1IGV

BOVINE CALBINDIN D9K BINDING MN2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k.

Andersson, M.Malmendal, A.Linse, S.Ivarsson, I.Forsen, S.Svensson, L.A.

(1997) Protein Sci 6: 1139-1147

  • DOI: 10.1002/pro.5560060602
  • Primary Citation of Related Structures:  
    1IG5, 1IGV

  • PubMed Abstract: 
  • 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 significantl ...

    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.


    Organizational Affiliation

    Department of Molecular Biophysics, Lund University, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN, INTESTINALA75Bos taurusMutation(s): 0 
Gene Names: synthetic geneS100GCALB3S100D
Find proteins for P02633 (Bos taurus)
Explore P02633 
Go to UniProtKB:  P02633
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.8α = 90
b = 33.8β = 90
c = 129.63γ = 90
Software Package:
Software NamePurpose
SIGMAAmodel building
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction
SIGMAAphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-04-18 
  • Released Date: 2001-04-25 
  • Deposition Author(s): Andersson, E.M.
  • This entry supersedes: 6ICB

Revision History 

  • Version 1.0: 2001-04-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description