2ZG8

Crystal Structure of Pd(allyl)/apo-H49AFr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Control of the coordination structure of organometallic palladium complexes in an apo-ferritin cage.

Abe, S.Niemeyer, J.Abe, M.Takezawa, Y.Ueno, T.Hikage, T.Erker, G.Watanabe, Y.

(2008) J Am Chem Soc 130: 10512-10514

  • DOI: https://doi.org/10.1021/ja802463a
  • Primary Citation of Related Structures:  
    2ZG7, 2ZG8, 2ZG9

  • PubMed Abstract: 

    We report the preparation of organometallic Pd(allyl) dinuclear complexes in protein cages of apo-Fr by reactions with [Pd(allyl)Cl]2 (allyl = eta3-C3H5). One of the dinuclear complexes is converted to a trinuclear complex by replacing a Pd-coordinated His residue to an Ala residue. These results suggest that multinuclear metal complexes with various coordination structures could be prepared by the deletion or introduction of His, Cys, and Glu at appropriate positions on protein surface.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chainA [auth X]174Equus caballusMutation(s): 1 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLL
Query on PLL

Download Ideal Coordinates CCD File 
H [auth X],
I [auth X],
J [auth X]
Palladium(II) allyl complex
C3 H5 Pd
WTWGCTVOVPTEEU-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth X]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PD
Query on PD

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B [auth X]PALLADIUM ION
Pd
MUJIDPITZJWBSW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth X],
E [auth X],
F [auth X],
G [auth X]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth X]
L [auth X]
M [auth X]
N [auth X]
O [auth X]
K [auth X],
L [auth X],
M [auth X],
N [auth X],
O [auth X],
P [auth X],
Q [auth X]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.339α = 90
b = 181.339β = 90
c = 181.339γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description