2W72

DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pattern of Cavities in Globins: The Case of Human Hemoglobin.

Savino, C.Miele, A.E.Draghi, F.Johnson, K.A.Sciara, G.Brunori, M.Vallone, B.

(2009) Biopolymers 91: 1097

  • DOI: 10.1002/bip.21201
  • Primary Citation of Related Structures:  
    2W72, 2W6V, 2W6W

  • PubMed Abstract: 
  • Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atom ...

    Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atoms. In particular, we present the high resolution structures of the Xe-adduct of deoxygenated wild type human hemoglobin and a quadruple mutant (L(B10)Y and H(E7)Q in alpha and beta chains). For the sake of comparison we also determined under the same experimental conditions the xenon complex of wild type sperm whale myoglobin. The analysis revealed that the number and position of Xe binding cavities are different in the alpha and beta subunits, the latter being more similar to myoglobin. Notably, no proximal Xe docking site was detected in hemoglobin, at variance with myoglobin. The pattern of internal cavities accessibility and affinity for xenon suggests a different role for the dynamics of ligand migration in the two types of hemoglobin chains as compared to myoglobin. The number and position of hydrophobic cavities in hemoglobin are briefly discussed also in comparison with the data available for other members of the globin superfamily.


    Organizational Affiliation

    University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy. linda.savino@uniroma1.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN HEMOGLOBIN AA141Homo sapiensMutation(s): 2 
Gene Names: HBA1HBA2
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN HEMOGLOBIN ABD146Homo sapiensMutation(s): 2 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
NIH Common Fund Data Resources
PHAROS  P68871
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN HEMOGLOBIN AC141Homo sapiensMutation(s): 2 
Gene Names: HBA1HBA2
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
XE
Query on XE

Download CCD File 
A, B, C, D
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

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A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.957α = 90
b = 82.447β = 99.6
c = 53.531γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations