WT swMb-MeNO

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives.

Herrera, V.E.Charles, T.P.Scott, T.G.Prather, K.Y.Nguyen, N.T.Sohl, C.D.Thomas, L.M.Richter-Addo, G.B.

(2023) Biochemistry 62: 1406-1419

  • DOI: https://doi.org/10.1021/acs.biochem.2c00725
  • Primary Citation of Related Structures:  
    6E02, 6E03, 6E04, 8F9H, 8F9I, 8F9J, 8F9N

  • PubMed Abstract: 

    Nitrosoalkanes (R-N═O; R = alkyl) are biological intermediates that form from the oxidative metabolism of various amine (RNH 2 ) drugs or from the reduction of nitroorganics (RNO 2 ). RNO compounds bind to and inhibit various heme proteins. However, structural information on the resulting Fe-RNO moieties remains limited. We report the preparation of ferrous wild-type and H64A sw Mb II -RNO derivatives (λ max 424 nm; R = Me, Et, Pr, i Pr) from the reactions of Mb III -H 2 O with dithionite and nitroalkanes. The apparent extent of formation of the wt Mb derivatives followed the order MeNO > EtNO > PrNO > i PrNO, whereas the order was the opposite for the H64A derivatives. Ferricyanide oxidation of the Mb II -RNO derivatives resulted in the formation of the ferric Mb III -H 2 O precursors with loss of the RNO ligands. X-ray crystal structures of the wt Mb II -RNO derivatives at 1.76-2.0 Å resoln. revealed N -binding of RNO to Fe and the presence of H-bonding interactions between the nitroso O-atoms and distal pocket His64. The nitroso O-atoms pointed in the general direction of the protein exterior, and the hydrophobic R groups pointed toward the protein interior. X-ray crystal structures for the H64A mutant derivatives were determined at 1.74-1.80 Å resoln. An analysis of the distal pocket amino acid surface landscape provided an explanation for the differences in ligand orientations adopted by the EtNO and PrNO ligands in their wt and H64A structures. Our results provide a good baseline for the structural analysis of RNO binding to heme proteins possessing small distal pockets.

  • Organizational Affiliation

    Department of Chemistry and Physics, Ivory V. Nelson Science Center, Lincoln University, Lincoln University, Pennsylvania 19352, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter catodonMutation(s): 0 
Gene Names: MB
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.354α = 90
b = 90.354β = 90
c = 45.332γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-08
    Changes: Database references