Abstract
This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of alkali metal ion complexes containing low-molecular-weight ligands of biological relevance, mostly obtained from the Cambridge Structural Database (the CSD version 5.35 updated to February 2014). These ligands include (i) amino acids and small peptides, (ii) nucleic acid constituents (excluding quadruplexes and other oligonucleotides), (iii) simple carbohydrates, and (iv) naturally occurring antibiotic ionophores. For some representative complexes of these ligands, some details on the environment of the metal coordination and structural characteristics are described.
Please cite as: Met. Ions Life Sci. 16 (2016) 27–101
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- aa:
-
amino acid
- Ade:
-
adenine
- Ado–2H:
-
adenosinate dianion
- ADP:
-
adenosine diphosphate
- ADPH2:
-
diprotonated adenosine diphosphate
- Ala–H:
-
alaninate monoanion
- AMP:
-
adenosine monophosphate
- AMPH:
-
monoprotonated adenosine monophosphate
- AppppA (Ap4A):
-
P 1,P 4-bis(5’-adenosyl)tetraphosphate
- ApU:
-
adenylyl-3’,5’-uridine
- ApT:
-
adenylyl-3’,5’-thymidine
- ATP:
-
adenosine 5’-triphosphate
- ATPH2:
-
diprotonated adenosine 5’-triphosphate
- C+ :
-
cytosinium monocation
- CCDC:
-
Cambridge Crystallographic Data Centre
- CDP:
-
cytidine diphosphate
- CDPcholine:
-
cytidine diphosphocholine
- CDPethanolamine:
-
cytidine diphosphoethanolamine
- Cha:
-
cyclohexylalanyl
- CMP:
-
cytidine monophosphate
- CMPH:
-
monoprotonated cytidine monophosphate
- CpG:
-
cytidylyl-3’,5’-guanosine
- CSD:
-
Cambridge Structural Database
- Cyt:
-
cytosine
- d:
-
deoxyribose
- d:
-
dexter (optical isomer named after Latin)
- dCMP:
-
deoxycytidine monophosphate
- d(CpG):
-
deoxycytidylyl-3’,5’-deoxyguanosine
- dien:
-
diethylenetriamine
- dGMP:
-
deoxyguanosine monophosphate
- DMSO:
-
dimethylformamide
- en:
-
ethylenediamine
- 9-Et-azacrown-Ade:
-
16-(2-(9H-adenin-9-yl)ethyl)-16-aza-1,4,7,10,13-pentaoxa-cyclooctadecane
- 1-EtThy:
-
N1-ethylthymine
- Fru:
-
fructose
- gA, gB, gC, gD:
-
gramicidin A, B, C, D
- Gal:
-
galactose
- Glc:
-
glucose
- GlyGly:
-
glycylglycine
- Gly–H:
-
glycinate monoanion
- GlyTyr:
-
glycyltyrosine
- GMP:
-
guanosine monophosphate
- GMPH:
-
monoprotonated guanosine monophosphate
- GpC:
-
guanylyl-3’,5’-cytidine
- Gua:
-
guanine
- HyIv:
-
hydroxyisovalerate
- Hyp:
-
hypoxanthine
- IMP:
-
inosine monophosphate
- IMPH:
-
monoprotonated inosine monophosphate
- Ino–H:
-
inosinate monoanion
- iPr:
-
isopropyl
- isoGuo:
-
isoguanosine
- l :
-
leavus (optical isomer named after Latin)
- L:
-
ligand
- Lac:
-
lactic acid
- M:
-
metal ion
- 1-Me-Cyt:
-
N1-methylcytosine
- 1-MeCyt–H:
-
N1-methylcytosinate monoanion
- Me4dae:
-
N,N,N’,N’-tetramethyl-1,2-diaminoethane
- 9-MeGua:
-
N9-methylguanine
- 1-MeThy:
-
N1-methylthymine
- 1-MeThy–H:
-
N1-methylthyminate monoanion
- 1-MeUra–H:
-
N1-methyluracilate monoanion
- MeVal:
-
methylvalyl
- NAD:
-
5’-nicotinamide-ribosyl-5’-adenyl-pyrophosphate
- O(P):
-
oxygen atom of the phosphate group
- 1-Pr-azacrown–Thy:
-
(3-(1-thyminyl)propyl)-4,13-diaza-18-crown-6
- Pro–H:
-
prolinate monoanion
- pTpT:
-
5’-phosphoryl-thymidylyl-3’,5’-thymidine
- THF:
-
tetrahydrofuran
- Thr–H:
-
threonate monoanion
- Thy:
-
thymine
- Thy–H:
-
thyminate monoanion
- TMP:
-
thymidine monophosphate
- UDP:
-
uridine 5’-diphosphate
- UDPglucose:
-
uridine diphosphate glucose
- UDPH:
-
monoprotonated uridine diphosphate
- UMP:
-
uridine monophosphate
- UMPH:
-
monoprotonated uridine monophosphate
- Ura:
-
uracil
- Urd–3H:
-
uridinate trianion
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D. Łowicki, A. Huczyński, BioMed Research International, 2013, 2013, Article ID 742149.
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Aoki, K., Murayama, K., Hu, NH. (2016). Solid State Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance. In: Sigel, A., Sigel, H., Sigel, R. (eds) The Alkali Metal Ions: Their Role for Life. Metal Ions in Life Sciences, vol 16. Springer, Cham. https://doi.org/10.1007/978-3-319-21756-7_3
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