5OT7

Elongation factor G-ribosome complex captures in the absence of inhibitors.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors.

Mace, K.Giudice, E.Chat, S.Gillet, R.

(2018) Nucleic Acids Res 46: 3211-3217

  • DOI: https://doi.org/10.1093/nar/gky081
  • Primary Citation of Related Structures:  
    5OT7

  • PubMed Abstract: 

    During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis.


  • Organizational Affiliation

    Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France.


Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25F [auth 6]178Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9G [auth 7]146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2H [auth A]235Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3I [auth B]207Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4J [auth C]208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5K [auth D]151Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6L [auth E]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7M [auth F]155Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8N [auth G]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9O [auth H]127Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10P [auth I]99Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11Q [auth J]119Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12R [auth K]125Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13S [auth L]119Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZT [auth M]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15U [auth N]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16V [auth O]84Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17W [auth P]100Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18X [auth Q]70Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Y [auth R]88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Z [auth S]99Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxAA [auth T]25Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GBA [auth U]687Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CA [auth V]78Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28DA [auth W]94Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29EA [auth X]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FA [auth Y]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GA [auth Z]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32HA [auth a]59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33IA [auth b]50Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34JA [auth c]48Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35KA [auth d]64Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36LA [auth e]37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1MA [auth f]227Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2NA [auth g]275Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3OA [auth h]205Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PA [auth i]208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5QA [auth j]179Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6RA [auth k]176Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL10SA [auth l]130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL11TA [auth m]140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein bL12UA [auth n]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13VA [auth o]139Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14WA [auth p]122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15XA [auth q]150Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16YA [auth r]141Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17ZA [auth s]118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18AB [auth t]99Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19BB [auth u]138Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20CB [auth v]117Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21DB [auth w]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22EB [auth x]113Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23FB [auth y]93Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24GB [auth z]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth 1]1,507Thermus thermophilus HB8
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA-PheB [auth 2]76Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNAC [auth 3]15Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
23S Ribosomal RNAD [auth 4]2,901Thermus thermophilus HB8
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S Ribosomal RNAE [auth 5]119Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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US [auth U]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

