Zinc in PDB 5k48: Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid

The structure of Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid, PDB code: 5k48 was solved by D.Zollman, M.Mcdonough, J.Brem, C.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.82 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.888, 79.542, 67.892, 90.00, 130.60, 90.00
R / Rfree (%)	16.6 / 19.4

The binding sites of Zinc atom in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid (pdb code 5k48). 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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid, PDB code: 5k48:
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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:16.3 occ:1.00 ND1 A:HIS116 2.0 13.3 1.0 NE2 A:HIS179 2.1 13.8 1.0 NE2 A:HIS114 2.1 12.4 1.0 S17 A:S5Z301 2.3 27.0 1.0 CE1 A:HIS116 3.0 15.1 1.0 CD2 A:HIS179 3.0 17.6 1.0 CG A:HIS116 3.0 13.5 1.0 CE1 A:HIS179 3.1 21.1 1.0 CE1 A:HIS114 3.1 11.9 1.0 CD2 A:HIS114 3.1 15.3 1.0 C16 A:S5Z301 3.3 28.0 1.0 CB A:HIS116 3.4 15.1 1.0 ZN A:ZN306 3.7 16.9 1.0 OD1 A:ASP118 4.1 17.4 1.0 NE2 A:HIS116 4.1 17.6 1.0 CD2 A:HIS116 4.1 13.7 1.0 ND1 A:HIS179 4.2 15.8 1.0 ND1 A:HIS114 4.2 9.9 1.0 CG A:HIS179 4.2 12.8 1.0 CB A:CYS198 4.2 14.7 1.0 CG A:HIS114 4.2 12.1 1.0 SG A:CYS198 4.3 13.3 1.0 ND2 A:ASN210 4.4 55.4 1.0 OD2 A:ASP118 4.6 18.5 1.0 C15 A:S5Z301 4.6 31.1 1.0 CG A:ASP118 4.7 16.4 1.0 CA A:HIS116 4.8 14.3 1.0

Zinc binding site 2 out of 6 in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:16.9 occ:1.00 OD2 A:ASP118 2.0 18.5 1.0 NE2 A:HIS240 2.1 11.9 1.0 SG A:CYS198 2.2 13.3 1.0 S17 A:S5Z301 2.3 27.0 1.0 CE1 A:HIS240 3.0 14.8 1.0 CD2 A:HIS240 3.1 20.0 1.0 CG A:ASP118 3.1 16.4 1.0 C16 A:S5Z301 3.4 28.0 1.0 CB A:CYS198 3.4 14.7 1.0 OD1 A:ASP118 3.6 17.4 1.0 NH2 A:ARG119 3.7 15.2 1.0 ZN A:ZN305 3.7 16.3 1.0 C14 A:S5Z301 4.0 30.6 1.0 NE A:ARG119 4.1 14.4 1.0 ND1 A:HIS240 4.1 15.5 1.0 CG A:HIS240 4.2 13.3 1.0 C15 A:S5Z301 4.2 31.1 1.0 CE1 A:HIS114 4.3 11.9 1.0 CZ A:ARG119 4.3 13.3 1.0 CB A:ASP118 4.3 12.8 1.0 NE2 A:HIS114 4.4 12.4 1.0 NE2 A:HIS179 4.5 13.8 1.0 CA A:CYS198 4.6 12.1 1.0 O A:HOH513 4.8 21.9 1.0 O A:HOH566 4.8 30.7 1.0 CE1 A:HIS179 4.8 21.1 1.0

Zinc binding site 3 out of 6 in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:22.9 occ:1.00 O2 A:FMT303 2.0 21.5 1.0 O1 A:FMT302 2.0 24.6 1.0 NE2 A:HIS153 2.0 19.8 1.0 C A:FMT303 2.7 22.8 1.0 CE1 A:HIS153 2.8 28.7 1.0 O1 A:FMT303 2.8 24.9 1.0 C A:FMT302 2.9 26.5 1.0 O2 A:FMT302 3.1 25.9 1.0 CD2 A:HIS153 3.2 18.2 1.0 ND1 A:HIS153 4.0 21.4 1.0 CG A:HIS153 4.2 21.2 1.0 CB A:ALA132 4.3 17.7 1.0 O A:HOH406 4.5 36.0 1.0 CG2 A:THR152 4.6 19.1 1.0 CA A:ALA132 4.9 19.8 1.0 O A:HOH410 5.0 43.4 1.0

