. 2002 Aug;11(8):1978–1983. doi: 10.1110/ps.4980102

Table 3.

Recognition sites participating in stabilization centers of type II restriction endonucleases

Enzyme	Type	PDB	SCs with recognition sites
BamHI	free	1bam	Asn 116–Val 156, Thr 144–Val 156,Gly 115–Val 156, Asn 55–Thr 153, Gly 56–Thr 153
	DNA	1bhm	Asn 116–Val 156,Gly 115–Val 156,Ile 117–Val 156, Asn 116–Thr 157, Asn 53–Thr 153, Asn 55–Thr 153, Gly 56–Thr 153
	DNA + Ca²⁺	2bam	Asn 116–Val 156, Asn 116–Thr 157, Ile 117–Val 156,Gly 115–Val 156, Asn 55–Thr 153, Gly 56–Thr 153
	DNA + Mn²⁺	3bam	Asn 116–Val 156,Ile 117–Val 156, Asn 116–Thr 157, Asn 53–Thr 153, Asn 55–Thr 153, Gly 56–Thr 153
	DNA*	1esg	Gly 115–Val 156
EcoRI	free	1qc9	Asn 141–Arg 203
	DNA	1eri	Ile 143–Arg 203,Glu 144–Arg 203, Phe 174–Arg 200
	DNA + Mn²⁺	1qps	Ile 143–Arg 203, Phe 174–Arg 200
FokI	free	2fok	Gln 12–Arg 228, Phe 178–Glu 220
	DNA	1fok	Phe 178–Glu 220
BglII	free	1es8	Ser 97–Ser 142
	DNA + Mg²⁺	1d2i	Asn 98–Ser 142,Asn 98–Leu 143
	DNA + Ca²⁺	1dfm	Asn 98–Leu 143
EcoRV	free	1rve	Thr 106–Gly 190, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA	4rve	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA	1eoo	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA	1eop	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA	1bgb	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA	1rva	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA + Mg²⁺	1rvb	Thr 106–Ile 189,Thr 106–Gly 190, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA + Mg²⁺	1rvc	Thr 106–Ile 189, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA + Ca²⁺	1az0	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA + Ca²⁺	1b94	Thr 106–Ile 189,Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
	DNA*	2rve	Thr 106–Gly 190, Leu 107–Asn 188, Gly 108–Asn 188, Gly 109–Asn 188, Tyr 110–Asn 188
PvuII	free	1pvu	His 84–Asn 141, Thr 82–Asn 141, His 83–Asn 141, Thr 82–Pro 142,His 84–Asn 141
	DNA	1eyu	Ser 81–Lys 143,Thr 82–Pro 142,His 83–Asn 141, His 84–Asn 141
	DNA	1pvi	Ser 81–Lys 143,Thr 82–Pro 142,His 83–Asn 141
	DNA	3pvi	Ser 81–Lys 143,Thr 82–Pro 142,His 83–Asn 141, His 84–Asn 141
	DNA + Ca²⁺	1f0o	His 83–Asn 141, His 83–Asn 140, His 84–Asn 140, His 84–Asn 141
BglI	DNA + Ca²⁺	1dmu	Asp 154–Val 280,Asp 154–Asp 281, Leu 155–Arg 279, Val 156–Val 278, Val 156–Arg 279, Arg 263–Arg 279, Pro 264–Arg 279
MunI	DNA	1d02	Lys 50–Gly 79, Asn 51–Gly 79, Leu 52–Gly 79, Tyr 53–Gly79, Ile 99–Val 151, Asp 103–Asp 155, Asp 103–Ile 156
NaeI	free	1ev7	Phe 98–Trp 120, Ser 99–Trp 120
	DNA	1iaw	Phe 98–Trp 120, Ser 99–Trp 120
NgoMIV	DNA + Mg²⁺	1fiu	Ser 40–Thr 224
BsoBI	DNA	1dcl	Tyr 24–Asp 246, Phe 28–Asp 246
Bse634I	DNA	1knv	Ile 149–Ala 193, Ala 193–Lys 235, Gly 194–Lys 235, Gly 194–Tyr 236
HincII	DNA + Na⁺	1kc6	Asn 141–Ile 208, Asn 141–Gln 209, Ala 139–Phe 210, Pro 140–Gln 209, Asn 141–Gln 209

Residues that interact with DNA are marked in bold. Neighboring residues are marked in italic. DNA* means complex with nonspecific substrate.