Solution structure of the imidazole complex of cytochrome C

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c

Banci, L.Bertini, I.Liu, G.Lu, J.Reddig, T.Tang, W.Wu, Y.Yao, Y.Zhu, D.

(2001) J Biol Inorg Chem 6: 628-637

  • DOI: https://doi.org/10.1007/s007750100240
  • Primary Citation of Related Structures:  
    1FI7, 1FI9

  • PubMed Abstract: 

    Although imidazole ligand binding to cytochrome c is not directly related to its physiological function, it has the potential to provide valuable information on the molecular and electronic structure of the protein. The solution structure of the imidazole adduct of oxidized horse heart cytochrome c (Im-cyt c) has been determined through 2D NMR spectroscopy. The Im-cyt c, 8 mM in 1.2 M imidazole solution at pH 5.7 and 313 K, provided altogether 2,542 NOEs (1,901 meaningful NOEs) and 194 pseudocontact shifts. The 35 conformers of the family show the RMSD values to the average structure of 0.063+/-0.007 nm for the backbone and 0.107+/-0.007 nm for all heavy atoms, respectively. The characterization of Im-cyt c is discussed in detail both in terms of structure and electronic properties. The replacement of the axial ligand Met80 with the exogenous imidazole ligand induces significant conformation changes in both backbone and side chains of the residues located in the distal axial ligand regions. The imidazole ligand binds essentially parallel to the imidazole of the proximal histidine, the two planes forming an angle of 8+/-7 degrees. The electron delocalization on the heme moiety and the magnetic susceptibility tensor are consistent with these structural features.

  • Organizational Affiliation

    Magnetic Resonance Center, University of Florence, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C104Equus caballusMutation(s): 0 
Find proteins for P00004 (Equus caballus)
Explore P00004 
Go to UniProtKB:  P00004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00004
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A]HEME C
C34 H34 Fe N4 O4
Query on IMD

Download Ideal Coordinates CCD File 
C3 H5 N2
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations