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. 2013 May 1;4:14. doi: 10.1186/1759-8753-4-14

Table 1.

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

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]

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.

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].

PDB: Protein Data Bank.