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Pregled bibliografske jedinice broj: 329048

Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination


Dokmanić, Ivan; Šikić, Mile; Tomić, Sanja
Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination // Acta crystallographica. Section D, Biological crystallography, 64 (2008), 3; 257-263 doi:10.1107/S090744490706595X (međunarodna recenzija, članak, znanstveni)


CROSBI ID: 329048 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination

Autori
Dokmanić, Ivan ; Šikić, Mile ; Tomić, Sanja

Izvornik
Acta crystallographica. Section D, Biological crystallography (0907-4449) 64 (2008), 3; 257-263

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
metal ions ; metal coordination number ; metal coordination sphere

Sažetak
Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution <1.5 A* and the set of nonredundant protein structures from the PDB. The former was used to determine the distances between each metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals.

Izvorni jezik
Engleski

Znanstvena područja
Fizika



POVEZANOST RADA


Projekti:
MZOS-022-0222148-2822 - Modeliranje i međudjelovanje kompleksa prijelaznih metala i bioliganada (Sabolović, Jasmina, MZOS ) ( CroRIS)
MZO-ZP-036-0362214-1987 - Modeliranje kompleksnih sustava (Jeren, Branko, MZO ) ( CroRIS)
MZOS-098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Tomić, Sanja, MZOS ) ( CroRIS)

Ustanove:
Fakultet elektrotehnike i računarstva, Zagreb,
Institut "Ruđer Bošković", Zagreb

Profili:

Avatar Url Sanja Tomić (autor)

Avatar Url Mile Šikić (autor)

Avatar Url Ivan Dokmanić (autor)

Poveznice na cjeloviti tekst rada:

doi scripts.iucr.org

Citiraj ovu publikaciju:

Dokmanić, Ivan; Šikić, Mile; Tomić, Sanja
Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination // Acta crystallographica. Section D, Biological crystallography, 64 (2008), 3; 257-263 doi:10.1107/S090744490706595X (međunarodna recenzija, članak, znanstveni)
Dokmanić, I., Šikić, M. & Tomić, S. (2008) Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination. Acta crystallographica. Section D, Biological crystallography, 64 (3), 257-263 doi:10.1107/S090744490706595X.
@article{article, author = {Dokmani\'{c}, Ivan and \v{S}iki\'{c}, Mile and Tomi\'{c}, Sanja}, year = {2008}, pages = {257-263}, DOI = {10.1107/S090744490706595X}, keywords = {metal ions, metal coordination number, metal coordination sphere}, journal = {Acta crystallographica. Section D, Biological crystallography}, doi = {10.1107/S090744490706595X}, volume = {64}, number = {3}, issn = {0907-4449}, title = {Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination}, keyword = {metal ions, metal coordination number, metal coordination sphere} }
@article{article, author = {Dokmani\'{c}, Ivan and \v{S}iki\'{c}, Mile and Tomi\'{c}, Sanja}, year = {2008}, pages = {257-263}, DOI = {10.1107/S090744490706595X}, keywords = {metal ions, metal coordination number, metal coordination sphere}, journal = {Acta crystallographica. Section D, Biological crystallography}, doi = {10.1107/S090744490706595X}, volume = {64}, number = {3}, issn = {0907-4449}, title = {Metals in proteins: correlation between the metal- ion type, coordination number and the amino-acid residues involved in the coordination}, keyword = {metal ions, metal coordination number, metal coordination sphere} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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