Zinc in PDB 5n4t: Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4), PDB code: 5n4t was solved by G.-B.Li, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.29 / 1.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.903, 80.148, 79.085, 90.00, 139.49, 90.00
R / Rfree (%)	17.5 / 19.6

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) (pdb code 5n4t). 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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4), PDB code: 5n4t:
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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.9 occ:1.00 ND1 A:HIS116 2.0 13.0 1.0 NE2 A:HIS114 2.1 9.2 1.0 NE2 A:HIS179 2.1 9.8 1.0 S20 A:R59504 2.3 12.2 1.0 CE1 A:HIS116 3.0 12.1 1.0 CE1 A:HIS179 3.0 11.2 1.0 CE1 A:HIS114 3.0 9.1 1.0 CD2 A:HIS114 3.0 9.2 1.0 CG A:HIS116 3.1 11.0 1.0 CD2 A:HIS179 3.1 8.9 1.0 C19 A:R59504 3.4 13.8 1.0 CB A:HIS116 3.5 10.9 1.0 ZN A:ZN502 3.9 11.6 1.0 OD1 A:ASP118 4.1 12.1 1.0 NE2 A:HIS116 4.1 13.2 1.0 ND1 A:HIS114 4.1 9.3 1.0 ND1 A:HIS179 4.1 10.7 1.0 CB A:CYS198 4.2 9.7 1.0 CD2 A:HIS116 4.2 12.5 1.0 CG A:HIS114 4.2 9.6 1.0 CG A:HIS179 4.2 9.1 1.0 SG A:CYS198 4.5 10.3 1.0 C18 A:R59504 4.7 18.9 1.0 OD2 A:ASP118 4.8 11.7 1.0 CG A:ASP118 4.9 10.7 1.0 CA A:HIS116 4.9 10.2 1.0 O A:HOH817 4.9 31.8 1.0

Zinc binding site 2 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.6 occ:1.00 OD2 A:ASP118 2.0 11.7 1.0 NE2 A:HIS240 2.1 10.4 1.0 SG A:CYS198 2.3 10.3 1.0 S20 A:R59504 2.3 12.2 1.0 CG A:ASP118 3.0 10.7 1.0 CE1 A:HIS240 3.1 10.5 1.0 CD2 A:HIS240 3.1 10.2 1.0 C19 A:R59504 3.4 13.8 1.0 OD1 A:ASP118 3.4 12.1 1.0 CB A:CYS198 3.4 9.7 1.0 NH2 A:ARG119 3.7 13.8 1.0 ZN A:ZN501 3.9 10.9 1.0 C18 A:R59504 3.9 18.9 1.0 NE A:ARG119 4.0 11.8 1.0 ND1 A:HIS240 4.2 11.0 1.0 CG A:HIS240 4.2 9.5 1.0 CZ A:ARG119 4.2 10.1 1.0 CE1 A:HIS114 4.3 9.1 1.0 CB A:ASP118 4.3 12.9 1.0 C02 A:R59504 4.4 29.1 1.0 NE2 A:HIS114 4.5 9.2 1.0 CA A:CYS198 4.7 9.3 1.0 O A:HOH612 4.8 13.1 1.0 O05 A:R59504 4.8 32.1 1.0 NE2 A:HIS179 4.8 9.8 1.0 C16 A:R59504 4.8 22.9 1.0 C03 A:R59504 4.9 29.5 1.0 CE1 A:HIS179 5.0 11.2 1.0

Zinc binding site 3 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:11.4 occ:1.00 O2 A:FMT505 1.9 8.2 0.5 O1 A:BEZ507 1.9 11.3 1.0 ND1 A:HIS251 2.1 9.5 1.0 O1 A:FMT505 2.1 20.1 0.5 C A:BEZ507 2.7 13.3 1.0 O2 A:BEZ507 2.8 13.8 1.0 C A:FMT505 2.8 8.6 0.5 CE1 A:HIS251 3.0 11.0 1.0 C A:FMT505 3.0 21.4 0.5 O1 A:FMT505 3.2 7.0 0.5 CG A:HIS251 3.2 8.3 1.0 CB A:HIS251 3.5 10.5 1.0 CA A:HIS251 3.8 9.7 1.0 C1 A:BEZ507 4.2 19.8 1.0 NE2 A:HIS251 4.2 11.1 1.0 O2 A:FMT505 4.2 21.2 0.5 CD2 A:HIS251 4.3 10.7 1.0 ND2 A:ASN254 4.3 13.4 1.0 CD2 A:LEU203 4.6 13.1 1.0 O A:HIS251 4.6 9.3 1.0 C A:HIS251 4.7 9.6 1.0 C2 A:BEZ507 4.9 21.5 1.0 N A:HIS251 4.9 9.1 1.0

