|General information||Species distribution||Numeration assumed||Sequence conservation||3D conservation||Contacts with DNA|
For all 13 structures possible Hbonds between protein and the DNA were anlyzed.
A potential Hbond was detected if an atom, capable of being H donor came nearer than 3.5 Å
to an H acceptor atom. Here Hbonds made by conserved amino acid residues are described.
|AA residue.atom||Nucleotide.atom||Average distance, Å||Models||Proteins|
|Gln104.n||800 phosphate oxygen||2,93||All except 10||All|
|Gln104.ne2||801 phosphate oxygen||2,92||All except 3 and 13||All except 434 cro|
|Gly114.n/ Lys114.n/ Tyr114.n||898 phosphate oxygen||2,99||All except 2, 7, 10, 11||All except 434 C1 repressor|
|Gln115.ne2||A801.n7||3,16||All except 7||All|
|Gln115.oe1||A801.n6||3,00||All except 2,3||All|
|Asn123.nd2||801 phosphate oxygen||3,14||All except 3, 12, 13||Lambda and 434 C1 repressors|
Here the overall picture of conservative Hbonds between conservative
part of HTH3 family and the DNA is shown. 2-nd and 3-rd alpha-helices
are colored pink, the DNA is shown as wireframe model, while DNAbackbone is shown as brown
strands. Contacting nucleotides and amino acid residues are shown as wireframe model,
and contacting atoms are shown as balls. Hbonds are shown as short brown lines.
The most conservative residue is Gln115, which is responsible for recognition of adenine 801 by bidentate Hbond. Adenine 801 is invariant in all studied binding sites. It is the only conservative Hbond with the DNA major groove atoms. There are three residues (104, 114 and 123) making Hbonds with DNA backbone phosphates. Two of them (Gln104 and Asn123) contact to forward strand phosphates, Gln 104 being bound to phosphates of two nucleotides. One residue (104) contacts to phosphate on the revers strand, and due to the fact, that it makes Hbond by it's backbone nitrogen, position 104 is occupied by different amino acids in different structures.