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

BMC Bioinformatics

Table 4 Three AIR sets used for docking Zif268 with DNA

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

(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.

ISSN: 1471-2105