3D7O

Human hemoglobin, nitrogen dioxide anion modified


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The nitrite anion binds to human hemoglobin via the uncommon O-nitrito mode.

Yi, J.Safo, M.K.Richter-Addo, G.B.

(2008) Biochemistry 47: 8247-8249

  • DOI: 10.1021/bi801015c

  • PubMed Abstract: 
  • The nitrite anion is known to oxidize and degrade hemoglobin (Hb). Recent literature reports suggest a nitrite reductase activity for Hb, converting nitrite into nitric oxide. Surprisingly, no structural information about Hb-nitrite interactions has ...

    The nitrite anion is known to oxidize and degrade hemoglobin (Hb). Recent literature reports suggest a nitrite reductase activity for Hb, converting nitrite into nitric oxide. Surprisingly, no structural information about Hb-nitrite interactions has been reported. We have determined the crystal structure of the ferric Hb-nitrite complex at 1.80 A resolution. The nitrite ligand adopts the uncommon O-nitrito binding mode. In addition, the nitrito conformations in the alpha and beta subunits are different, reflecting subtle effects of the distal His in orienting the nitrite ligand in the O-nitrito binding mode.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBN
Query on MBN

Download SDF File 
Download CCD File 
A
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

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Download CCD File 
A, B
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
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: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.538α = 90.00
b = 53.538β = 90.00
c = 191.770γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata scaling
REFMACrefinement
MOLREPphasing
d*TREKdata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance