Instructor: Dr. Natalia Tretyakova, Ph.D. «hyperlink "mailto:[email protected]"»    -   6-3432
  PDB reference correction and design Dr.chem., Ph.D. Aris Kaksis, Associate Prof. mailto:[email protected]
                                          DNA sequence specific binding Proteins 3
  Catabolite Gene Activator Protein Act1 with DNA 30 bp fragment
 
1CGP.PDB
 
---> C chain 5'-GCGAA AA GTGTGAC A T A T |GT C ACAC TTTTCG-3' chain D --->
<--- C chain    3'-GCTT TTCACACTG| T A T A CA G TGTG AAAA GCG-5' chain D <---
 
Binding TATA Box Protein on DNA 16 base pair specific Site fragment
 
1YTF.PDB
 
<--- F chain 3'-ACA T ACA T A T A TTTTG-5' chain F <---
---> E chain 5'-TGT A TGT A T A T AAAAC-3' chain E --->
 
U turn binding protein Ihf with DNA 35 = 20+15 base paire fragment
 
1IHF.PDB
 
 
<--- C35 chain 3'-CGGTGC AAC AAA TT GAAA GC AATGC TTTTTT GGC-5' chain C35 <---
 ---> E20 chain    5'-CCACG TTGTTT AA CTATT CG|TTACG AA AA AA CCGG-3' chain D15 --->
 
Human Protein SRY binding DNA 8 base pair fragment
 
1HRY.PDB
 
<--- B chain 3'-GTTTGTGC-5' chain B <---
---> B chain 5'-C AAACACG-3' chain B --->
 
Estrogen O Receptor on 18 base paire DNA box fragment
 
1HCQ.PDB
 
---> C chain 5'-CC A GG T C A C  A G T G  A  CC T G-3' chain C --->  
   <--- D chain 3'-G T CC A G T G T C A  C T GG A  CC-5' chain D <---
 
RiboNuclease with  deoxy AAAA ssDNA chaine fragment
 
1RBJ.PDB
 
Restriction EndoNuclease bamH with 12 base paire DNA specific site
 
1BHN.PDB
 
---> C chain 5'- T A T GG A T CC  A T A-3' chain C --->  
    <--- D chain 3'- T A  CC T A GG T A T
 
Restriction EndoNuclease Eco RvRI on 12 base pair DNA specific site
 
1RVA.PDB
 
---> C chain 5'-AA  A G  A T A T C T T -3' chain C --->  
  <--- D chain 3'- T T C T A T A  G A  AA
 
Restriction EndoNuclease PvuII with 13 base paire DNA specific site
 
1PVI.PDB
 
---> C chain 5'- T G A CC A  GC T GG T C-3' chain C --->  
   <--- D chain   3'-C T GG T CG A  CC A  G T