Zinc binding site 4 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:10.1 occ:1.00 ND1 B:HIS116 2.0 10.8 1.0 NE2 B:HIS179 2.0 8.8 1.0 NE2 B:HIS114 2.1 8.2 1.0 S20 B:R59304 2.3 11.2 1.0 CE1 B:HIS116 2.9 12.3 1.0 CE1 B:HIS179 3.0 9.8 1.0 CG B:HIS116 3.0 10.3 1.0 CE1 B:HIS114 3.1 8.9 1.0 CD2 B:HIS179 3.1 9.6 1.0 CD2 B:HIS114 3.1 8.1 1.0 C19 B:R59304 3.3 13.4 1.0 CB B:HIS116 3.4 10.6 1.0 ZN B:ZN302 3.9 10.8 1.0 NE2 B:HIS116 4.1 12.2 1.0 OD1 B:ASP118 4.1 10.9 1.0 ND1 B:HIS179 4.1 9.4 1.0 CD2 B:HIS116 4.1 11.1 1.0 ND1 B:HIS114 4.2 9.4 1.0 CB B:CYS198 4.2 10.3 1.0 CG B:HIS179 4.2 9.7 1.0 CG B:HIS114 4.2 9.3 1.0 SG B:CYS198 4.5 10.2 1.0 C18 B:R59304 4.7 20.6 1.0 OD2 B:ASP118 4.8 12.1 1.0 CG B:ASP118 4.9 11.6 1.0 CA B:HIS116 4.9 10.4 1.0

Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.8 occ:1.00 OD2 B:ASP118 2.0 12.1 1.0 NE2 B:HIS240 2.1 10.4 1.0 SG B:CYS198 2.3 10.2 1.0 S20 B:R59304 2.4 11.2 1.0 CG B:ASP118 3.0 11.6 1.0 CE1 B:HIS240 3.1 9.4 1.0 CD2 B:HIS240 3.1 10.5 1.0 C19 B:R59304 3.3 13.4 1.0 OD1 B:ASP118 3.4 10.9 1.0 CB B:CYS198 3.4 10.3 1.0 NH2 B:ARG119 3.7 15.4 1.0 C18 B:R59304 3.9 20.6 1.0 ZN B:ZN301 3.9 10.1 1.0 NE B:ARG119 4.0 11.9 1.0 ND1 B:HIS240 4.2 10.2 1.0 CG B:HIS240 4.2 9.1 1.0 CZ B:ARG119 4.3 12.1 1.0 C02 B:R59304 4.3 33.1 1.0 CE1 B:HIS114 4.3 8.9 1.0 CB B:ASP118 4.4 11.9 1.0 NE2 B:HIS114 4.5 8.2 1.0 O04 B:R59304 4.7 34.6 1.0 O B:HOH420 4.7 13.6 1.0 CA B:CYS198 4.7 8.6 1.0 NE2 B:HIS179 4.8 8.8 1.0 C16 B:R59304 4.8 26.0 1.0 C03 B:R59304 4.9 34.1 1.0 CE1 B:HIS179 5.0 9.8 1.0 N01 B:R59304 5.0 30.4 1.0

Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:14.6 occ:1.00 O2 B:BEZ306 1.9 18.3 1.0 O1 B:FMT305 2.0 13.6 1.0 ND1 B:HIS251 2.1 11.8 1.0 C B:BEZ306 2.7 20.9 1.0 O1 B:BEZ306 2.8 18.9 1.0 C B:FMT305 3.0 17.0 1.0 CE1 B:HIS251 3.0 12.1 1.0 CG B:HIS251 3.1 12.0 1.0 O2 B:FMT305 3.3 16.5 1.0 CB B:HIS251 3.5 11.1 1.0 CA B:HIS251 3.8 10.4 1.0 C1 B:BEZ306 4.1 28.6 1.0 NE2 B:HIS251 4.2 11.7 1.0 CD2 B:HIS251 4.2 10.9 1.0 ND2 B:ASN254 4.4 16.6 1.0 O B:HIS251 4.6 11.9 1.0 C B:HIS251 4.7 10.5 1.0 CD2 B:LEU203 4.8 14.2 1.0 C6 B:BEZ306 4.8 29.5 1.0 N B:HIS251 4.9 11.6 1.0

G.B.Li, J.Brem, R.Lesniak, M.I.Abboud, C.T.Lohans, I.J.Clifton, S.Y.Yang, J.C.Jimenez-Castellanos, M.B.Avison, J.Spencer, M.A.Mcdonough, C.J.Schofield. Crystallographic Analyses of Isoquinoline Complexes Reveal A New Mode of Metallo-Beta-Lactamase Inhibition. Chem. Commun. (Camb.) V. 53 5806 2017.
ISSN: ESSN 1364-548X
PubMed: 28470248
DOI: 10.1039/C7CC02394D