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NS [auth C],
PS [auth M],
XS [auth e]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 4],
AI [auth 4],
AJ [auth 4],
AK [auth 4],
AL [auth 4],
AM [auth 4],
AN [auth 4],
AO [auth 4],
AP [auth 4],
AQ [auth 4],
AR [auth 4],
AS [auth 4],
AT [auth q],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 4],
BI [auth 4],
BJ [auth 4],
BK [auth 4],
BL [auth 4],
BM [auth 4],
BN [auth 4],
BO [auth 4],
BP [auth 4],
BQ [auth 4],
BR [auth 4],
BS [auth 4],
BT [auth t],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 4],
CI [auth 4],
CJ [auth 4],
CK [auth 4],
CL [auth 4],
CM [auth 4],
CN [auth 4],
CO [auth 4],
CP [auth 4],
CQ [auth 4],
CR [auth 4],
CS [auth 4],
CT [auth t],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 4],
DH [auth 4],
DI [auth 4],
DJ [auth 4],
DK [auth 4],
DL [auth 4],
DM [auth 4],
DN [auth 4],
DO [auth 4],
DP [auth 4],
DQ [auth 4],
DR [auth 4],
DS [auth 4],
DT [auth u],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 4],
EH [auth 4],
EI [auth 4],
EJ [auth 4],
EK [auth 4],
EL [auth 4],
EM [auth 4],
EN [auth 4],
EO [auth 4],
EP [auth 4],
EQ [auth 4],
ER [auth 4],
ES [auth 4],
ET [auth x],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 4],
FH [auth 4],
FI [auth 4],
FJ [auth 4],
FK [auth 4],
FL [auth 4],
FM [auth 4],
FN [auth 4],
FO [auth 4],
FP [auth 4],
FQ [auth 4],
FR [auth 4],
FS [auth 4],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 4],
GH [auth 4],
GI [auth 4],
GJ [auth 4],
GK [auth 4],
GL [auth 4],
GM [auth 4],
GN [auth 4],
GO [auth 4],
GP [auth 4],
GQ [auth 4],
GR [auth 4],
GS [auth 4],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 4],
HH [auth 4],
HI [auth 4],
HJ [auth 4],
HK [auth 4],
HL [auth 4],
HM [auth 4],
HN [auth 4],
HO [auth 4],
HP [auth 4],
HQ [auth 4],
HR [auth 4],
HS [auth 4],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 4],
IH [auth 4],
II [auth 4],
IJ [auth 4],
IK [auth 4],
IL [auth 4],
IM [auth 4],
IN [auth 4],
IO [auth 4],
IP [auth 4],
IQ [auth 4],
IR [auth 4],
IS [auth 4],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 4],
JH [auth 4],
JI [auth 4],
JJ [auth 4],
JK [auth 4],
JL [auth 4],
JM [auth 4],
JN [auth 4],
JO [auth 4],
JP [auth 4],
JQ [auth 4],
JR [auth 4],
JS [auth 4],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 4],
KH [auth 4],
KI [auth 4],
KJ [auth 4],
KK [auth 4],
KL [auth 4],
KM [auth 4],
KN [auth 4],
KO [auth 4],
KP [auth 4],
KQ [auth 4],
KR [auth 4],
KS [auth 4],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 4],
LH [auth 4],
LI [auth 4],
LJ [auth 4],
LK [auth 4],
LL [auth 4],
LM [auth 4],
LN [auth 4],
LO [auth 4],
LP [auth 4],
LQ [auth 4],
LR [auth 4],
LS [auth 4],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 4],
MH [auth 4],
MI [auth 4],
MJ [auth 4],
MK [auth 4],
ML [auth 4],
MM [auth 4],
MN [auth 4],
MO [auth 4],
MP [auth 4],
MQ [auth 4],
MR [auth 4],
MS [auth 4],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 4],
NH [auth 4],
NI [auth 4],
NJ [auth 4],
NK [auth 4],
NL [auth 4],
NM [auth 4],
NN [auth 4],
NO [auth 4],
NP [auth 4],
NQ [auth 4],
NR [auth 4],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 4],
OH [auth 4],
OI [auth 4],
OJ [auth 4],
OK [auth 4],
OL [auth 4],
OM [auth 4],
ON [auth 4],
OO [auth 4],
OP [auth 4],
OQ [auth 4],
OR [auth 4],
OS [auth D],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 4],
PH [auth 4],
PI [auth 4],
PJ [auth 4],
PK [auth 4],
PL [auth 4],
PM [auth 4],
PN [auth 4],
PO [auth 4],
PP [auth 4],
PQ [auth 4],
PR [auth 4],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 4],
QH [auth 4],
QI [auth 4],
QJ [auth 4],
QK [auth 4],
QL [auth 4],
QM [auth 4],
QN [auth 4],
QO [auth 4],
QP [auth 4],
QQ [auth 4],
QR [auth 4],
QS [auth O],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 4],
RH [auth 4],
RI [auth 4],
RJ [auth 4],
RK [auth 4],
RL [auth 4],
RM [auth 4],
RN [auth 4],
RO [auth 4],
RP [auth 4],
RQ [auth 4],
RR [auth 4],
RS [auth O],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 4],
SH [auth 4],
SI [auth 4],
SJ [auth 4],
SK [auth 4],
SL [auth 4],
SM [auth 4],
SN [auth 4],
SO [auth 4],
SP [auth 4],
SQ [auth 4],
SR [auth 4],
SS [auth S],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 4],
TH [auth 4],
TI [auth 4],
TJ [auth 4],
TK [auth 4],
TL [auth 4],
TM [auth 4],
TN [auth 4],
TO [auth 4],
TP [auth 4],
TQ [auth 4],
TR [auth 4],
TS [auth U],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 4],
UH [auth 4],
UI [auth 4],
UJ [auth 4],
UK [auth 4],
UL [auth 4],
UM [auth 4],
UN [auth 4],
UO [auth 4],
UP [auth 4],
UQ [auth 4],
UR [auth 4],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 4],
VH [auth 4],
VI [auth 4],
VJ [auth 4],
VK [auth 4],
VL [auth 4],
VM [auth 4],
VN [auth 4],
VO [auth 4],
VP [auth 4],
VQ [auth 4],
VR [auth 4],
VS [auth c],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 4],
WH [auth 4],
WI [auth 4],
WJ [auth 4],
WK [auth 4],
WL [auth 4],
WM [auth 4],
WN [auth 4],
WO [auth 4],
WP [auth 4],
WQ [auth 4],
WR [auth 4],
WS [auth e],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 4],
XH [auth 4],
XI [auth 4],
XJ [auth 4],
XK [auth 4],
XL [auth 4],
XM [auth 4],
XN [auth 4],
XO [auth 4],
XP [auth 4],
XQ [auth 4],
XR [auth 4],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 4],
YH [auth 4],
YI [auth 4],
YJ [auth 4],
YK [auth 4],
YL [auth 4],
YM [auth 4],
YN [auth 4],
YO [auth 4],
YP [auth 4],
YQ [auth 4],
YR [auth 4],
YS [auth h],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 4],
ZH [auth 4],
ZI [auth 4],
ZJ [auth 4],
ZK [auth 4],
ZL [auth 4],
ZM [auth 4],
ZN [auth 4],
ZO [auth 4],
ZP [auth 4],
ZQ [auth 4],
ZR [auth 4],
ZS [auth i]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N