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Table 1 Available 3-D X-ray structures of the group II intron

From: Now on display: a gallery of group II intron structures at different stages of catalysis

PDB id Resolution (Å) Metals Splicing stage Activity Construct Reference
4DS6 3.64 NH4+/Mg2+ 5′-exon hydrolysis (pre) No (active site mutant) OiD1-6-G359A [29]
4FAQ 3.11 K+/Ca2+ 5′-exon hydrolysis (pre) No (nonfunctional divalent ion) Oi5eD1-5 [30]
4FAR 2.86 K+/Mg2+ 5′-exon hydrolysis (post) Yes Oi5eD1-5 [30]
4FAU 2.87 Li+/Mg2+ Intermediate Partial (nonfunctional monovalent ion) Oi5eD1-5 [30]
3IGIa 3.13 K+/Mg2+ Postcatalytic ligand-bound Yes OiD1-6 [26, 27]
4E8M 3.50 K+/Mg2+ Ligand-free Yes OiD1-5 [30]
4E8P 3.28 Rb+/Mg2+ Ligand-free Yes OiD1-5 [30]
4E8R 3.36 Cs+/Mg2+ Ligand-free Partial (nonfunctional monovalent ion) OiD1-5 [30]
4E8Q 2.84 Tl+/Mg2+ Ligand-free Yes OiD1-5 [30]
4E8N 2.96 NH4+/Mg2+ Ligand-free Yes OiD1-5 [30]
4E8V 3.99 K+/Ba2+ Ligand-free No (nonfunctional divalent ion) OiD1-5 [30]
4FAX 3.10 Na+/Mg2+ Ligand-free No (nonfunctional monovalent ion) OiD1-5 [30]
4FB0 3.22 K+/Mg2+ Ligand-free Partial (active site mutant) OiD1-5-C377G [30]
4E8Kb 3.03 K+/Ca2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [30]
4E8T 3.34 K+/Ca2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [30]
4FAW 2.70 K+/Mg2+ SER (post) Yes OiD1-5 [30]
  1. a Additional PDB entries 3BWP, 3EOH and 3G78 represent the same form of the group II intron in the state following 3′-exon hydrolysis as 3IGI, which results from the most recent refinement. These depositions were obtained by applying different integration and refinement procedures against the same set of experimental crystallographic data.
  2. b PDB entry 3EOG represents the same form of the group II intron in the state preceding the SER reaction as 4E8K, but was solved at a lower resolution (3.39 Å) using construct OiD1-6 [31].
  3. PDB: Protein Data Bank.