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PDBsum entry 1cdp
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protein metals links
Calcium binding PDB id
1cdp

 

 

 

 

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Contents
Protein chain
109 a.a. *
Metals
_CD ×2
Waters ×73
* Residue conservation analysis
PDB id:
1cdp
Name: Calcium binding
Title: Restrained least squares refinement of native (calcium) and cadmium- substituted carp parvalbumin using x-ray crystallographic data at 1.6-angstroms resolution
Structure: Cadmium-substituted calcium-binding parvalbumin b. Chain: a. Engineered: yes
Source: Cyprinus carpio. Common carp. Organism_taxid: 7962
Resolution:
1.60Å     R-factor:   0.164    
Authors: A.L.Swain,R.H.Kretsinger,E.L.Amma
Key ref: A.L.Swain et al. (1989). Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution. J Biol Chem, 264, 16620-16628. PubMed id: 2777802
Date:
24-Jan-90     Release date:   15-Oct-90    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P02618  (PRVB_CYPCA) -  Parvalbumin beta from Cyprinus carpio
Seq:
Struc: 		108 a.a.
108 a.a.
Key:    Secondary structure  CATH domain

 

 
J Biol Chem 264:16620-16628 (1989)
PubMed id: 2777802  
 
 
Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.
A.L.Swain, R.H.Kretsinger, E.L.Amma.
 
