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Solid State Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance

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Part of the book series:Metal Ions in Life Sciences ((MILS,volume 16))

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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Abbreviations

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):

P1,P4-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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Authors and Affiliations

  1. Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, 441-8580, Japan

    Katsuyuki Aoki

  2. Graduate School of Biomedical Engineering, Tohoku University, Aoba, Sendai, 980-8575, Japan

    Kazutaka Murayama

  3. Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China

    Ning-Hai Hu

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  1. Katsuyuki Aoki

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  2. Kazutaka Murayama

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  1. Department of Chemistry Inorganic Chemistry, University of Basel, Basel, Basel Stadt, Switzerland

    Astrid Sigel

  2. Department of Chemistry Inorganic Chemistry, University of Basel, Basel, Switzerland

    Helmut Sigel

  3. Department of Chemistry, University of Zürich, Zürich, Switzerland

    Roland K. O. Sigel

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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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