3D7O | pdb_00003d7o

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 18630930 Search on PubMed
DOI: https://doi.org/10.1021/bi801015c
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MBN Query on MBN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TOLUENE C₇ H₈ YXFVVABEGXRONW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NO2 Query on NO2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

Yi, J.

Safo, M.K.

Richter-Addo, G.B.

Revision History (Full details and data files)

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