. Author manuscript; available in PMC: 2010 Jan 15.

Published in final edited form as: J Phys Chem B. 2009 Jan 15;113(2):511–521. doi: 10.1021/jp8057838

Table 2.

Primary contacts between protein and DNA. (only contacts with frequencies larger than 0.10 are shown)

	Monomer-DNA			Dimer-DNA
	H-bond	Salt-bridge	Water-med.	H-bond	Salt-bridge	Water-med.
Mg²⁺		1.00 (G25,O2P)				0.90 (C24,O3S)
Ser53	--	--	--	0.43 (G23,O2P)
Thr56	0.82 (A3,O1P)			0.62 (G4,O1P)
Arg57	0.46 (C27,O1P)	0.15 (C27,O1P)	0.10 (C27,O1P)	0.96 (C26,O1P)	0.66 (C26,O1P)	0.31 (C26,O1P)
Asn58	0.39 (A3,O1P)			0.45 (G4,O1P)		0.20 (G4,O1P)
Lys60	--	--	--	0.33 (A3,O2P)
Asn80			0.15 (C26,O2P)	0.79 (C26,O2P)
Asp86			0.48 (C26,O2P)
			0.22 (G25,O3S)
Arg87	0.21 (C27,O1P)	0.15 (C27,O1P)	0.25 (C26,O1P)	0.65 (C26,O2P)	0.20 (C26,O2P)	0.58 (G25,O2P)
His89			0.22 (C26,O1P)			0.19 (G25,O2P)
Gln120	0.44 (G9,H22)
Arg125	0.86 (C11,O3S)	0.64 (C12,O2P)		0.15 (C13,O2P)	0.22 (C13,O2P)
	0.90 (C12,O2P)
Asp128			0.20 (C24,O2P)			0.25 (C12,O3S)
Lys196	0.37 (C10,O4S)			0.68 (C11,O2P)	0.53 (C11,O2P)
Asp199			0.15 (C12,O2P)	--	--	--