Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

Table 1

The hydrogen bonds with occupancy over 30%.

Base	Nonmodeled system			Modeled system
Position	Protein	DNA	HDO	Protein	DNA	HDO
0	Gly302-N	T0-O2P	74.88%	Thr270-N	T0-O2P	83.19%
				Gln305-N	T0-O1P	63.73%
1	Asp301_OD2^(1)	A1-N6	39.41%	Asp301_OD1^(1)	A1-N6	60.35%
				Asp301_OD1^(1)	A1-N7	58.47%
	Gln339-NE2	A1-O1P	50.89%	Gln339-NE2	A1-O1P	88.85%
2				Asp301_OD1^(1)	T2-O4	47.65%
	Gln373-NE2	T2-O1P	35.44%	Gln373-NE2	T2-O1P	67.05%
3	Gln407-NE2	A3-O2P	53.24%	Gln407-NE2	A3-O2P	58.90%
4	Gln441-NE2	T4-O1P	63.73%	Gln441-NE2	T4-O1P	86.36%
5	Gln475-NE2	A5-O2P	30.78%	Gln475-NE2	A5-O2P	45.92%
6	Gln509-NE2	A6-O2P	63.56%	Gln509-NE2	A6-O2P	79.03%
7	Gln543-NE2	A7-O2P	96.01%	Gln543-NE2	A7-O2P	94.18%
8	Asp539-OD2	C8-N4	30.23%	Asp539-OD2	C8-N4	35.44%
	Gln577-NE2	C8-O1P	92.68%	Gln577-NE2	C8-O1P	63.73%
9	Asp573-OD1	C9-N4	36.77%	Asp573-OD1	C9-N4	34.11%
	Asp573-OD2	C9-N4	30.28%	Asp573-OD2	C9-N4	60.90%
	Gln611-NE2	C9-O1P	54.08%	Gln611-NE2	C9-O1P	90.18%
10	Gln645-NE2	T10-O1P	88.19%	Gln645-NE2	T10-O1P	88.85%
11	Gln679-NE2	A11-O2P	73.21%	Gln679-NE2	A11-O2P	88.52%
12	Gln713-NE2	A12-O2P	88.69%	Gln713-NE2	A12-O2P	81.70%
13				Gln747-NE2	C13-O1P	57.90%
14	Asp743-OD2	C14-N4	64.73%	Asp743-OD2	C14-N4	85.69%
	Gln781-OE2	C14-O3	32.78%
15	Asp743-OD2	C15-N4	60.12%	Asp777-OD1	C15-N4	61.40%
				Asp777-OD2	C15-N4	37.27%
	Lys814-NZ	C15-O1P	57.90%	Lys814-NZ	C15-O2P	99.83%
16				Lys848-NZ	T16-O1P	83.86%
17				Gly811-O	C17-N4	88.02%
				Gly881-N	C17-O1P	35.62%
19				Asp845-OD1	A19-N6	43.43%

The index of a repeat that a residue belongs to.
HDO is the abbreviation of hydrogen bond occupancy.
DNA base belonging to the sense strand of DNA.
Hydrogen bonds in bold and nonbold reflect the specific and nonspecific interactions, respectively. Bold in italics denotes the specific and water-mediated hydrogen bonds.