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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F03%3A00008726%21RIV08-MSM-14310___
rdf:type
skos:Concept n18:Vysledek
dcterms:description
We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, satin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the. hexa-co We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, satin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the. hexa-co We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, satin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the. hexa-co
dcterms:title
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
skos:prefLabel
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
skos:notation
RIV/00216224:14310/03:00008726!RIV08-MSM-14310___
n4:strany
368
n4:aktivita
n13:P
n4:aktivity
P(LN00A016)
n4:cisloPeriodika
3
n4:dodaniDat
n5:2008
n4:domaciTvurceVysledku
n14:4347374
n4:druhVysledku
n10:J
n4:duvernostUdaju
n16:S
n4:entitaPredkladatele
n8:predkladatel
n4:idSjednocenehoVysledku
602248
n4:idVysledku
RIV/00216224:14310/03:00008726
n4:jazykVysledku
n9:eng
n4:klicovaSlova
coordination number of zinc ion; zinc-containing enzyme; phosphotriesterase; molecular dynamics; quantum mechanics
n4:klicoveSlovo
n6:zinc-containing%20enzyme n6:phosphotriesterase n6:coordination%20number%20of%20zinc%20ion n6:molecular%20dynamics n6:quantum%20mechanics
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[6ED727CD49CD]
n4:nazevZdroje
Journal of Computational Chemistry
n4:obor
n17:CE
n4:pocetDomacichTvurcuVysledku
1
n4:pocetTvurcuVysledku
4
n4:projekt
n12:LN00A016
n4:rokUplatneniVysledku
n5:2003
n4:svazekPeriodika
24
n4:tvurceVysledku
Koča, Jaroslav Zhan, Chang-Guo Ornstein, Rick Rittenhouse, Robert
s:issn
0192-8651
s:numberOfPages
11
n7:organizacniJednotka
14310