Zinc in PDB 5y6e: Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12), PDB code: 5y6e was solved by G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.355, 74.452, 64.456, 90.00, 129.46, 90.00
R / Rfree (%)	13.7 / 17.3

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) (pdb code 5y6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12), PDB code: 5y6e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.5 occ:1.00 ND1 A:HIS116 2.0 9.3 1.0 NE2 A:HIS114 2.0 6.6 1.0 NE2 A:HIS179 2.1 7.6 1.0 S14 A:8PO304 2.3 9.8 1.0 CE1 A:HIS116 3.0 11.6 1.0 CE1 A:HIS114 3.0 6.2 1.0 CE1 A:HIS179 3.0 5.9 1.0 CD2 A:HIS114 3.0 7.1 1.0 CG A:HIS116 3.0 8.9 1.0 CD2 A:HIS179 3.1 7.2 1.0 C13 A:8PO304 3.3 9.9 1.0 CB A:HIS116 3.4 7.8 1.0 ZN A:ZN302 3.7 10.4 1.0 OD1 A:ASP118 4.0 9.7 1.0 ND1 A:HIS114 4.1 7.1 1.0 NE2 A:HIS116 4.1 9.9 1.0 ND1 A:HIS179 4.1 4.4 1.0 CD2 A:HIS116 4.1 8.6 1.0 CG A:HIS114 4.1 5.1 1.0 CB A:CYS198 4.2 8.5 1.0 CG A:HIS179 4.2 5.3 1.0 SG A:CYS198 4.4 8.9 1.0 OD2 A:ASP118 4.7 8.5 1.0 C12 A:8PO304 4.7 8.9 1.0 CG A:ASP118 4.7 7.8 1.0 CA A:HIS116 4.8 7.8 1.0 ND2 A:ASN210 4.9 21.6 1.0

Zinc binding site 2 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.4 occ:1.00 OD2 A:ASP118 2.0 8.5 1.0 NE2 A:HIS240 2.1 6.4 1.0 S14 A:8PO304 2.3 9.8 1.0 SG A:CYS198 2.4 8.9 1.0 CE1 A:HIS240 3.0 5.6 1.0 CG A:ASP118 3.0 7.8 1.0 CD2 A:HIS240 3.1 6.6 1.0 C13 A:8PO304 3.4 9.9 1.0 OD1 A:ASP118 3.4 9.7 1.0 CB A:CYS198 3.5 8.5 1.0 O18 A:8PO304 3.6 10.9 1.0 NH2 A:ARG119 3.6 11.2 1.0 C12 A:8PO304 3.6 8.9 1.0 ZN A:ZN301 3.7 7.5 1.0 N09 A:8PO304 3.9 8.0 1.0 NE A:ARG119 4.0 8.5 1.0 ND1 A:HIS240 4.1 7.2 1.0 C10 A:8PO304 4.2 14.2 1.0 CG A:HIS240 4.2 5.2 1.0 CZ A:ARG119 4.2 8.4 1.0 CE1 A:HIS114 4.3 6.2 1.0 CB A:ASP118 4.3 6.9 1.0 NE2 A:HIS114 4.5 6.6 1.0 NE2 A:HIS179 4.6 7.6 1.0 C16 A:8PO304 4.6 13.1 1.0 CA A:CYS198 4.7 4.9 1.0 CE1 A:HIS179 4.7 5.9 1.0 O A:HOH474 4.8 10.1 1.0 C01 A:8PO304 5.0 11.4 1.0

Zinc binding site 3 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.7 occ:1.00 O1 A:FMT306 1.7 16.6 1.0 O2 A:FMT305 2.0 13.0 1.0 ND1 A:HIS251 2.1 4.4 1.0 C A:FMT305 2.7 15.5 1.0 O1 A:FMT305 2.8 12.0 1.0 C A:FMT306 2.8 18.9 1.0 CE1 A:HIS251 3.0 9.7 1.0 CG A:HIS251 3.1 9.1 1.0 O2 A:FMT306 3.3 15.5 1.0 CB A:HIS251 3.4 9.7 1.0 CA A:HIS251 3.7 6.0 1.0 NE2 A:HIS251 4.2 7.1 1.0 CD2 A:HIS251 4.2 8.9 1.0 ND2 A:ASN254 4.5 10.8 1.0 O A:HIS251 4.5 9.2 1.0 CD2 A:LEU203 4.6 7.9 1.0 C A:HIS251 4.6 11.0 1.0 N A:HIS251 4.9 7.3 1.0

