5UT8

Deoxy form of sperm whale myoglobin H64A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  

  • 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 re ...

    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

    Department of Chemistry and Chemical Biology , Stevens Institute of Technology , Castle Point on Hudson , Hoboken , New Jersey 07030 , United States.,Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States.,Department of Pharmacology and Chemical Biology , University of Pittsburgh , 200 Lothrop Street , Pittsburgh , Pennsylvania 15213 , United States.,Heart, Lung, Blood and Vascular Medicine Institute , University of Pittsburgh School of Medicine , 3550 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 1 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.399α = 90.00
b = 90.399β = 90.00
c = 45.271γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKLdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-3000data scaling
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection
  • Version 1.2: 2018-08-22
    Type: Data collection, Database references
  • Version 1.3: 2018-08-29
    Type: Data collection, Database references
  • Version 1.4: 2019-11-27
    Type: Author supporting evidence