PDBsum entry 2dn3

Oxygen storage/transport

PDB id: 2dn3

Contents

Protein chains

141 a.a. *

146 a.a. *

Ligands

HEM-CMO ×2

Waters ×212

* Residue conservation analysis

PDB id:

2dn3

Name:

Oxygen storage/transport

Title:

1.25a resolution crystal structure of human hemoglobin in the carbonmonoxy form

Structure:

Hemoglobin alpha subunit. Chain: a. Synonym: hemoglobin alpha chain, alpha-globin. Hemoglobin beta subunit. Chain: b. Synonym: hemoglobin beta chain, beta-globin

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: red cell. Tissue: red cell

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.25Å R-factor: 0.183

Authors:

S.-Y.Park,T.Yokoyama,N.Shibayama,Y.Shiro,J.R.Tame

Key ref:

S.Y.Park et al. (2006). 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J Mol Biol, 360, 690-701. PubMed id: 16765986 DOI: 10.1016/j.jmb.2006.05.036

Date:

25-Apr-06 Release date: 09-May-06

Protein chain

P69905  (HBA_HUMAN) -  Hemoglobin subunit alpha from Homo sapiens

Seq: 142 a.a.

Struc: 141 a.a.

Protein chain

P68871  (HBB_HUMAN) -  Hemoglobin subunit beta from Homo sapiens

Seq: 147 a.a.

Struc: 146 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1016/j.jmb.2006.05.036

J Mol Biol 360:690-701 (2006)

PubMed id: 16765986

1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms.

S.Y.Park, T.Yokoyama, N.Shibayama, Y.Shiro, J.R.Tame.

ABSTRACT

The most recent refinement of the crystallographic structure of oxyhaemoglobin (oxyHb) was completed in 1983, and differences between this real-space refined model and later R state models have been interpreted as evidence of crystallisation artefacts, or numerous sub-states. We have refined models of deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with other Hb structures. It is shown that the older structures reflect the software used in refinement, and many differences with newer structures are unlikely to be physiologically relevant. The improved accuracy of our models clarifies the disagreement between NMR and X-ray studies of oxyHb, the NMR experiments suggesting a hydrogen bond to exist between the distal histidine and oxygen ligand of both the alpha and beta-subunits. The high-resolution crystal structure also reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin. We also propose a new set of relatively fixed residues to act as a frame of reference; this set contains a similar number of atoms to the well-known "BGH" frame yet shows a much smaller rmsd value between R and T state models of HbA.

Selected figure(s)

Figure 1.
Figure 1. Stereo view of the final 2mF[o]–DF[c] electron density map for oxyHbA, showing (a) the ligand at the α haem and (b) the β chain. In the α subunit, a small peak of density (roughly 1.5σ) is found about 2.2 Å from the oxygen ligand and 3.1 Å from Leu29. Leu29 shows some sign of adopting more than one rotamer, which may allow a partially occupied water molecule into the haem pocket. Density is contoured at 1.5σ. It can be seen that the O2 atom of the ligand, not directly bonded to the haem, is better defined in the α pocket than in the β haem pocket density. The lower electron density in the β subunits is indicative of a weaker bond to the distal histidine and greater rotation about the Fe–O bond. Temperature factors for the O2 atoms are similar (35 Å^2and 33 Å^2 in the α and β subunits, respectively).

Figure 2.
Figure 2. Stereo view of the final 2mF[o]–DF[c] electron density map for COHb, showing (a) the α haem and (b) the β haem. Density is contoured at 1.5σ. The C termini of the α and β subunits are shown in (c) and (d), respectively. Tyr141α and Tyr145β show substantial shifts compared to PDB 1HHO.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 690-701) copyright 2006.