3D7O

Human hemoglobin, nitrogen dioxide anion modified

• PDB DOI: https://doi.org/10.2210/pdb3D7O/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2008-05-21 Released: 2009-05-05 
• Deposition Author(s): Yi, J., Safo, M.K., Richter-Addo, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

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

• PubMed: 18630930 
• DOI: https://doi.org/10.1021/bi801015c
• Primary Citation of Related Structures:  
  3D7O


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.46 kDa 
• Atom Count: 2,468 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MBN	E [auth A]	TOLUENE C7 H8 YXFVVABEGXRONW-UHFFFAOYSA-N
NO2	C [auth A], F [auth B]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.538	α = 90
b = 53.538	β = 90
c = 191.77	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Yi, J., Safo, M.K., Richter-Addo, G.B.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description