6CF0

Sperm Whale Myoglobin H64V Mutant with Nitrite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.

Wang, B.Shi, Y.Tejero, J.Powell, S.M.Thomas, L.M.Gladwin, M.T.Shiva, S.Zhang, Y.Richter-Addo, G.B.

(2018) Biochemistry 57: 4788-4802

  • DOI: 10.1021/acs.biochem.8b00542
  • Primary Citation of Related Structures:  
    5VZQ, 5VZN, 5VZP, 5VZO, 5UTD, 5UTA, 5UTC, 5UTB, 5UT7, 5UT9, 5UT8, 6CF0

  • PubMed Abstract: 
  • The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated ...

    The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb III and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb III and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb II -mediated reductions of nitrite to NO and structural data for the wt and mutant Mb II -NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.


    Organizational Affiliation

    Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA154Physeter catodonMutation(s): 1 
Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.15α = 90
b = 90.15β = 90
c = 45.324γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

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: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence