5ILM

H64A sperm whale myoglobin with a Fe-chlorophenyl moiety

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations.

Wang, B., Thomas, L.M., Richter-Addo, G.B.

(2016) J Inorg Biochem 164: 1-4

  • DOI: https://doi.org/10.1016/j.jinorgbio.2016.06.028
  • Primary Citation of Related Structures:  
    5IKS, 5ILE, 5ILM, 5ILP, 5ILR

  • PubMed Abstract: 

    Bioorganometallic Fe-C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures of four new sperm whale mutant myoglobin derivatives with Fe-aryl moieties, namely H64A-tolyl-m, H64A-chlorophenyl-p, H64Q-tolyl-m, and H64Q-chlorophenyl-p, have been determined at 1.7-1.9Å resolution. The structures reveal conformational preferences for the substituted aryls resulting from attachment of the aryl ligands to Fe at the site of net -NHNH 2 release from the precursor hydrazines, and show distal pocket changes that readily accommodate these bulky ligands.

    • Organizational Affiliation: 

    Department of Chemistry and Biochemistry, and Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman 73019, United States.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 2 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4HE
Query on 4HE
Download Ideal Coordinates CCD File 
B [auth A](4-chlorophenyl)[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)di(propanoato)(2-)]iron
C40 H36 Cl Fe N4 O4
FEKAGXWHIKBYKT-HXFTUNQESA-L
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.599α = 90
b = 90.599β = 90
c = 45.121γ = 120
Software Package:
Software NamePurpose
HKL-3000phasing
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE 1213674

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description