Sodium (YMDB00020)

Identification
YMDB IDYMDB00020
NameSodium
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionSodium, also known as Na+ or sodium ion, belongs to the class of inorganic compounds known as homogeneous alkali metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a alkali metal atom. Sodium is a weakly acidic compound (based on its pKa). Sodium exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 11Na
  • NA
  • Na(+)
  • Na+
  • Natrium
  • Sodium
  • Sodium cation
  • Sodium ion
  • Sodium(1+)
CAS number7440-23-5
WeightAverage: 22.98976928
Monoisotopic: 22.989769675
InChI KeyFKNQFGJONOIPTF-UHFFFAOYSA-N
InChIInChI=1S/Na/q+1
IUPAC Namesodium(1+) ion
Traditional IUPAC Namesodium(1+) ion
Chemical FormulaNa
SMILES[Na+]
Chemical Taxonomy
Description belongs to the class of inorganic compounds known as homogeneous alkali metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a alkali metal atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous alkali metal compounds
Sub ClassNot Available
Direct ParentHomogeneous alkali metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous alkali metal
Molecular FrameworkNot Available
External Descriptors
Physical Properties
StateSolid
Charge1
Melting point97.82 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
logP-0.77ChemAxon
pKa (Strongest Acidic)3.09ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity0 m³·mol⁻¹ChemAxon
Polarizability1.78 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
  • extracellular
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Methane metabolismec00680 Map00680
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
1740 ± 237 µM hops, malted barleyanaerobicBaker's yeastAlcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
1740 ± 0 µM grape juiceanaerobicBaker's yeastAlcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Conversion Details Here
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9000000000-fba837e9c7559de06780JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-9000000000-fba837e9c7559de06780JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9000000000-fba837e9c7559de06780JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-9000000000-1d278094c49273af723fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-1d278094c49273af723fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-1d278094c49273af723fJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Catty, P., de Kerchove d'Exaerde, A., Goffeau, A. (1997). "The complete inventory of the yeast Saccharomyces cerevisiae P-type transport ATPases." FEBS Lett 409:325-332.9224683
  • Benito, B., Garciadeblas, B., Rodriguez-Navarro, A. (2002). "Potassium- or sodium-efflux ATPase, a key enzyme in the evolution of fungi." Microbiology 148:933-941.11932440
  • Logg, K., Warringer, J., Hashemi, S. H., Kall, M., Blomberg, A. (2008). "The sodium pump Ena1p provides mechanistic insight into the salt sensitivity of vacuolar protein sorting mutants." Biochim Biophys Acta 1783:974-984.18395523
  • Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
  • Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID29101
HMDB IDHMDB00588
Pubchem Compound ID923
Kegg IDC01330
ChemSpider ID24770394
FOODB IDFDB031052
WikipediaSodium
BioCyc IDNA+

Transporters

Protein Details
1. Sodium transport ATPase 1
General function:
Involved in nucleotide binding
Specific function:
This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the sodium or lithium ions to allow salt tolerance. Is negatively modulated by SIS2/HAL3
Gene Name:
ENA1
Uniprot ID:
P13587
Molecular weight:
120356.0
Reactions
ATP + H(2)O + Na(+)(In) → ADP + phosphate + Na(+)(Out).
Protein Details
2. Sodium transport ATPase 5
General function:
Involved in nucleotide binding
Specific function:
This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of sodium or lithium ions to allow salt tolerance
Gene Name:
ENA5
Uniprot ID:
Q12691
Molecular weight:
120295.0
Reactions
ATP + H(2)O + Na(+)(In) → ADP + phosphate + Na(+)(Out).
Protein Details
3. Sodium transport ATPase 2
General function:
Involved in nucleotide binding
Specific function:
This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of sodium or lithiums ions to allow salt tolerance
Gene Name:
ENA2
Uniprot ID:
Q01896
Molecular weight:
120316.0
Reactions
ATP + H(2)O + Na(+)(In) → ADP + phosphate + Na(+)(Out).
Protein Details
4. Na(+)/H(+) antiporter
General function:
Involved in sodium:hydrogen antiporter activity
Specific function:
Sodium export from cell, takes up external protons in exchange for internal sodium ions
Gene Name:
NHA1
Uniprot ID:
Q99271
Molecular weight:
109368.0