2RGI

Crystal structure of Ca2+-free S100A2 at 1.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

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This is version 1.1 of the entry. See complete history

Literature

Crystal structure of Ca2+ -free S100A2 at 1.6-A resolution.

Koch, M.Diez, J.Fritz, G.

(2008) J.Mol.Biol. 378: 931-940

  • DOI: 10.1016/j.jmb.2008.03.019

  • PubMed Abstract: 
  • S100A2 is an EF hand-containing Ca(2+)-binding protein of the family of S100 proteins. The protein is localized exclusively in the nucleus and is involved in cell cycle regulation. It attracted most interest by its function as a tumor suppressor via ...

    S100A2 is an EF hand-containing Ca(2+)-binding protein of the family of S100 proteins. The protein is localized exclusively in the nucleus and is involved in cell cycle regulation. It attracted most interest by its function as a tumor suppressor via p53 interaction. We determined the crystal structure of homodimeric S100A2 in the Ca(2+)-free state at 1.6-A resolution. The structure revealed structural differences between subunits A and B, especially in the conformation of a loop that connects the N- and C-terminal EF hands and represents a part of the target-binding site in S100 proteins. Analysis of the hydrogen bonding network and molecular dynamics calculations indicate that one of the two observed conformations is more stable. The structure revealed Na(+) bound to each N-terminal EF hand of both subunits coordinated by oxygen atoms of the backbone carbonyl and water molecules. Comparison with the structures of Ca(2+)-free S100A3 and S100A6 suggests that Na(+) might occupy the S100-specific EF hand in the Ca(2+)-free state.


    Organizational Affiliation

    Fachbereich Biologie, Universität Konstanz, Postfach M665, Universitätsstrasse 10, 78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A2
A, B
98Homo sapiensMutation(s): 4 
Gene Names: S100A2 (S100L)
Find proteins for P29034 (Homo sapiens)
Go to Gene View: S100A2
Go to UniProtKB:  P29034
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.516α = 90.00
b = 57.820β = 90.00
c = 59.794γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance