2ZG7

Crystal Structure of Pd(allyl)/apo-Fr

PDB DOI: https://doi.org/10.2210/pdb2ZG7/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Equus caballus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-18 Released: 2008-08-26
Deposition Author(s): Abe, S., Niemeyer, J., Abe, M., Ueno, T., Hikage, T., Erker, G., Watanabe, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.202
R-Value Work: 0.176
R-Value Observed: 0.177

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 18636721 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 21.46 kDa
Atom Count: 1,795
Modelled Residue Count: 173
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth X]	174	Equus caballus	Mutation(s): 0 Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791 Go to UniProtKB: P02791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLL Query on PLL Download Ideal Coordinates CCD File SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X]	G [auth X], H [auth X], I [auth X], J [auth X]	Palladium(II) allyl complex C₃ H₅ Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N		Interactions Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Interactions & Density Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] SDF format, chain E [auth X] SDF format, chain F [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X]	C [auth X], D [auth X], E [auth X], F [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain L [auth X] SDF format, chain M [auth X] SDF format, chain N [auth X] SDF format, chain O [auth X] SDF format, chain P [auth X] SDF format, chain Q [auth X] SDF format, chain R [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] MOL2 format, chain M [auth X] MOL2 format, chain N [auth X] MOL2 format, chain O [auth X] MOL2 format, chain P [auth X] MOL2 format, chain Q [auth X] MOL2 format, chain R [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X] mmCIF format, chain M [auth X] mmCIF format, chain N [auth X] mmCIF format, chain O [auth X] mmCIF format, chain P [auth X] mmCIF format, chain Q [auth X] mmCIF format, chain R [auth X]	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], R [auth X]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Interactions & Density Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.202
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.45	α = 90
b = 181.45	β = 90
c = 181.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

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: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description