Yang, S.Li, J.Zou, Y.Zhou, A.L.Maniccia, H.Mao, F.Zhao, R.Malchow, S.Zhao, J.Johnson, X.Hu, E.Krogstad, and Z.R.Liu (2008).
Rational design of protein-based MRI contrast agents.
  J Am Chem Soc, 130, 9260-9267.  
18699778 J.O.Schulze, C.Quedenau, Y.Roske, T.Adam, H.Schüler, J.Behlke, A.P.Turnbull, V.Sievert, C.Scheich, U.Mueller, U.Heinemann, and K.Büssow (2008).
Structural and functional characterization of human Iba proteins.
  FEBS J, 275, 4627-4640.
PDB codes: 2jjz 2vtg
16637059 L.L.Clainche, M.Figuet, V.Montjardet-Bas, S.Blanchard, and C.Vita (2006).
Modulating the affinity and the selectivity of engineered calmodulin EF-Hand peptides for lanthanides.
  Biotechnol Bioeng, 95, 29-36.  
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