. Author manuscript; available in PMC: 2022 Jul 14.

Published in final edited form as: Chem Rev. 2021 Jun 15;121(13):7957–8094. doi: 10.1021/acs.chemrev.1c00138

Table 3.

Relevant inter-Zn(II), Zn(II)-water, amino acid side chains-water, and hydrolysis product-enzyme distances in the active site of MBLs obtained from X-ray crystallographic structures of EP(^a) or EI(^b) complexes. Res. : crystal structure resolution (in Å); ch. : crystal structure chain; ref. : reference publication for the crystal structure.

Penicillins					Distance (Å)
PDB code	Enzyme	Res.(Å)	Hydrolyzed β-lactam (adduct)	Ref.	Ch.	Zn1-Zn2	Wat1-Zn1	Wat1-Zn2	Wat2-Zn2	C7O-Zn1	C7O-Zn2	C3O-Zn2	N4-Zn2
3Q6X	NDM-1^a (B1)	1.3	ampicillin (EP)	²⁵⁸	A	4.6	2.1	3.0	-	2.4	4.3	2.2	2.2
3Q6X	NDM-1^a (B1)	1.3	ampicillin (EP)	²⁵⁸	B	4.6	2.0	3.0	-	2.5	4.3	2.2	2.2
4EYF	NDM-1^a (B1)	1.8	benzylpenicillin (EP)	²²⁹	A	4.6	1.9	3.1	-	2.5	4.4	2.2	2.2
4EYF	NDM-1^a (B1)	1.8	benzylpenicillin (EP)	²²⁹	B	4.6	2.0	3.1	-	2.4	4.4	2.1	2.2
4EY2	NDM-1^a (B1)	1.2	methicillin (EP)	²²⁹	A	4.6	2.0	3.0	-	2.5	4.4	2.2	2.1
4EY2	NDM-1^a (B1)	1.2	methicillin (EP)	²²⁹	B	4.6	2.0	3.0	-	2.5	4.4	2.2	2.2
4EYB	NDM-1^a (B1)	1.2	oxacillin (EP)	²²⁹	A	4.5	2.0	2.9	-	2.5	4.4	2.2	2.1
4EYB	NDM-1^a (B1)	1.2	oxacillin (EP)	²²⁹	B	4.6	2.0	3.0	-	2.5	4.4	2.1	2.1
Cephalosporins
PDB code	Enzyme	Res.(Å)	Hydrolyzed β-lactam (adduct)	Ref.	Ch.	Zn1-Zn2	Wat1-Zn1	Wat1-Zn2	Wat2-Zn2	C8O-Zn1	C8O-Zn2	C4O-Zn2	N5-Zn2
2AIO	L1 (B3)^a	1.7	moxalactam (EP)	³³⁰	A	3.7	2.0	2.2	_-	2.4	4.2	2.3	2.4
4RL0	NDM-1^b (B1)	1.3	cefuroxime (EI)	³²⁹	A	3.8	2.0	2.2	-	2.8	4.2	2.1	2.4
4RL0	NDM-1^b (B1)	1.3	cefuroxime (EI)	³²⁹	B	3.8	2.0	2.2	-	2.9	4.2	2.2	2.3
4RL2	NDM-1^a (B1)	2.0	cephalexin (EP)	³²⁹	A	4.5	1.8	3.0	-	2.5	4.3	2.3	2.4
4RL2	NDM-1^a (B1)	2.0	cephalexin (EP)	³²⁹	B	4.5	2.0	2.8	-	2.4	4.3	2.3	2.4
Carbapenems
PDB code	Enzyme	Res.(Å)	Hydrolyzed β-lactam (adduct)	Ref.	Ch.	Zn1-Zn2	Wat1-Zn1	Wat1-Zn2	Wat2-Zn2	C7O-Zn1	C7O-Zn2	C3O-Zn2	N4-Zn2
5N5I	VIM-1^a (B1)	2.2	meropenem (EP)	²⁵⁹	A	3.5	1.8	2.3	-	6.0; 6.4	6.3; 5.8	2.6	3.0
4EYL	NDM-1^a (B1)	1.9	meropenem (EP)	²²⁹	A	4.0	-	-	-	2.3	2.5	3.0	2.2
4EYL	NDM-1^a (B1)	1.9	meropenem (EP)	²²⁹	B	3.9	-	-	-	2.2	2.7	2.9	2.3
4RBS	NDM-1^a (B1)	2.4	meropenem (EP)	To be published (Kim, Y. et al)	A	4.0	-	-	-	2.0	3.3	3.0	2.1
4RBS	NDM-1^a (B1)	2.4	meropenem (EP)	To be published (Kim, Y. et al)	B	4.0				2.2	3.0	3.1	2.1
5YPN	NDM-1 (B1) ^b	2.12	meropenem (EI²)	³²⁸	A	4.1	-	-	-	2.0	2.6	3.0	2.0
5YPN	NDM-1 (B1) ^b	2.12	meropenem (EI²)	³²⁸	B	4.3	-	-	-	2.2	2.9	2.7	2.0
5YPM	NDM-1 (B1) ^b	2.15	meropenem (EI¹)	³²⁸	A	4.2	-	-	-	2.1	3.2	2.6	2.0
					B	4.2	-	-	-	2.1	3.0	2.4	2.0
					C	4.2	-	-	-	2.1	3.1	2.5	1.9
					D	4.2	-	-	-	2.0	3.2	2.3	2.0
					E	4.2	-	-	-	2.2	3.1	2.4	2.0
					F	4.3	-	-	-	2.1	3.2	2.4	2.0
					G	4.2	-	-	-	2.3	2.8	2.3	1.9
					H	3.9	-	-	-	2.3	3.0	2.6	2.0
							Wat1-H118	Wat1-D120	Wat1-H196	Wat1-Zn2	Wat2-Zn2	C3O-Zn2	N4-Zn2
1X8I	CphA (B2)^a	1.9	biapenem (EP)	²⁴⁵	A		2.7	2.8	4.0	3.4	-	2.4	2.2