X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin at 2·0 Å resolution. Stabilization of the fluoride ion by hydrogen bonding to Arg66 (E10)

Martino Bolognesi, Alessandro Coda, Francesco Frigerio, Giuseppina Gatti, Paolo Ascenzi, Maurizio Brunori

Research output: Contribution to journalArticle

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Abstract

The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2·0 Å resolution; the crystallographic R-factor is 13·6%. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2·2 Å from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.

Original languageEnglish
Pages (from-to)621-625
Number of pages5
JournalJournal of Molecular Biology
Volume213
Issue number4
DOIs
Publication statusPublished - Jun 20 1990

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Aplysia
Myoglobin
Hydrogen Bonding
Fluorides
X-Rays
Ions
Heme
Sperm Whale
R388
Hydrogen
Ligands
Propionates
Hemoglobins
Iron
Metals
Oxygen
Water

ASJC Scopus subject areas

  • Molecular Biology
  • Virology

Cite this

X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin at 2·0 Å resolution. Stabilization of the fluoride ion by hydrogen bonding to Arg66 (E10). / Bolognesi, Martino; Coda, Alessandro; Frigerio, Francesco; Gatti, Giuseppina; Ascenzi, Paolo; Brunori, Maurizio.

In: Journal of Molecular Biology, Vol. 213, No. 4, 20.06.1990, p. 621-625.

Research output: Contribution to journalArticle

Bolognesi, Martino ; Coda, Alessandro ; Frigerio, Francesco ; Gatti, Giuseppina ; Ascenzi, Paolo ; Brunori, Maurizio. / X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin at 2·0 Å resolution. Stabilization of the fluoride ion by hydrogen bonding to Arg66 (E10). In: Journal of Molecular Biology. 1990 ; Vol. 213, No. 4. pp. 621-625.
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abstract = "The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2·0 {\AA} resolution; the crystallographic R-factor is 13·6{\%}. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2·2 {\AA} from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.",
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N2 - The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2·0 Å resolution; the crystallographic R-factor is 13·6%. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2·2 Å from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.

AB - The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2·0 Å resolution; the crystallographic R-factor is 13·6%. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2·2 Å from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.

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