3RUE - JenaLib

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Title :   ALTERNATIVE ANALOGS AS VIABLE SUBSTRATES OF UDP-HEXOSE 4-EPIMERASES

Authors :   V. S. Bhatt, W. Guan, P. G. Wang

Date :   05 May 11 (Deposition) - 25 May 11 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,S,b
Biol. Unit 1: A,S  (1x)
Biol. Unit 2: B (1x),b (1x)

Keywords :   Rossmann Fold, Udp-Hexose 4-Epimerases, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. S. Bhatt, W. Guan, P. G. Wang
Alternative Analogs As Viable Substrates Of Udp-Hexose 4-Epimerases
To Be Published
PubMed: search

Molecule 1 - WBGU
	Chains	:	A, B, S, b
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	WBGU
	Organism Scientific	:	PLESIOMONAS SHIGELLOIDES
	Organism Taxid	:	703

		1	2	3	4
Asymmetric Unit	:	A	B	S	b
Biological Unit 1 (1x)	:	A		S
Biological Unit 2 (1x)	:		B (1x)		b (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	UNL	4	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	UNL	2	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:23 , ALA A:25 , GLY A:26 , PHE A:27 , ILE A:28 , ASP A:47 , ASN A:48 , SER A:50 , THR A:51 , GLY A:52 , GLY A:77 , ASP A:78 , ILE A:79 , GLN A:98 , ALA A:100 , THR A:117 , ALA A:140 , ALA A:141 , TYR A:166 , LYS A:170 , VAL A:196	BINDING SITE FOR RESIDUE NAD A 344
2	AC2	SOFTWARE	GLY B:23 , ALA B:25 , GLY B:26 , PHE B:27 , ILE B:28 , ASP B:47 , ASN B:48 , PHE B:49 , SER B:50 , THR B:51 , GLY B:52 , GLY B:77 , ASP B:78 , ILE B:79 , GLN B:98 , ALA B:99 , ALA B:100 , THR B:117 , ALA B:141 , TYR B:166 , LYS B:170 , TYR B:193 , ASN B:195 , VAL B:196	BINDING SITE FOR RESIDUE NAD B 343
3	AC3	SOFTWARE	GLY S:23 , ALA S:25 , GLY S:26 , PHE S:27 , ILE S:28 , ASN S:48 , SER S:50 , THR S:51 , GLY S:52 , GLY S:77 , ASP S:78 , ILE S:79 , GLN S:98 , ALA S:99 , ALA S:100 , LEU S:101 , THR S:117 , ALA S:140 , TYR S:166 , LYS S:170 , TYR S:193 , VAL S:196	BINDING SITE FOR RESIDUE NAD S 343
4	AC4	SOFTWARE	GLY b:23 , ALA b:25 , GLY b:26 , PHE b:27 , ILE b:28 , ASP b:47 , ASN b:48 , SER b:50 , THR b:51 , GLY b:52 , GLY b:77 , ASP b:78 , ILE b:79 , GLN b:98 , ALA b:99 , ALA b:100 , THR b:117 , ALA b:140 , TYR b:166 , LYS b:170 , TYR b:193 , VAL b:196	BINDING SITE FOR RESIDUE NAD b 343

(no "SS Bond" information available for 3RUE)

Asymmetric Unit

No.	Residues
1	Leu A:152	-	Pro A:153
2	Leu B:152	-	Pro B:153
3	Leu S:152	-	Pro S:153
4	Leu b:152	-	Pro b:153

(no "SAP(SNP)/Variant" information available for 3RUE)

(no "PROSITE Motif" information available for 3RUE)

(no "Exon" information available for 3RUE)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:336
 aligned with GNE_PLESH | Q7BJX9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
            GNE_PLESH     4 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHHIDKLSIKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 344
               SCOP domains d3ruea_ A: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeee..ee...........hhhhhhhhhhhhh...eee.....ee..eehhhhhhhhhhhhh.hhhhh.eeeee.....eehhhhhhhhhhhhhh...-----.eee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rue A   1 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHH-----IKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      |  -  |    300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                        287   293

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with GNE_PLESH | Q7BJX9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
            GNE_PLESH     4 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHHIDKLSIKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 344
               SCOP domains d3rueb_ B: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeee..ee...........hhhhhhhhhhhhh...eee.....ee..eehhhhhhhhhhhhh.hhhhh.eeeee.....eehhhhhhhhhhhhhh...-----.eee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rue B   1 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHH-----IKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      |  -  |    300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                        287   293

Chain S from PDB  Type:PROTEIN  Length:336
 aligned with GNE_PLESH | Q7BJX9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
            GNE_PLESH     4 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHHIDKLSIKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 344
               SCOP domains d3rues_ S: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh..hhhhhh.eeeee....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeee..ee...........hhhhhhhhhhhhh...eee.....ee..eehhhhhhhhhhhhh.hhhhh.eeeee.....eehhhhhhhhhhhhhh...-----.eee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rue S   1 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHH-----IKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      |  -  |    300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                        287   293

Chain b from PDB  Type:PROTEIN  Length:336
 aligned with GNE_PLESH | Q7BJX9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
            GNE_PLESH     4 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHHIDKLSIKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 344
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh..hhhhhh.eeeee....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeee..ee...........hhhhhhhhhhhhh...eee.....ee..eehhhhhhhhhhhhh.hhhhh.eeeee.....eehhhhhhhhhhhhhh...-----.eee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rue b   1 YMSRYEEITQQLIFSPKTWLITGVAGFIGSNLLEKLLKLNQVVIGLDNFSTGHQYNLDEVKTLVSTEQWSRFCFIEGDIRDLTTCEQVMKGVDHVLHQAALGSVPRSIVDPITTNATNITGFLNILHAAKNAQVQSFTYAASSSTYGDHPALPKVEENIGNPLSPYAVTKYVNEIYAQVYARTYGFKTIGLRYFNVFGRRQDPNGAYAAVIPKWTAAMLKGDDVYINGDGETSRDFCYIDNVIQMNILSALAKDSAKDNIYNVAVGDRTTLNELSGYIYDELNLIHH-----IKYREFRSGDVRHSQADVTKAIDLLKYRPNIKIREGLRLSMPWYVRFLK 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      |  -  |    300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                        287   293

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: automated matches (114)

Plesiomonas shigelloides [TaxId: 703] (9)

1a	d3ruea_	A:
1b	d3rueb_	B:
1c	d3rues_	S:

(no "CATH Domain" information available for 3RUE)

(no "Pfam Domain" information available for 3RUE)

Asymmetric Unit(hide GO term definitions)

Chain A,B,S,b (GNE_PLESH | Q7BJX9)

molecular function
	GO:0003974	UDP-N-acetylglucosamine 4-epimerase activity	Catalysis of the reaction: UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-galactosamine.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016857	racemase and epimerase activity, acting on carbohydrates and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
	GO:0009243	O antigen biosynthetic process	The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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	Cis Peptide Bonds
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		Leu b:152 - Pro b:153	[ RasMol ]

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	GNE_PLESH \| Q7BJX9	:	3lu1 3ru7 3ru9 3rua 3ruc 3rud 3ruf 3ruh

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Ligands, Modified Residues, Ions (2, 8)

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