4N8T

Human hemoglobin nitric oxide adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystallographic characterization of the nitric oxide derivative of R-state human hemoglobin.

Yi, J.Soares, A.S.Richter-Addo, G.B.

(2014) Nitric Oxide 39: 46-50

  • DOI: https://doi.org/10.1016/j.niox.2014.04.001
  • Primary Citation of Related Structures:  
    4N8T

  • PubMed Abstract: 

    Nitric oxide (NO) is a signaling agent that is biosynthesized in vivo. NO binds to the heme center in human hemoglobin (Hb) to form the HbNO adduct. This reaction of NO with Hb has been studied for many decades. Of continued interest has been the effect that the bound NO ligand has on the geometrical parameters of the resulting heme-NO active site. Although the crystal structure of a T-state human HbNO complex has been published previously, that of the high affinity R-state HbNO derivative has not been reported to date. We have crystallized and solved the three-dimensional X-ray structure of R-state human HbNO to 1.90 Å resolution. The differences in the FeNO bond parameters and H-bonding patterns between the α and β subunits contribute to understanding of the observed enhanced stability of the α(FeNO) moieties relative to the β(FeNO) moieties in human R-state HbNO.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA; Department of Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta146Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MBN
Query on MBN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
G [auth A]NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
NO
Query on NO

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.567α = 90
b = 53.567β = 90
c = 192.499γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description