Zinc binding site 4 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:7.4 occ:1.00 NE2 B:HIS114 2.0 5.8 1.0 ND1 B:HIS116 2.0 10.2 1.0 NE2 B:HIS179 2.1 6.0 1.0 S14 B:8PO304 2.3 9.1 1.0 CE1 B:HIS114 2.9 7.4 1.0 CE1 B:HIS116 3.0 12.6 1.0 CE1 B:HIS179 3.0 5.9 1.0 CG B:HIS116 3.0 8.1 1.0 CD2 B:HIS114 3.0 5.8 1.0 CD2 B:HIS179 3.1 7.1 1.0 C13 B:8PO304 3.3 8.2 1.0 CB B:HIS116 3.4 8.5 1.0 ZN B:ZN302 3.7 9.8 1.0 OD1 B:ASP118 3.9 8.8 1.0 ND1 B:HIS114 4.1 6.8 1.0 NE2 B:HIS116 4.1 10.5 1.0 ND1 B:HIS179 4.1 5.3 1.0 CG B:HIS114 4.1 5.5 1.0 CD2 B:HIS116 4.1 8.9 1.0 CB B:CYS198 4.2 7.3 1.0 CG B:HIS179 4.2 5.6 1.0 SG B:CYS198 4.4 8.1 1.0 OD2 B:ASP118 4.7 8.8 1.0 C12 B:8PO304 4.7 9.4 1.0 CG B:ASP118 4.7 8.2 1.0 CA B:HIS116 4.8 7.7 1.0 ND2 B:ASN210 4.8 16.2 1.0

Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:9.8 occ:1.00 OD2 B:ASP118 2.0 8.8 1.0 NE2 B:HIS240 2.1 6.3 1.0 S14 B:8PO304 2.3 9.1 1.0 SG B:CYS198 2.4 8.1 1.0 CE1 B:HIS240 3.0 6.4 1.0 CG B:ASP118 3.0 8.2 1.0 CD2 B:HIS240 3.1 5.6 1.0 OD1 B:ASP118 3.4 8.8 1.0 C13 B:8PO304 3.4 8.2 1.0 CB B:CYS198 3.5 7.3 1.0 O18 B:8PO304 3.6 10.9 1.0 NH2 B:ARG119 3.6 11.0 1.0 C12 B:8PO304 3.7 9.4 1.0 ZN B:ZN301 3.7 7.4 1.0 N09 B:8PO304 3.9 8.2 1.0 NE B:ARG119 4.0 6.5 1.0 ND1 B:HIS240 4.1 7.0 1.0 CZ B:ARG119 4.2 7.2 1.0 CG B:HIS240 4.2 5.5 1.0 C10 B:8PO304 4.2 13.1 1.0 CE1 B:HIS114 4.3 7.4 1.0 CB B:ASP118 4.3 6.0 1.0 NE2 B:HIS114 4.5 5.8 1.0 NE2 B:HIS179 4.6 6.0 1.0 C16 B:8PO304 4.6 11.4 1.0 CA B:CYS198 4.7 5.3 1.0 CE1 B:HIS179 4.7 5.9 1.0 O B:HOH501 4.9 9.2 1.0 C01 B:8PO304 5.0 10.4 1.0

Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Hydroxyphenyl)- 2-((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 12) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.3 occ:1.00 O1 B:FMT306 1.9 18.8 1.0 O2 B:FMT305 2.1 12.9 1.0 ND1 B:HIS251 2.1 7.5 1.0 C B:FMT305 2.7 15.6 1.0 O1 B:FMT305 2.8 15.6 1.0 C B:FMT306 2.9 12.8 1.0 CE1 B:HIS251 3.0 11.0 1.0 CG B:HIS251 3.1 10.1 1.0 O2 B:FMT306 3.4 15.4 1.0 CB B:HIS251 3.4 9.1 1.0 CA B:HIS251 3.7 6.2 1.0 NE2 B:HIS251 4.1 8.1 1.0 CD2 B:HIS251 4.2 9.8 1.0 ND2 B:ASN254 4.5 10.4 1.0 O B:HIS251 4.5 7.3 1.0 CD2 B:LEU203 4.6 10.3 1.0 C B:HIS251 4.6 9.2 1.0 N B:HIS251 4.8 8.2 1.0

S.Liu, L.Jing, Z.-J.Yu, C.Wu, Y.Zheng, E.Zhang, Q.Chen, Y.Yu, L.Guo, Y.Wu, G.-B.Li. ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid Derivatives As Metallo-Beta-Lactamase Inhibitors: Synthesis, Kinetic and Crystallographic Studies. Eur J Med Chem V. 145 649 2018.
ISSN: ISSN 1768-3254
PubMed: 29353720
DOI: 10.1016/J.EJMECH.2018.01.032