  ABSTRACT  
 
Carp parvalbumin coordinates calcium through one carbonyl oxygen atom and the oxygen-containing side chains of 5 amino acid residues, or 4 residues and a water molecule, in a helix-loop-helix structural motif. Other calcium-binding proteins, including calmodulin and troponin C, also possess this unique calcium-binding design, which is designated EF-hand or calmodulin fold. Parvalbumin has two such sites, labeled CD and EF. Each of the calcium-binding sites of refined structures of proteins belonging to this group has a 7-oxygen coordination sphere except those of the structure of parvalbumin as it was reported in 1975. This structure had been refined at 1.9 A using difference Fourier techniques on film data. The CD site appeared to be 6-coordinate and the EF site 8-coordinate. Results of NMR experiments using 113Cd-substituted parvalbumin, however, indicate that the sites are similar to one another with coordination number greater than 6. To resolve the inconsistency between crystallographic and NMR results, 1.6 A area detector data was collected for native and cadmium-substituted parvalbumin; the structures have been refined to R factors of 18.7% and 16.4%, respectively, with acceptable geometry and low errors in atomic coordinates. Differences between the parvalbumin structure described in 1975 and the present structure are addressed, including the discovery of 7-coordination for both the CD and EF sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20857506 E.Papaleo, and G.Invernizzi (2011).
Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: Remodeling induced by mutation of calcium coordinating residues.
  Biopolymers, 95, 117-126.  
21287610 M.T.Henzl, J.J.Tanner, and A.Tan (2011).
Solution structures of chicken parvalbumin 3 in the Ca(2+) -free and Ca(2+) -bound states.
  Proteins, 79, 752-764.
PDB codes: 2kyc 2kyf
20156445 J.P.Schuermann, A.Tan, J.J.Tanner, and M.T.Henzl (2010).
Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states.
  J Mol Biol, 397, 991.
PDB codes: 2kqy 3fs7
18684507 M.Kirberger, and J.J.Yang (2008).
Structural differences between Pb2+- and Ca2+-binding sites in proteins: implications with respect to toxicity.
  J Inorg Biochem, 102, 1901-1909.  
18305196 N.Juranić, J.J.Dannenberg, G.Cornilescu, P.Salvador, E.Atanasova, H.C.Ahn, S.Macura, J.L.Markley, and F.G.Prendergast (2008).
Structural dependencies of protein backbone 2JNC' couplings.
  Protein Sci, 17, 768-776.  
12382287 C.Charron, B.Vitoux, and A.Aubry (2002).
Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus.
  Biopolymers, 65, 263-273.  
11818024 K.Truong, and M.Ikura (2002).
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach.
  BMC Bioinformatics, 3, 1.  
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.  
11753432 S.L.Kazmirski, R.L.Isaacson, C.An, A.Buckle, C.M.Johnson, V.Daggett, and A.R.Fersht (2002).
Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.
  Nat Struct Biol, 9, 112-116.
PDB code: 1kcq
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.  
11717497 J.Jia, N.Borregaard, K.Lollike, and M.Cygler (2001).
Structure of Ca(2+)-loaded human grancalcin.
  Acta Crystallogr D Biol Crystallogr, 57, 1843-1849.
PDB codes: 1k94 1k95
  10739249 R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, and D.J.Nelson (2000).
X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).
  Protein Sci, 9, 73-82.
PDB code: 1bu3
10545329 E.J.van Asselt, A.J.Dijkstra, K.H.Kalk, B.Takacs, W.Keck, and B.W.Dijkstra (1999).
Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand.
  Structure, 7, 1167-1180.
PDB codes: 1qus 1qut
  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
10545326 M.S.Cates, M.B.Berry, E.L.Ho, Q.Li, J.D.Potter, and G.N.Phillips (1999).
Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin.
  Structure, 7, 1269-1278.
PDB codes: 1b8c 1b8l 1b8r 1b9a
9519413 H.Matsumura, T.Shiba, T.Inoue, S.Harada, and Y.Kai (1998).
A novel mode of target recognition suggested by the 2.0 A structure of holo S100B from bovine brain.
  Structure, 6, 233-241.
PDB code: 1mho
9585577 R.R.Biekofsky, S.R.Martin, J.P.Browne, P.M.Bayley, and J.Feeney (1998).
Ca2+ coordination to backbone carbonyl oxygen atoms in calmodulin and other EF-hand proteins: 15N chemical shifts as probes for monitoring individual-site Ca2+ coordination.
  Biochemistry, 37, 7617-7629.  
9037719 A.R.Khan, K.A.Johnson, J.Braam, and M.N.James (1997).
Comparative modeling of the three-dimensional structure of the calmodulin-related TCH2 protein from Arabidopsis.
  Proteins, 27, 144-153.
PDB code: 1avj
8652520 G.S.Shaw, and B.D.Sykes (1996).
NMR solution structure of a synthetic troponin C heterodimeric domain.
  Biochemistry, 35, 7429-7438.
PDB code: 1pon
9162944 L.Zhang, and J.Hermans (1996).
Hydrophilicity of cavities in proteins.
  Proteins, 24, 433-438.  
  7613474 C.Donaldson, K.R.Barber, C.M.Kay, and G.S.Shaw (1995).
Human S100b protein: formation of a tetramer from synthetic calcium-binding site peptides.
  Protein Sci, 4, 765-772.  
  7670374 N.N.Khechinashvili, J.Janin, and F.Rodier (1995).
Thermodynamics of the temperature-induced unfolding of globular proteins.
  Protein Sci, 4, 1315-1324.  
7552750 S.M.Gagné, S.Tsuda, M.X.Li, L.B.Smillie, and B.D.Sykes (1995).
Structures of the troponin C regulatory domains in the apo and calcium-saturated states.
  Nat Struct Biol, 2, 784-789.
PDB codes: 1tnp 1tnq
  7920247 G.S.Shaw, R.S.Hodges, C.M.Kay, and B.D.Sykes (1994).
Relative stabilities of synthetic peptide homo- and heterodimeric troponin-C domains.
  Protein Sci, 3, 1010-1019.  
7899550 J.J.Falke, S.K.Drake, A.L.Hazard, and O.B.Peersen (1994).
Molecular tuning of ion binding to calcium signaling proteins.
  Q Rev Biophys, 27, 219-290.  
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
  8453381 S.T.Rao, S.Wu, K.A.Satyshur, K.Y.Ling, C.Kung, and M.Sundaralingam (1993).
Structure of Paramecium tetraurelia calmodulin at 1.8 A resolution.
  Protein Sci, 2, 436-447.
PDB code: 1clm
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 codes are shown on the right.

 

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