1M8S

Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 5.9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas at 1.9A resolutio

Xu, S.Gu, L.Jiang, T.Zhou, Y.Lin, Z.

(2003) Biochem.Biophys.Res.Commun. 300: 271-277

  • Primary Citation of Related Structures:  1M8R

  • PubMed Abstract: 
  • Phospholipase A(2) coordinates Ca(2+) ion through three carbonyl oxygen atoms of residues 28, 30, and 32, two carboxyl oxygen atoms of residue Asp49, and two (or one) water molecules, forming seven (or six) coordinate geometry of Ca(2+) ligands. Two ...

    Phospholipase A(2) coordinates Ca(2+) ion through three carbonyl oxygen atoms of residues 28, 30, and 32, two carboxyl oxygen atoms of residue Asp49, and two (or one) water molecules, forming seven (or six) coordinate geometry of Ca(2+) ligands. Two crystal structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas (i.e., Agkistrodon blomhoffii brevicaudus) at different pH values (5.9 and 7.4) were determined to 1.9A resolution by the isomorphous difference Fourier method. The well-refined structures revealed that a Cd(2+) ion occupied the position expected for a Ca(2+) ion, and that the substitution of Cd(2+) for Ca(2+) resulted in detectable changes in the metal-binding region: one of the carboxyl oxygen atoms from residue Asp49 was farther from the metal ion while the other one was closer and there were no water molecules coordinating to the metal ion. Thus the Cd(2+)-binding region appears to have four coordinating oxygen ligands. The cadmium binding to the enzyme induced no other significant conformational change in the enzyme molecule elsewhere. The mechanism for divalent cadmium cation to support substrate binding but not catalysis is discussed.


    Related Citations: 
    • Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide
      Zhao, H.,Tang, L.,Wang, X.,Zhou, Y.,Lin, Z.
      (1998) TOXICON 36: 875
    • Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution
      Wang, X.,Yang, J.,Gui, L.,Lin, Z.,Chen, Y.,Zhou, Y.
      (1996) J.MOL.BIOL. 255: 669


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phospholipase a2
A
124Gloydius halysEC: 3.1.1.4
Find proteins for O42191 (Gloydius halys)
Go to UniProtKB:  O42191
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU1
Query on BU1

Download SDF File 
Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.202 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 83.160α = 90.00
b = 83.160β = 90.00
c = 32.780γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance