2H9J

Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Configurations of nickel-cyclam antiviral complexes and protein recognition.

Hunter, T.M., McNae, I.W., Simpson, D.P., Smith, A.M., Moggach, S., White, F., Walkinshaw, M.D., Parsons, S., Sadler, P.J.

(2007) Chemistry 13: 40-50

  • DOI: 10.1002/chem.200601334
  • Primary Citation of Related Structures:  
    2H9K, 2H9J

  • PubMed Abstract: 

    • Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to the CXCR4 co-receptor. We have investigated configurational equilibria of Ni(II)-cyclam derivatives, since these are important for receptor recognition. Crystallographic studies sh ...

    Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to the CXCR4 co-receptor. We have investigated configurational equilibria of Ni(II)-cyclam derivatives, since these are important for receptor recognition. Crystallographic studies show that both trans and cis configurations are readily formed: [Ni(cyclam)(OAc)(2)] x H(2)O adopts the trans-III configuration with axial monodentate acetates, as does [Ni(benzylcyclam)(NO(3))(2)] with axial nitrate ligands, whereas [Ni(benzylcyclam)(OAc)](OAc)2 x H(2)O has an unusual folded cis-V configuration with Ni(II) coordination to bidentate acetate. UV/Vis and NMR studies show that the octahedral trans-III configuration slowly converts to square-planar trans-I in aqueous solution. For Ni(II)-xylylbicyclam, a mixture of cis-V and trans-I configurations was detected in solution. X-ray diffraction studies showed that crystals of lysozyme soaked in Ni(II)-cyclam or Ni(II) (2)-xylylbicyclam contain two major binding sites, one involving Ni(II) coordination to Asp101 and hydrophobic interactions between the cyclam ring and Trp62 and Trp63, and the second hydrophobic interactions with Trp123. For Ni(II)-cyclam bound to Asp101, the cis-V configuration predominates.

    Organizational Affiliation: 

    School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme C A129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MM5
Query on MM5
Download Ideal Coordinates CCD File 
A
1,1'-[1,4-PHENYLENEBIS(METHYLENE)]BIS[1,4,8,11-TETRAAZACYCLOTETRADECANE]NI(II)
C28 H48 N8 Ni2
XVYSAVBBVPTNSF-AHOGKBPJAJ		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.577α = 90
b = 77.577β = 90
c = 38.355γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance