Sodium (ECMDB02908) (M2MDB000470)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesTransporters (19)XML
Proteins (19)
Record Information
Version2.0
Creation Date2012-05-31 13:57:21 -0600
Update Date2015-09-17 16:24:10 -0600
Secondary Accession Numbers
  • ECMDB02908
Identification
Name:Sodium
DescriptionSodium is a metallic element that is soluble in water in nearly all of its compounds, and is thus present in great quantities in the Earth's oceans and other stagnant bodies of water. In these bodies it is mostly counterbalanced by the chloride ion, causing evaporated ocean water solids to consist mostly of sodium chloride, or common table salt. Sodium ion is also a component of many minerals. Export of sodium from the cell provides the driving force for several secondary active transporters membrane transport proteins, which import glucose, amino acids, and other nutrients into the cell by use of the sodium gradient.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Sodium
  • Sodium ion
Chemical Formula:Na
Weight:Average: 22.9898
Monoisotopic: 22.989769675
InChI Key:FKNQFGJONOIPTF-UHFFFAOYSA-N
InChI:InChI=1S/Na/q+1
CAS number:7440-23-5
IUPAC Name:sodium(1+) ion
Traditional IUPAC Name:sodium(1+) ion
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
State:Solid
Charge:1
Melting point:97.82 °C
Experimental Properties:
PropertyValueSource
LogP:1.011PhysProp
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
Reactions:
SMPDB Pathways:
Biosynthesis of siderophore group nonribosomal peptidesPW000760 ThumbThumb?image type=greyscaleThumb?image type=simple
D-Glutamine and D-glutamate metabolismPW000769 ThumbThumb?image type=greyscaleThumb?image type=simple
GLYCINE BIOSYNTHESISPW000808 ThumbThumb?image type=greyscaleThumb?image type=simple
Galactose metabolismPW000821 ThumbThumb?image type=greyscaleThumb?image type=simple
Glutathione metabolismPW000833 ThumbThumb?image type=greyscaleThumb?image type=simple
L-glutamate metabolismPW000789 ThumbThumb?image type=greyscaleThumb?image type=simple
Porphyrin metabolismPW000936 ThumbThumb?image type=greyscaleThumb?image type=simple
glutathione metabolism IIPW001927 ThumbThumb?image type=greyscaleThumb?image type=simple
glutathione metabolism IIIPW002018 ThumbThumb?image type=greyscaleThumb?image type=simple
inner membrane transportPW000786 ThumbThumb?image type=greyscaleThumb?image type=simple
isoleucine biosynthesisPW000818 ThumbThumb?image type=greyscaleThumb?image type=simple
peptidoglycan biosynthesis IPW000906 ThumbThumb?image type=greyscaleThumb?image type=simple
peptidoglycan biosynthesis I 2PW002062 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-25bf08b0ab99f8116a31View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9000000000-fba837e9c7559de06780View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-9000000000-fba837e9c7559de06780View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9000000000-fba837e9c7559de06780View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-9000000000-1d278094c49273af723fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-1d278094c49273af723fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-1d278094c49273af723fView in MoNA
References
References:
  • Achard JM, Hadchouel J, Faure S, Jeunemaitre X: Inherited sodium avid states. Adv Chronic Kidney Dis. 2006 Apr;13(2):118-23. Pubmed: 16580612
  • Felder RA, Jose PA: Mechanisms of disease: the role of GRK4 in the etiology of essential hypertension and salt sensitivity. Nat Clin Pract Nephrol. 2006 Nov;2(11):637-50. Pubmed: 17066056
  • Fox CS, Larson MG, Hwang SJ, Leip EP, Rifai N, Levy D, Benjamin EJ, Murabito JM, Meigs JB, Vasan RS: Cross-sectional relations of serum aldosterone and urine sodium excretion to urinary albumin excretion in a community-based sample. Kidney Int. 2006 Jun;69(11):2064-9. Pubmed: 16572107
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • SCHULTZ, S. G., WILSON, N. L., EPSTEIN, W. (1962). "Cation transport in Escherichia coli. II. Intracellular chloride concentration." J Gen Physiol 46:159-166. Pubmed: 13909522
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID26708
HMDB IDHMDB00588
Pubchem Compound ID923
Kegg IDC01330
ChemSpider ID899
WikipediaSodium
BioCyc IDNA+
EcoCyc IDNA+
Ligand ExpoNA

Transporters

Protein Details
1. Melibiose carrier protein
General function:
Involved in transporter activity
Specific function:
Responsible for melibiose transport. It is capable of using hydrogen, sodium, and lithium cations as coupling cations for cotransport, depending on the particular sugar transported (symport system)
Gene Name:
melB
Uniprot ID:
P02921
Molecular weight:
52217
Protein Details
2. Sodium/proline symporter
General function:
Involved in proline:sodium symporter activity
Specific function:
Catalyzes the sodium-dependent uptake of extracellular L-proline. This protein is also capable of using lithium as the transport cation. Also catalyzes the uptake of propionate
Gene Name:
putP
Uniprot ID:
P07117
Molecular weight:
54344
Protein Details
3. Uncharacterized transporter yaaJ
General function:
Involved in sodium:amino acid symporter activity
Specific function:
Specific function unknown
Gene Name:
yaaJ
Uniprot ID:
P30143
Molecular weight:
51662
Protein Details
4. Sodium/glutamate symport carrier protein
General function:
Involved in glutamate:sodium symporter activity
Specific function:
Catalyzes the sodium-dependent uptake of extracellular glutamate
Gene Name:
gltS
Uniprot ID:
P0AER8
Molecular weight:
42425
Protein Details
5. Multidrug translocase mdfA
General function:
Involved in transmembrane transport
Specific function:
Efflux pump driven by the proton motive force. Confers resistance to basic, aromatic and lipophilic drugs as well as neutral, non-aromatic, zwitterionic or non-aromatic hydrophilic antibiotics
Gene Name:
cmr
Uniprot ID:
P0AEY8
Molecular weight:
44320
Protein Details
6. Serine/threonine transporter sstT
General function:
Involved in sodium:dicarboxylate symporter activity
Specific function:
Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
Gene Name:
sstT
Uniprot ID:
P0AGE4
Molecular weight:
43477
Protein Details
7. Sodium/pantothenate symporter
General function:
Involved in sodium ion transmembrane transporter activity
Specific function:
Catalyzes the sodium-dependent uptake of extracellular pantothenate
Gene Name:
panF
Uniprot ID:
P16256
Molecular weight:
51717
Protein Details
8. Cation/acetate symporter ActP
General function:
Involved in transporter activity
Specific function:
Transports acetate. Also able to transport glycolate
Gene Name:
actP
Uniprot ID:
P32705
Molecular weight:
59197
Protein Details
9. Multidrug resistance protein mdtK
General function:
Involved in drug transmembrane transporter activity
Specific function:
Multidrug efflux pump that functions probably as a Na(+)/drug antiporter. Confers resistance to many drugs such as fluoroquinolones (norfloxacin, ciprofloxacin, enoxacin), tetraphenylphosphonium ion (TPP), deoxycholate, doxorubicin, trimethoprim, chloramphenicol, fosfomycin, acriflavine, ethidium bromide and benzalkonium
Gene Name:
mdtK
Uniprot ID:
P37340
Molecular weight:
49447
Protein Details
10. Calcium/proton antiporter
General function:
Involved in cation transmembrane transporter activity
Specific function:
According to PubMed:8496184 the natural activity of this protein is as a calcium/proton antiporter, but it can act as a weak sodium/proton antiporter. The presence of a preferred substrate and normal pH cytoplasmic values might prevent significant sodium/proton antiporter activity
Gene Name:
chaA
Uniprot ID:
P31801
Molecular weight:
39168
Protein Details
11. Na(+)/H(+) antiporter nhaA
General function:
Involved in sodium ion transport
Specific function:
Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. Catalyzes the exchange of 2 H(+) per Na(+). Can mediate sodium uptake when a transmembrane pH gradient is applied. Active at alkaline pH. Activity is strongly down- regulated below pH 6.5
Gene Name:
nhaA
Uniprot ID:
P13738
Molecular weight:
41355
Protein Details
12. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
13. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
14. Uncharacterized symporter yidK
General function:
Involved in transporter activity
Specific function:
Specific function unknown
Gene Name:
yidK
Uniprot ID:
P31448
Molecular weight:
62084
Protein Details
15. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
16. Inner membrane protein yrbG
General function:
Involved in transmembrane transport
Specific function:
Specific function unknown
Gene Name:
yrbG
Uniprot ID:
P45394
Molecular weight:
34740
Protein Details
17. Na(+)/H(+) antiporter nhaB
General function:
Involved in sodium:hydrogen antiporter activity
Specific function:
Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. Catalyzes the exchange of 3 H(+) per 2 Na(+). Has a high affinity for sodium, but can also transport lithium. Activity is weakly pH-dependent. Essential for regulation of intracellular pH under alkaline conditions
Gene Name:
nhaB
Uniprot ID:
P0AFA7
Molecular weight:
56728
Protein Details
18. Branched-chain amino acid transport system 2 carrier protein
General function:
Involved in branched-chain aliphatic amino acid transmembrane transporter activity
Specific function:
Component of the LIV-II transport system for branched- chain amino acids. This LIV-II transport system may be H(+)- coupled
Gene Name:
brnQ
Uniprot ID:
P0AD99
Molecular weight:
46208
Protein Details
19. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368