6TC3

Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ornithine capture by a translating ribosome controls bacterial polyamine synthesis.

Herrero Del Valle, A.Seip, B.Cervera-Marzal, I.Sacheau, G.Seefeldt, A.C.Innis, C.A.

(2020) Nat Microbiol 5: 554-561

  • DOI: 10.1038/s41564-020-0669-1
  • Primary Citation of Related Structures:  
    6TBV, 6TC3

  • PubMed Abstract: 
  • Polyamines are essential metabolites that play an important role in cell growth, stress adaptation and microbial virulence 1-3 . To survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues 2 ...

    Polyamines are essential metabolites that play an important role in cell growth, stress adaptation and microbial virulence 1-3 . To survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues 2 . Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF 4 , via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryogenic electron microscopy structure of an Escherichia coli ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor 1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.


    Organizational Affiliation

    Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France. axel.innis@inserm.fr.



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Entity ID: 2
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30S ribosomal protein S2B [auth S021]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3C [auth S031]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4D [auth S041]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5E [auth S051]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6F [auth S061]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7G [auth S071]179Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8H [auth S081]130Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9I [auth S091]130Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10J [auth S101]103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11K [auth S111]129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S12L [auth S121]124Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S13M [auth S131]118Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S14N [auth S141]102Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S15O [auth S151]89Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S16P [auth S161]82Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17Q [auth S171]84Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S18R [auth S181]75Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S19S [auth S191]92Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20T [auth S201]87Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S21U [auth S211]71Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L2X [auth L021]273Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3Y [auth L031]209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4Z [auth L041]201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5AA [auth L051]179Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6BA [auth L061]177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L9CA [auth L091]149Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L31DA [auth L311]70Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L13EA [auth L131]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14FA [auth L141]123Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15GA [auth L151]144Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16HA [auth L161]136Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L17IA [auth L171]127Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18JA [auth