3HHB

THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of human deoxyhaemoglobin at 1.74 A resolution

Fermi, G.Perutz, M.F.Shaanan, B.Fourme, R.

(1984) J.Mol.Biol. 175: 159-174

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of human deoxyhaemoglobin was refined at 1.74 A resolution using data collected on film at room temperature from a synchrotron X-ray source. The crystallographic R-factor is 16.0%. The estimated error in atomic positions is 0.1 A overal ...

    The structure of human deoxyhaemoglobin was refined at 1.74 A resolution using data collected on film at room temperature from a synchrotron X-ray source. The crystallographic R-factor is 16.0%. The estimated error in atomic positions is 0.1 A overall, 0.14 A for main-chain atoms of internal segments, and 0.05 A for the iron atoms. The effects of intermolecular contacts on the structure were investigated; such contacts cause only highly localized distortions, as judged from the degree of molecular asymmetry that they induce. The geometry of the iron-nitrogen complex closely resembles that of the deoxymyoglobin structure of Takano (1977) and of the 5-co-ordinated model compounds of Hoard (1975) and Jameson et al. (1980). The distance of the iron from the mean plane of N(porphyrin) is 0.40(5) A and 0.36(5) A, respectively, at the alpha and beta haems, in contrast to the corresponding distance of +0.12(8) A and -0.11(8) A in oxyhaemoglobin ( Shaanan , 1983); the Fe-N epsilon (F8) bond length is 2.12(4) A and the Fe-N(porphyrin) bond length is 2.06(2) A; the last is also in good agreement with extended X-ray fluorescence spectroscopy measurements on deoxyhaemoglobin ( Eisenberger et al., 1978; Perutz et al., 1982). The haems are domed toward the proximal side; the separation between the mean planes of N(porphyrin) and C(porphyrin) being 0.16(6) A and 0.10(6) A, respectively at the alpha and beta haems. At the alpha haems, the normals to the mean pyrrole planes are tilted uniformly toward the haem centre, by about three degrees relative to the haem normal, and there is a folding of about four degrees of the haem about an axis running between the methene carbons that are between the pyrrole rings bearing like-type side-chains. At the beta haems, there is no such folding, and only pyrroles II and IV (those eclipsed by His F8) are appreciably tilted, by about eight degrees. The independence of these parameters from restraints imposed on the model was verified by unrestrained refinement of the entire molecule starting from a structure with modified haem geometry.


    Related Citations: 
    • Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 2.5 Angstroms Resolution, Refinement of the Atomic Model
      Fermi, G.
      (1975) J.Mol.Biol. 97: 237
    • Three-Dimensional Fourier Synthesis of Human Deoxyhemoglobin at 2.5 Angstroms Resolution, I.X-Ray Analysis
      Teneyck, L.F.,Arnone, A.
      (1976) J.Mol.Biol. 100: 3
    • Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 3.5 Angstroms Resolution
      Muirhead, H.,Greer, J.
      (1970) Nature 228: 516
    • Regulation of Oxygen Affinity of Hemoglobin. Influence of Structure of the Globin on the Heme Iron
      Perutz, M.F.
      (1979) Annu.Rev.Biochem. 48: 327
    • Fermi, G.,Perutz, M.F.
      (1981) Haemoglobin and Myoglobin. Atlas of Molecular Structures in Biology 2: --
    • Stereochemistry of Iron in Deoxyhaemoglobin
      Perutz, M.F.,Hasnain, S.S.,Duke, P.J.,Sessler, J.L.,Hahn, J.E.
      (1982) Nature 295: 535



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
A, C
141Homo sapiensGene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (DEOXY) (BETA CHAIN)
B, D
146Pan troglodytesGene Names: HBB
Find proteins for P68873 (Pan troglodytes)
Go to Gene View: HBB
Go to UniProtKB:  P68873
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.150α = 90.00
b = 83.590β = 99.34
c = 53.800γ = 90.00

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1984-03-07 
  • Released Date: 1984-07-18 
  • Deposition Author(s): Fermi, G., Perutz, M.F.
  • This entry supersedes: 1HHB

Revision History 

  • Version 1.0: 1984-07-18
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance