Modified nucleotides of Haloarcula marismortui and H. halobium 23S rRNA and estimates of equivalent nucleotides in E. coli.
For Haloarcula, if the equivalent nucleotide is modified in E. coli it is also listed along with the S. cerevisiae and human equivalent as well.

^a Numbering as in PDB entry 1JJ2. Asterisks indicate the corresponding nucleotides not visible in the crystal structure of the large subunit H. marismortui at 2.4 angstroms (Klein et al., 2001; Ban et al., 2001). Modified nucleotides are indicated according to Kirpekar et al., 2005.

^b Numbering according to Genbank entry J01695, annotated at the Gutell lab Comparative RNA website.

^c Numbering of modifications according to Piekna-Przybylska et al., 2007 (people.biochem.umass.edu/sfournier/fournierlab/snornadb/).

^d Numbering according to U13369, modifications indicated according to Maden, 1990 and Ofengand and Bakin, 1997.

23S RNA (the 8 positions are those of H.marismortui)

- m1A 628 (EC571) in hairpin 25.1 of Domain II
- Gm 1950 (Ec1909) in helix 69 of Domain IV  very close to Pur-37 of tRNA
in site A<----I question this. Two sources that I checked, Yusupov et al. 2001
and the E. coli Cryo-em structure, say this nucleotide contacts the P-site tRNA.
I didn't look up the residue of tRNA yet or check other sources yet.
- Psi, Psi at positions 1956+1958 (Ec 1915+1917) in hairpin 69 of Domain
IV, 1915 contacts tRNA in site A and 1917 is adjacent(*).
- Um 2587 (Ec 2552) in hairpin 92 (the so-called A-loop) of Domain V
- Gm 2588 (Ec2553) in the same hairpin 92 of Domain  V.
- m3U 2619 (Ec 2584) in region between hairpin 90 and 93 (*) in Domain V.
- Psi 2621 (Ec 2586) in the same region between hairpin 90 and 93 (*) in Domain
V.

2619 (Ec2584) and 2621 (Ec2586) contact the tRNA in the P site.

- WRONG! Psi 2606 (Ec 2580) in H. halobium (H. salinarum) is in the stem of helix 90 in Domain V

Pseudouridines (only) of Haloarcula marismortui 23S rRNA and H. halobium (H. salinarum) 23S rRNA and estimates of equivalent positions in E. coli and other Halo species.

^a Numbering as in PDB entry 1JJ2. Asterisks indicate the corresponding nucleotides not visible in the crystal structure of the large subunit Haloarcula marismortui at 2.4 angstroms (Klein et al. 2001; Ban et al. 2001). Modified nucleotides are indicated according to Kirpekar et al. 2005.

^b Numbering according to Genbank entry J01695, annotated at the Gutell lab Comparative RNA website.

^c Numbering according to sequence of 23S rRNA sequence of Haloferax volcanii from http://archaea.ucsc.edu/cgi-bin/hgc?hgsid=482213&g=htcGetDna2&table=&i=mixed&o=1600054&l=1600054&r=1602908&getDnaPos=chr%3A1%2C600%2C055-1%2C602%2C908&db=haloVolc1&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA

^d Numbering according to sequence of 23S rRNA sequence of Halobacterium halobium (H. salinarum) from GenBank: X03407.1. Pseudouridines according to secondary structure in Ofengand and Bakin and positions even match numbers used there.