2EB9

Crystal Structure of Cu(II)(Sal-Leu)/apo-Myoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and Structure Analysis of Artificial Metalloproteins: Selective Coordination of His64 to Copper Complexes with Square-Planar Structure in the apo-Myoglobin Scaffold

Abe, S.Ueno, T.Reddy, P.A.N.Okazaki, S.Hikage, T.Suzuki, A.Yamane, T.Nakajima, H.Watanabe, Y.

(2007) Inorg Chem 46: 5137-5139

  • DOI: 10.1021/ic070289m
  • Primary Citation of Related Structures:  
    2EB9, 2EB8

  • PubMed Abstract: 
  • apo-Myoglobin (apo-Mb) was reconstituted with three copper complexes: CuII(Sal-Phe) (1; Sal-Phe = N-salicylidene-L-phenylalanato), CuII(Sal-Leu) (2; Sal-Leu = N-salicylidene-L-leucinato), and CuII(Sal-Ala) (3; Sal-Ala = N-salicylidene-L-alanato). The ...

    apo-Myoglobin (apo-Mb) was reconstituted with three copper complexes: CuII(Sal-Phe) (1; Sal-Phe = N-salicylidene-L-phenylalanato), CuII(Sal-Leu) (2; Sal-Leu = N-salicylidene-L-leucinato), and CuII(Sal-Ala) (3; Sal-Ala = N-salicylidene-L-alanato). The crystal structures of 1.apo-Mb (1.65 Angstrom resolution) and 2.apo-Mb (1.8 Angstrom resolution) show that the coordination geometry around the CuII atom in apo-Mb is distorted square-planar with tridentate Sal-X and a Nepsilon atom of His64 in the apo-Mb cavity and the plane of these copper complexes is perpendicular to that of heme. These results suggest that the apo-Mb cavity can hold metal complexes with various coordination geometries.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA154Physeter catodonMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUS
Query on CUS

Download CCD File 
A
(N-SALICYLIDEN-L-LEUCINATO)-COPPER(II)
C13 H15 Cu N O3
KPMFLJZVJBUURT-QUJLGKBQDT
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.58α = 90
b = 57.901β = 90
c = 75.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance