9K0Z | pdb_00009k0z

EF-G2 bound 70S ribosome complex of M. smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structural analyses reveal a unique role for elongation factor G2 (EF-G2) in Mycobacteria.

Baid, P.Sengupta, J.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70161
  • Primary Citation of Related Structures:  
    9K0Z, 9K10

  • PubMed Abstract: 

    The gene-encoding translation elongation factor G (EF-G) has undergone gene duplication across various bacterial species including Mycobacteria, and in mammalian mitochondria, leading to the emergence of the paralogue elongation factor G2 (EF-G2). Our study reveals that mycobacterial EF-G2, unlike EF-G1, neither participates in ribosome-recycling nor significantly contributes to overall translation, suggesting that it plays an alternative role in Mycobacteria. Remarkably, our investigation found a significant overexpression of mycobacterial EF-G2 during the stationary growth phase. Moreover, EF-G2 lacks ribosome-dependent GTPase activity, an observation consistent with previous reports. Cryo-EM analysis of the M. smegmatis 70S ribosome purified from the nutrient-starved (stationary) phase and complexed with EF-G2 unveiled the structural basis for its inability to hydrolyse GTP in a ribosome-dependent manner. Furthermore, we report an unprecedented binding mode of two EF-G2 copies on the 50S ribosomal subunit that impedes subunit association, thereby preventing the formation of active 70S ribosomes. Thus, instead of performing canonical functions, mycobacterial EF-G2 acts as a translation repressor during nutrient starvation. Altogether, our findings shed light on the multifaceted mechanisms by which EF-G2 modulates protein synthesis under nutrient-limited conditions, providing insights into adaptive strategies employed by Mycobacteria to survive in hostile environments.


  • Organizational Affiliation

    Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein bL37B [auth 3]23Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL12D [auth 5]69Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS63 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translation elongation factor EF-GE [auth 7]709Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_6535
UniProt
Find proteins for A0R6G0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3H [auth C]208Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4I [auth D]200Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5J [auth E]180Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6K [auth F]96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0A2U9Q0X2 (Mycolicibacterium smegmatis (strain MKD8))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7L [auth G]155Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8M [auth H]131Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9N [auth I]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10O [auth J]99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11P [auth K]115Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12Q [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13R [auth M]116Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14BS [auth N]60Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15T [auth O]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16U [auth P]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17V [auth Q]94Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18BW [auth R]65Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19X [auth S]82Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20Y [auth T]85Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23Z [auth U]97Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2AA [auth V]228Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25BA [auth W]192Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27CA [auth X]79Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28DA [auth Y]63Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29EA [auth Z]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30FA [auth a]59Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32GA [auth b]54Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AHA [auth c]49Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34IA [auth d]46Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35JA [auth e]63Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36KA [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31LA [auth g]48Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2MA [auth i]275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3NA [auth j]214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4OA [auth k]209Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5PA [auth l]182Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6QA [auth m]176Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9RA [auth n]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10SA [auth o]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS62 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11TA [auth p]133Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS45 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13UA [auth q]146Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14VA [auth r]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15WA [auth s]145Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I7G436 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16XA [auth t]136Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17YA [auth u]118Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18ZA [auth v]126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I7FGD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19AB [auth w]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20BB [auth x]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21CB [auth y]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22DB [auth z]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24EB [auth 1]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChains LengthOrganismImage
P/P-site Phe-tRNA(Phe)A [auth 2]76Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNA fragmentC [auth 4]18Mycolicibacterium smegmatis MC2 155
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S ribosomal RNAF [auth A]1,511Mycolicibacterium smegmatis MC2 155
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S ribosomal RNAG [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 58
MoleculeChains LengthOrganismImage
23S ribosomal RNAFB [auth h]3,127Mycolicibacterium smegmatis MC2 155
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

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HB [auth 7]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
PHE
Query on PHE

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GB [auth 2]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN

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JB [auth N]
LB [auth R]
NB [auth Y]
OB [auth c]
PB [auth f]
JB [auth N],
LB [auth R],
NB [auth Y],
OB [auth c],
PB [auth f],
QB [auth g]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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IB [auth F]
KB [auth R]
MB [auth X]
RB [auth i]
SB [auth i]
IB [auth F],
KB [auth R],
MB [auth X],
RB [auth i],
SB [auth i],
TB [auth i],
UB [auth l],
VB [auth t],
WB [auth z],
XB [auth h],
YB [auth h],
ZB [auth h]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaSPF/2021/000141
Science and Engineering Research Board (SERB)IndiaCRG/2019/001788
Council of Scientific & Industrial Research (CSIR)IndiaMLP-139

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release