L181]117Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L19KA [auth L191]115Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L20LA [auth L201]118Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L21MA [auth L211]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22NA [auth L221]110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23OA [auth L231]100Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L24PA [auth L241]104Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25QA [auth L251]94Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L27RA [auth L271]85Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28SA [auth L281]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29TA [auth L291]63Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L30UA [auth L301]59Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L32VA [auth L321]57Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L33WA [auth L331]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34XA [auth L341]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35YA [auth L351]65Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L36ZA [auth L361]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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SpeFLAB [auth SPE1]34Escherichia coli K-12Mutation(s): 0 
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16S rRNAA [auth 16S1]1534Escherichia coli K-12
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23S rRNAV [auth 23S1]2897Escherichia coli K-12
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5S rRNAW [auth 05S1]120Escherichia coli K-12
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    mRNABB [auth MRN1]7Escherichia coli K-12
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    P-site Arg-tRNACB [auth PTR1]76Escherichia coli K-12
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    Ligands 5 Unique
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    ORN
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    XL [auth 23S1]L-ornithine
    C5 H12 N2 O2
    AHLPHDHHMVZTML-BYPYZUCNSA-N
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    ZN
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    ALB [auth L311], OL [auth S021], SNB [auth L361]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
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    K
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    AF [auth 16S1] , AW [auth 23S1] , AX [auth 23S1] , AY [auth 23S1] , AZ [auth 23S1] , BF [auth 16S1] , BW [auth 23S1] , BX [auth 23S1] , 
    AF [auth 16S1], AW [auth 23S1], AX [auth 23S1], AY [auth 23S1], AZ [auth 23S1], BF [auth 16S1], BW [auth 23S1], BX [auth 23S1], BY [auth 23S1], BZ [auth 23S1], CF [auth 16S1], CW [auth 23S1], CX [auth 23S1], CY [auth 23S1], CZ [auth 23S1], DF [auth 16S1], DW [auth 23S1], DX [auth 23S1], DY [auth 23S1], DZ [auth 23S1], EF [auth 16S1], EW [auth 23S1], EX [auth 23S1], EY [auth 23S1], EZ [auth 23S1], FF [auth 16S1], FW [auth 23S1], FX [auth 23S1], FY [auth 23S1], FZ [auth 23S1], GF [auth 16S1], GW [auth 23S1], GX [auth 23S1], GY [auth 23S1], GZ [auth 23S1], HF [auth 16S1], HW [auth 23S1], HX [auth 23S1], HY [auth 23S1], HZ [auth 23S1], IF [auth 16S1], IV [auth 23S1], IW [auth 23S1], IX [auth 23S1], IY [auth 23S1], IZ [auth 23S1], JF [auth 16S1], JV [auth 23S1], JW [auth 23S1], JX [auth 23S1], JY [auth 23S1], JZ [auth 23S1], KF [auth 16S1], KV [auth 23S1], KW [auth 23S1], KX [auth 23S1], KY [auth 23S1], LF [auth 16S1], LV [auth 23S1], LW [auth 23S1], LX [auth 23S1], LY [auth 23S1], ME [auth 16S1], MF [auth 16S1], MV [auth 23S1], MW [auth 23S1], MX [auth 23S1], MY [auth 23S1], NE [auth 16S1], NF [auth 16S1], NIB [auth 05S1], NL [auth 16S1], NV [auth 23S1], NW [auth 23S1], NX [auth 23S1], NY [auth 23S1], OE [auth 16S1], OF [auth 16S1], OV [auth 23S1], OW [auth 23S1], OX [auth 23S1], OY [auth 23S1], PE [auth 16S1], PF [auth 16S1], PV [auth 23S1], PW [auth 23S1], PX [auth 23S1], PY [auth 23S1], QE [auth 16S1], QF [auth 16S1], QV [auth 23S1], QW [auth 23S1], QX [auth 23S1], QY [auth 23S1], RE [auth 16S1], RF [auth 16S1], RV [auth 23S1], RW [auth 23S1], RX [auth 23S1], RY [auth 23S1], SE [auth 16S1], SF [auth 16S1], SV [auth 23S1], SW [auth 23S1], SX [auth 23S1], SY [auth 23S1], TE [auth 16S1], TF [auth 16S1], TV [auth 23S1], TW [auth 23S1], TX [auth 23S1], TY [auth 23S1], UE [auth 16S1], UF [auth 16S1], UV [auth 23S1], UW [auth 23S1], UX [auth 23S1], UY [auth 23S1], VE [auth 16S1], VF [auth 16S1], VV [auth 23S1], VW [auth 23S1], VX [auth 23S1], VY [auth 23S1], WE [auth 16S1], WF [auth 16S1], WV [auth 23S1], WW [auth 23S1], WX [auth 23S1], WY [auth 23S1], XE [auth 16S1], XF [auth 16S1], XJB [auth L031], XV [auth 23S1], XW [auth 23S1], XX [auth 23S1], XY [auth 23S1], YE [auth 16S1], YV [auth 23S1], YW [auth 23S1], YX [auth 23S1], YY [auth 23S1], ZE [auth 16S1], ZV [auth 23S1], ZW [auth 23S1], ZX [auth 23S1], ZY [auth 23S1]
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
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    MG
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    AC [auth 16S1] , AD [auth 16S1] , AE [auth 16S1] , AM [auth 23S1] , AN [auth 23S1] , AO [auth 23S1] , AP [auth 23S1] , AQ [auth 23S1] , 
    AC [auth 16S1], AD [auth 16S1], AE [auth 16S1], AM [auth 23S1], AN [auth 23S1], AO [auth 23S1], AP [auth 23S1], AQ [auth 23S1], AR [auth 23S1], AS [auth 23S1], AT [auth 23S1], AU [auth 23S1], AV [auth 23S1], BC [auth 16S1], BD [auth 16S1], BE [auth 16S1], BM [auth 23S1], BN [auth 23S1], BO [auth 23S1], BOB [auth PTR1], BP [auth 23S1], BQ [auth 23S1], BR [auth 23S1], BS [auth 23S1], BT [auth 23S1], BU [auth 23S1], BV [auth 23S1], CC [auth 16S1], CD [auth 16S1], CE [auth 16S1], CM [auth 23S1], CN [auth 23S1], CO [auth 23S1], CP [auth 23S1], CQ [auth 23S1], CR [auth 23S1], CS [auth 23S1], CT [auth 23S1], CU [auth 23S1], CV [auth 23S1], DB [auth 16S1], DC [auth 16S1], DD [auth 16S1], DE [auth 16S1], DM [auth 23S1], DN [auth 23S1], DO [auth 23S1], DP [auth 23S1], DQ [auth 23S1], DR [auth 23S1], DS [auth 23S1], DT [auth 23S1], DU [auth 23S1], DV [auth 23S1], EB [auth 16S1], EC [auth 16S1], ED [auth 16S1], EE [auth 16S1], EM [auth 23S1], EN [auth 23S1], EO [auth 23S1], EP [auth 23S1], EQ [auth 23S1], ER [auth 23S1], ES [auth 23S1], ET [auth 23S1], EU [auth 23S1], EV [auth 23S1], FB [auth 16S1], FC [auth 16S1], FD [auth 16S1], FE [auth 16S1], FM [auth 23S1], FN [auth 23S1], FO [auth 23S1], FP [auth 23S1], FQ [auth 23S1], FR [auth 23S1], FS [auth 23S1], FT [auth 23S1], FU [auth 23S1], FV [auth 23S1], GB [auth 16S1], GC [auth 16S1], GD [auth 16S1], GE [auth 16S1], GM [auth 23S1], GN [auth 23S1], GO [auth 23S1], GP [auth 23S1], GQ [auth 23S1], GR [auth 23S1], GS [auth 23S1], GT [auth 23S1], GU [auth 23S1], GV [auth 23S1], HB [auth 16S1], HC [auth 16S1], HD [auth 16S1], HE [auth 16S1], HM [auth 23S1], HN [auth 23S1], HO [auth 23S1], HP [auth 23S1], HQ [auth 23S1], HR [auth 23S1], HS [auth 23S1], HT [auth 23S1], HU [auth 23S1], HV [auth 23S1], IB [auth 16S1], IC [auth 16S1], ID [auth 16S1], IE [auth 16S1], IIB [auth 23S1], IM [auth 23S1], IN [auth 23S1], IO [auth 23S1], IP [auth 23S1], IQ [auth 23S1], IR [auth 23S1], IS [auth 23S1], IT [auth 23S1], IU [auth 23S1], JB [auth 16S1], JC [auth 16S1], JD [auth 16S1], JE [auth 16S1], JIB [auth 23S1], JM [auth 23S1], JN [auth 23S1], JO [auth 23S1], JP [auth 23S1], JQ [auth 23S1], JR [auth 23S1], JS [auth 23S1], JT [auth 23S1], JU [auth 23S1], KB [auth 16S1], KC [auth 16S1], KD [auth 16S1], KE [auth 16S1], KIB [auth 23S1], KM [auth 23S1], KN [auth 23S1], KO [auth 23S1], KP [auth 23S1], KQ [auth 23S1], KR [auth 23S1], KS [auth 23S1], KT [auth 23S1], KU [auth 23S1], LB [auth 16S1], LC [auth 16S1], LD [auth 16S1], LE [auth 16S1], LIB [auth 23S1], LM [auth 23S1], LN [auth 23S1], LO [auth 23S1], LP [auth 23S1], LQ [auth 23S1], LR [auth 23S1], LS [auth 23S1], LT [auth 23S1], LU [auth 23S1], MB [auth 16S1], MC [auth 16S1], MD [auth 16S1], MIB [auth 23S1], MM [auth 23S1], MN [auth 23S1], MO [auth 23S1], MP [auth 23S1], MQ [auth 23S1], MR [auth 23S1], MS [auth 23S1], MT [auth 23S1], MU [auth 23S1], NB [auth 16S1], NC [auth 16S1], ND [auth 16S1], NM [auth 23S1], NN [auth 23S1], NO [auth 23S1], NP [auth 23S1], NQ [auth 23S1], NR [auth 23S1], NS [auth 23S1], NT [auth 23S1], NU [auth 23S1], OB [auth 16S1], OC [auth 16S1], OD [auth 16S1], OM [auth 23S1], ON [auth 23S1], OO [auth 23S1], OP [auth 23S1], OQ [auth 23S1], OR [auth 23S1], OS [auth 23S1], OT [auth 23S1], OU [auth 23S1], PB [auth 16S1], PC [auth 16S1], PD [auth 16S1], PM [auth 23S1], PN [auth 23S1], PO [auth 23S1], PP [auth 23S1], PQ [auth 23S1], PR [auth 23S1], PS [auth 23S1], PT [auth 23S1], PU [auth 23S1], QB [auth 16S1], QC [auth 16S1], QD [auth 16S1], QM [auth 23S1], QN [auth 23S1], QO [auth 23S1], QP [auth 23S1], QQ [auth 23S1], QR [auth 23S1], QS [auth 23S1], QT [auth 23S1], QU [auth 23S1], RB [auth 16S1], RC [auth 16S1], RD [auth 16S1], RM [auth 23S1], RN [auth 23S1], RO [auth 23S1], RP [auth 23S1], RQ [auth 23S1], RR [auth 23S1], RS [auth 23S1], RT [auth 23S1], RU [auth 23S1], SB [auth 16S1], SC [auth 16S1], SD [auth 16S1], SM [auth 23S1], SN [auth 23S1], SO [auth 23S1], SP [auth 23S1], SQ [auth 23S1], SR [auth 23S1], SS [auth 23S1], ST [auth 23S1], SU [auth 23S1], TB [auth 16S1], TC [auth 16S1], TD [auth 16S1], TM [auth 23S1], TMB [auth L231], TN [auth 23S1], TNB [auth SPE1], TO [auth 23S1], TP [auth 23S1], TQ [auth 23S1], TR [auth 23S1], TS [auth 23S1], TT [auth 23S1], TU [auth 23S1], UB [auth 16S1], UC [auth 16S1], UD [auth 16S1], UM [auth 23S1], UN [auth 23S1], UO [auth 23S1], UP [auth 23S1], UQ [auth 23S1], UR [auth 23S1], US [auth 23S1], UT [auth 23S1], UU [auth 23S1], VB [auth 16S1], VC [auth 16S1], VD [auth 16S1], VM [auth 23S1], VN [auth 23S1], VO [auth 23S1], VP [auth 23S1], VQ [auth 23S1], VR [auth 23S1], VS [auth 23S1], VT [auth 23S1], VU [auth 23S1], WB [auth 16S1], WC [auth 16S1], WD [auth 16S1], WM [auth 23S1], WN [auth 23S1], WO [auth 23S1], WP [auth 23S1], WQ [auth 23S1], WR [auth 23S1], WS [auth 23S1], WT [auth 23S1], WU [auth 23S1], XB [auth 16S1], XC [auth 16S1], XD [auth 16S1], XM [auth 23S1], XN [auth 23S1], XO [auth 23S1], XP [auth 23S1], XQ [auth 23S1], XR [auth 23S1], XS [auth 23S1], XT [auth 23S1], XU [auth 23S1], YB [auth 16S1], YC [auth 16S1], YD [auth 16S1], YL [auth 23S1], YM [auth 23S1], YN [auth 23S1], YO [auth 23S1], YP [auth 23S1], YQ [auth 23S1], YR [auth 23S1], YS [auth 23S1], YT [auth 23S1], YU [auth 23S1], ZB [auth 16S1], ZC [auth 16S1], ZD [auth 16S1], ZL [auth 23S1], ZM [auth 23S1], ZN [auth 23S1], ZO [auth 23S1], ZP [auth 23S1], ZQ [auth 23S1], ZR [auth 23S1], ZS [auth 23S1], ZT [auth 23S1], ZU [auth 23S1]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
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    UNX
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