1JDO

SPERM WHALE MYOGLOBIN (FERROUS, NITRIC OXIDE BOUND)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nitric oxide myoglobin: crystal structure and analysis of ligand geometry.

Brucker, E.A.Olson, J.S.Ikeda-Saito, M.Phillips Jr., G.N.

(1998) Proteins 30: 352-356

  • Primary Citation of Related Structures:  1HJT

  • PubMed Abstract: 
  • The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 angstroms resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112 degrees. ...

    The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 angstroms resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112 degrees. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the N(epsilon) atom of histidine64 is located 2.8 angstroms away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
154Physeter catodonGene Names: MB
Find proteins for P02185 (Physeter catodon)
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
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
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 91.506α = 90.00
b = 91.506β = 90.00
c = 45.853γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
SHELXL-96phasing
XSCALEdata scaling
X-PLORphasing
X-PLORmodel building
SHELXL-96model building
XDSdata reduction
SHELXL-96refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance