HTH3 family

Conserved Hbonds 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.

List of conservative Hbonds between conservative part of HTH3 family and the DNA

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.