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Table 4 Three AIR sets used for docking Zif268 with DNA

From: An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking

No Molecule Zinc finger 1 Zinc finger 2 Zinc finger 3
(i) Zif268 R18, S19, D20, E21, R24, I28, H25 R46, D48, H49, H53, T56 H74, S75, D76, E77, K79, R80
  DNA G10, T13, T13, G8, G8, G6, G7 G7, C17, G6, G4, C3 G4, C18, A20, G2, C19, G2
(ii) Zif268 R18, R24 R46, D48, H49 R74, R80
  DNA G10, G8 G7, C17, G6 G4, G2
(iii) Zif268 S19, I28 D48, T56 D76, R80
  DNA T13, G6 C17, C3 A20, G2
  1. (i) The first AIR set was derived on the basis of hydrogen bonds and van der Waals contacts in all residues and bases from the interface of Zif268-DNA X-ray crystal structure. (ii) The second AIR set was derived on the basis of sequence-specific hydrogen bonds between the residues and bases. (iii) Two AIRs for each domain in the third AIR set were derived on the basis of van der Waals or hydrogen bond contacts.