Table 2.

List of homeodomain proteins and details of interactions made by mutational “hot spot” residyes (PDB accession code Protein database accession codes can be found at http://www.rcsb.org/pdb/). Crystal structures of native proteins complexed with DNA were used to complete this table. Each residue has distinctive and highly conserved roles. In some proteins, Arg52 is replaced by Lys52 but similar hydrogen bonding patterns are maintained.

Protein	Species	Homeodomain family	PDB accession code	Arg5 (hydrogen bond with)	Arg52 (salt bridge with)	Arg53 (salt bridge with)
MATα2	Yeast	Homeodomain	1APL	N3 on A	E17	PO4 on C
			1AKH	O2 on T	E56	PO4 on G
			1K61	O4′1	on T PO4	on A
			1MNM	O4′	on	A
			1YRN	O4′	on	G
MATa1	Yeast	Homeodomain	1AKH	O4 on T	Replaced by Lys	PO4 on A
			1YRN			PO4 on T
UBX	Fruit fly	Homeodomain	1B8I	N3 on A	E17	PO4 on C
				O2 on T		PO4 on G
				O4′	on	T
				O4′	on	A
PBX	Fruit fly	Hemeodomain	1B8I	N3 on A	Replaced by Lys	PO4 on A
				N3 on G		PO4 on T
				N7 on G
				O6 on G
				O2 on T
				O4′	on	T
				O4′	on	G
Engrailed	Fruit fly	Homeodomain	3HDD	N2 on G	Replaced by Lys	PO4 on G
				O2 on T		PO4 on T
				O4′	on T PO4	on C
				O4′	on	A
Antennapedia	Fruit fly	Homeodomain	9ANT	N2 on G	E17	PO4 on C
				N3 on A		PO4 on G
				O2 on T
				O4′	on	T
				O4′	on	A
Even-skipped	Fruit fly	Homeodomain	1JGG	N3 on A	E17	PO4 on A
				O2 on T	E56	PO4 on A
				O4′	on	T
Paired-box	Fruit fly	Paired-homeo	1FJL	N2 on G	E17	PO4 on C
				N3 on A		PO4 on T
				O2 on T		PO4 on A
				O4′	on	T
				O4′	on	A
MSX-1	Mouse	Homeodomain	1IG7	O2 on T	E17	PO4 on C
				O4′	on A PO4	on T
				O4′	on	T
HOXa9	Mouse	Homeodomain	1PUF	N3 on A	E17	PO4 on G
				O2 on T		PO4 on T
				O2 on C
				O4′	on	C
PBX1	Mouse	Homeodomain	1PUF	N3 on A	Replaced by Lys	PO4 on A
				O2 on T		PO4 on T
				O4′	on	T
				O4′	on	A
HOXB1	Human	Homeodomain	1B72	O2 on T	E17	PO4 on C
				O4′	on T PO4	on T
				O4′	on	G
PBX1	Human	Homeodomain	1B72	O2 on T	Replaced by Lys	PO4 on C
				O4′	on T PO4	on C
				O4′	on	A
				O4′	on	G
OCT-1	Human	POU-homeo	1OCT	N2 on G	E17	PO4 on C
			1CQT	N4 on C	E56	PO4 on T
			1E3O	N7 on G		PO4 on A
			1HF0	O4 on T
			1GT0	O6 on G
				O4′	on	A
PIT-1	Human	POU-homeo	1AU7	N3 on A	E17	PO4 on C
				O2 on T	E56	PO4 on T
				O2 on C
				O4′	on	A
HNF1α	Human	POU-homeo	1IC8	O2 on C	E56	PO4 on C
				O2 on T		PO4 on T
				O4′	on	C
				O4′	on	A