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

  • Katsuyuki AokiEmail author
  • Kazutaka Murayama
  • Ning-Hai Hu
Chapter
Part of the Metal Ions in Life Sciences book series (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.

Keywords

Alkali metal ions Amino acids Antibiotic ionophores Carbohydrates Crystal structures Nucleic acid constituents Peptides 

Abbreviations

Regarding the abbreviations of amino acids see Table 1.

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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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Katsuyuki Aoki
    • 1
    Email author
  • Kazutaka Murayama
    • 2
  • Ning-Hai Hu
    • 3
  1. 1.Department of Environmental and Life SciencesToyohashi University of TechnologyToyohashiJapan
  2. 2.Graduate School of Biomedical EngineeringTohoku UniversitySendaiJapan
  3. 3.Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunChina

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