Zinc binding site 4 out of 6 in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:18.2 occ:1.00 ND1 B:HIS116 2.0 20.9 1.0 NE2 B:HIS179 2.1 16.0 1.0 NE2 B:HIS114 2.1 12.3 1.0 S17 B:S5Z301 2.3 26.9 1.0 CE1 B:HIS116 3.0 22.9 1.0 CD2 B:HIS179 3.0 13.5 1.0 CE1 B:HIS114 3.0 16.1 1.0 CG B:HIS116 3.0 17.6 1.0 CE1 B:HIS179 3.1 17.2 1.0 CD2 B:HIS114 3.1 12.6 1.0 C16 B:S5Z301 3.3 29.3 1.0 CB B:HIS116 3.4 18.3 1.0 ZN B:ZN305 3.7 18.9 1.0 NE2 B:HIS116 4.1 20.9 1.0 OD1 B:ASP118 4.1 19.1 1.0 ND1 B:HIS114 4.1 11.8 1.0 CD2 B:HIS116 4.1 19.4 1.0 ND1 B:HIS179 4.2 20.6 1.0 CG B:HIS179 4.2 13.5 1.0 CG B:HIS114 4.2 13.6 1.0 CB B:CYS198 4.2 12.3 1.0 SG B:CYS198 4.3 12.3 1.0 C15 B:S5Z301 4.5 32.5 1.0 OD2 B:ASP118 4.7 18.4 1.0 ND2 B:ASN210 4.7 52.0 1.0 CG B:ASP118 4.8 20.7 1.0 CA B:HIS116 4.8 19.4 1.0

Zinc binding site 5 out of 6 in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:18.9 occ:1.00 OD2 B:ASP118 2.1 18.4 1.0 NE2 B:HIS240 2.1 16.8 1.0 SG B:CYS198 2.3 12.3 1.0 S17 B:S5Z301 2.3 26.9 1.0 CD2 B:HIS240 3.0 17.3 1.0 CE1 B:HIS240 3.1 16.4 1.0 CG B:ASP118 3.1 20.7 1.0 C16 B:S5Z301 3.4 29.3 1.0 CB B:CYS198 3.4 12.3 1.0 OD1 B:ASP118 3.5 19.1 1.0 NH2 B:ARG119 3.7 14.4 1.0 ZN B:ZN304 3.7 18.2 1.0 C14 B:S5Z301 4.0 33.3 1.0 NE B:ARG119 4.1 16.6 1.0 ND1 B:HIS240 4.1 16.5 1.0 CG B:HIS240 4.1 18.2 1.0 C15 B:S5Z301 4.2 32.5 1.0 CE1 B:HIS114 4.3 16.1 1.0 CZ B:ARG119 4.3 21.7 1.0 CB B:ASP118 4.4 19.8 1.0 NE2 B:HIS114 4.4 12.3 1.0 NE2 B:HIS179 4.6 16.0 1.0 CA B:CYS198 4.7 11.9 1.0 O B:HOH480 4.7 24.3 1.0 CE1 B:HIS179 4.8 17.2 1.0

Zinc binding site 6 out of 6 in the Vim-2 Metallo Beta Lactamase in Complex with 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid


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 3-(Mercaptomethyl)-[1,1'- Biphenyl]-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:20.4 occ:1.00 O2 B:FMT303 2.0 19.5 1.0 O2 B:FMT302 2.0 19.7 1.0 NE2 B:HIS153 2.1 19.0 1.0 C B:FMT302 2.8 21.5 1.0 O1 B:FMT302 2.9 23.1 1.0 C B:FMT303 2.9 21.8 1.0 CE1 B:HIS153 2.9 21.3 1.0 O1 B:FMT303 3.0 22.9 1.0 CD2 B:HIS153 3.2 18.0 1.0 ND1 B:HIS153 4.1 21.9 1.0 CG B:HIS153 4.3 17.7 1.0 CB B:ALA132 4.3 16.2 1.0 O B:HOH410 4.8 31.2 1.0 CA B:ALA132 4.9 20.1 1.0 CG2 B:THR152 4.9 21.0 1.0

R.Cain, J.Brem, D.Zollman, M.A.Mcdonough, R.M.Johnson, J.Spencer, A.Makena, M.I.Abboud, S.Cahill, S.Y.Lee, P.J.Mchugh, C.J.Schofield, C.W.G.Fishwick. In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-Beta-Lactamase Inhibitors. J. Med. Chem. V. 61 1255 2018.
ISSN: ISSN 1520-4804
PubMed: 29271657
DOI: 10.1021/ACS.JMEDCHEM.7B01728