2Z8A

Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with CO Bound to HEME and in the Presence of 3 Atoms of XE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis

Nienhaus, K.Knapp, J.E.Palladino, P.Royer Jr., W.E.Nienhaus, G.U.

(2007) Biochemistry 46: 14018-14031

  • DOI: 10.1021/bi7016798
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin o ...

    Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.


    Organizational Affiliation

    Institute of Biophysics, University of Ulm, 89069 Ulm, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Globin-1A, B146Scapharca inaequivalvisMutation(s): 1 
Gene Names: HBI
Find proteins for P02213 (Anadara inaequivalvis)
Explore P02213 
Go to UniProtKB:  P02213
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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

Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.66α = 90
b = 43.39β = 122.02
c = 82.29γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
BIOCARSdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description