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Table 2 Occurrence of metal atoms in the representatives of the 49 fold superfamilies that are common to Bacteria, Archaea and Eukarya

From: On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

Name Zn Fe Cd Ni Cu Mn Mg
S13-like H2TH domain 3 (38) 0 0 0 0 0 3 (18)
S15/NS1 RNA-binding domain 1 (18) 0 0 0 0 0 1 (17)
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthases 5 (21) 0 0 0 0 0 1 (2)
Ribosomal protein L11, C-terminal domain 0 0 0 0 0 0 1 (4)
5' to 3' exonuclease, C-terminal subdomain 2 (3) 0 0 0 0 2 (2) 2 (2)
Ribosomal protein S7 1 (18) 0 0 0 0 0 1 (15)
Translation proteins SH3-like domain 0 0 3 (57a) 0 0 0 1 (19)
Ribosomal protein L14 0 0 1 (19a) 0 0 0 1 (19)
Nucleic acid-binding proteins 15 (59) 0 2(1+19a) 1 (1) 1 (1) 4 (10) 10 (50)
Translation proteins 1 (6) 0 1 (19a) 0 0 0 8 (40)
EF-Tu/eEF-1α/eIF2-γ C-terminal domain 1 (6) 0 0 0 0 0 4 (18)
ValRS/IleRS/LeuRS editing domain 2 (7) 0 0 0 0 0 1 (2)
Metallo-dependent hydrolases 9 (50) 2 (9) 2 (4) 2 (32) 1 (2) 2 (2) 2 (4)
HAD-like 1 0 0 1 0 0 14 (35)
Ribosomal proteins L15p and L18e 0 0 2 (38a) 0 0 0 2 (38)
PIN domain-like 2 (3) 0 0 0 0 2 (2) 2 (2)
NAD(P)-binding Rossmann-fold domains 13 (89) 0 3 (7) 2 (2) 1 (1) 7 (14) 11 (20)
Initiation factor IF2/eIF5b, domain 3 0 0 0 0 0 0 1 (1)
Ribosomal protein S2 1 (18) 0 0 0 0 0 1 (15)
Class I glutamine amidotransferase-like 3 (4) 0 1 (2) 1 (4) 0 1 (10) 5 (5)
Nucleotidylyl transferase 8 (24) 0 1 (6) 0 0 2 (2) 9 (15)
Adenine nucleotide α hydrolases-like 8 (24) 0 1 (6) 0 0 3 (3) 13 (34)
FAD/NAD(P)-binding domain 1 (1) 0 0 0 0 1 (2) 2 (3)
P-loop containing nucleoside triphosphate hydrolases 18 (45) 0 3 (13) 2 (2) 0 8 (12) 108 (455)
Anticodon-binding domain of Class II aaRS 2 (15) 0 0 0 0 0 1 (4)
Actin-like ATPase domain 2 (3) 0 1 (1) 0 0 1 (1) 7 (38)
Ribonuclease H-like 8 (43) 0 3 (3+19a) 0 0 8 (15) 10 (76)
Translational machinery components 1 (18) 0 1 (19a) 0 0 0 2 (34)
S-adenosylmethionine-dependent methyltransferases 1 (1) 0 1 (1) 1 (1) 0 0 1 (3)
Class II aaRS and biotin synthetases 2 (15) 0 0 0 0 4 (4) 5 (13)
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0 0 0 0 0 1 (2) 11 (25)
Creatinase/aminopeptidase 2 (3) 0 0 0 0 2 (8) 0
DNA clamp 1 (1) 0 0 0 0 0 1 (1)
Ribosomal protein S5 domain 2-like 4 (39) 0 2 (2) 0 0 0 12 (49)
Ribosomal protein S8 1 (19) 0 0 0 0 0 1 (15)
Ribosomal protein L6 0 0 1 (19a) 0 0 0 1 (19)
DNA ligase/mRNA capping enzyme, catalytic domain 2 (3) 0 0 0 0 1 (1) 1 (1)
Metallo-hydrolase/oxidoreductase 4 (33) 1 (1) 2 (1+2b) 0 0 1 (1) 0
FKBP-like 4 (4) 1 (1) 0 0 0 0 0
Ribosomal protein L10e    1 (19a) 0 0 0 1 (19)
dsRNA-binding domain-like 1 (18) 0 0 0 0 0 1 (15)
Ribosomal protein L22 0 0 1 (19a)   0 0 1 (19)
EF-G/eEF-2 domains III and V 0 0 0 0 0 0 2 (2)
α-L RNA-binding motif 1 (18) 0 0 0 0 0 1 (15)
Threonyl-tRNA synthetase (ThrRS), second 'additional' domain 1 (3) 0 0 0 0 0 0
RBP11-like subunits of RNA polymerase 3 (21) 0 0 0 0 2 (14) 3 (7)
Ribosomal protein L5 0 0 1 (19a) 0 0 0 1 (20)
Ribosomal protein L1 0 0 0 0 0 0 1 (1)
β and β' subunits of DNA dependent RNA-polymerase 4 (22) 0 0 0 0 2 (14) 4 (10)
  1. Fold superfamily names are from the SCOP database [174]; metal content is from the Protein Data Bank [140]. The figures show the non-redundant numbers of hits, the figures in parentheses show the total number of hits (see text for details).
  2. a – Proteins of the large ribosomal subunit, whose crystals were soaked in CdCl2 during sample preparation ([147, 148], 19 different PDB entries).
  3. b – Cd-substituted Zn-dependent metallo-beta-lactamase [175].