Zinc in PDB 5fqc: Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C:
3.5.2.6;

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C, PDB code: 5fqc was solved by J.Brem, R.Cain, M.A.Mcdonough, I.J.Clifton, C.W.G.Fishwick, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.89 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.931, 79.152, 67.135, 90.00, 130.16, 90.00
R / Rfree (%)	15.5 / 18.5

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C (pdb code 5fqc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C, PDB code: 5fqc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:11.7 occ:1.00 O18 A:OK3600 2.0 11.2 1.0 ND1 A:HIS116 2.0 11.6 1.0 NE2 A:HIS179 2.0 9.9 1.0 NE2 A:HIS114 2.0 9.6 1.0 O19 A:OK3600 2.6 15.2 1.0 CD2 A:HIS179 3.0 10.7 1.0 CE1 A:HIS114 3.0 9.2 1.0 CE1 A:HIS116 3.0 11.9 1.0 B17 A:OK3600 3.0 19.7 1.0 CG A:HIS116 3.0 11.6 1.0 CE1 A:HIS179 3.1 9.9 1.0 CD2 A:HIS114 3.1 10.0 1.0 CB A:HIS116 3.3 11.4 1.0 O16 A:OK3600 3.9 13.5 1.0 NE2 A:HIS116 4.1 12.3 1.0 OD1 A:ASP118 4.1 12.3 1.0 ND1 A:HIS114 4.1 9.7 1.0 CD2 A:HIS116 4.1 11.9 1.0 ND1 A:HIS179 4.1 10.6 1.0 CG A:HIS179 4.1 11.0 1.0 CG A:HIS114 4.2 10.2 1.0 C12 A:OK3600 4.2 17.0 1.0 ZN A:ZN501 4.3 13.5 1.0 N11 A:OK3600 4.5 18.3 1.0 SG A:CYS198 4.5 11.8 1.0 CB A:CYS198 4.5 12.3 1.0 CA A:HIS116 4.7 11.8 1.0 O A:HOH2147 4.7 20.3 1.0 O26 A:OK3600 4.9 12.2 1.0 OD1 A:ASN210 4.9 19.9 1.0 N A:HIS116 4.9 11.9 1.0 OD2 A:ASP118 5.0 12.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.5 occ:1.00 O16 A:OK3600 2.0 13.5 1.0 NE2 A:HIS240 2.0 10.2 1.0 O26 A:OK3600 2.2 12.2 1.0 OD2 A:ASP118 2.3 12.3 1.0 SG A:CYS198 2.3 11.8 1.0 C15 A:OK3600 3.0 14.3 1.0 CD2 A:HIS240 3.0 10.5 1.0 CE1 A:HIS240 3.1 10.4 1.0 O18 A:OK3600 3.1 11.2 1.0 B17 A:OK3600 3.1 19.7 1.0 C24 A:OK3600 3.1 14.7 1.0 CG A:ASP118 3.4 12.2 1.0 C20 A:OK3600 3.4 15.0 1.0 CB A:CYS198 3.4 12.3 1.0 OD1 A:ASP118 3.8 12.3 1.0 NH2 A:ARG119 4.0 12.9 1.0 O19 A:OK3600 4.0 15.2 1.0 C14 A:OK3600 4.0 13.7 1.0 ND1 A:HIS240 4.2 10.8 1.0 CG A:HIS240 4.2 10.8 1.0 C12 A:OK3600 4.3 17.0 1.0 O25 A:OK3600 4.3 14.5 1.0 O A:HOH2156 4.3 12.6 1.0 ZN A:ZN500 4.3 11.7 1.0 C13 A:OK3600 4.4 16.2 1.0 CE1 A:HIS179 4.5 9.9 1.0 NE2 A:HIS179 4.5 9.9 1.0 CA A:CYS198 4.5 12.5 1.0 NE A:ARG119 4.5 12.2 1.0 CB A:ASP118 4.6 12.7 1.0 C21 A:OK3600 4.7 15.8 1.0 CZ A:ARG119 4.8 12.4 1.0 CE1 A:HIS114 4.8 9.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:17.4 occ:1.00 O1 A:FMT401 1.8 22.1 1.0 NE2 A:HIS153 2.0 15.0 1.0 O1 A:FMT400 2.1 20.1 1.0 C A:FMT401 2.5 23.2 1.0 O2 A:FMT401 2.6 22.2 1.0 CE1 A:HIS153 2.9 15.8 1.0 CD2 A:HIS153 3.1 13.9 1.0 C A:FMT400 3.1 22.3 1.0 O2 A:FMT400 3.4 23.1 1.0 ND1 A:HIS153 4.0 15.2 1.0 CB A:ALA132 4.2 14.1 1.0 CG A:HIS153 4.2 14.0 1.0 O A:HOH2096 4.5 39.9 1.0 CG2 A:THR152 4.8 15.0 1.0 CA A:ALA132 4.9 14.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:12.2 occ:1.00 O18 B:OK3600 1.9 12.9 1.0 NE2 B:HIS179 2.0 9.4 1.0 ND1 B:HIS116 2.0 11.4 1.0 NE2 B:HIS114 2.1 11.2 1.0 O19 B:OK3600 2.5 9.9 1.0 CE1 B:HIS116 3.0 12.4 1.0 CD2 B:HIS179 3.0 9.9 1.0 B17 B:OK3600 3.0 19.9 1.0 CE1 B:HIS114 3.0 10.6 1.0 CE1 B:HIS179 3.0 9.8 1.0 CG B:HIS116 3.0 12.0 1.0 CD2 B:HIS114 3.1 11.9 1.0 CB B:HIS116 3.4 11.3 1.0 O16 B:OK3600 3.8 10.5 1.0 ND1 B:HIS179 4.1 10.2 1.0 NE2 B:HIS116 4.1 13.0 1.0 ND1 B:HIS114 4.1 10.3 1.0 CG B:HIS179 4.1 10.1 1.0 CD2 B:HIS116 4.1 12.7 1.0 OD1 B:ASP118 4.2 11.6 1.0 CG B:HIS114 4.2 11.1 1.0 C12 B:OK3600 4.2 11.9 1.0 ZN B:ZN501 4.4 12.8 1.0 SG B:CYS198 4.4 11.4 1.0 CB B:CYS198 4.5 11.2 1.0 N11 B:OK3600 4.5 13.2 1.0 CA B:HIS116 4.7 11.2 1.0 O B:HOH2156 4.8 20.8 1.0 OD1 B:ASN210 4.9 17.9 1.0 O26 B:OK3600 4.9 12.8 1.0 N B:HIS116 5.0 10.5 1.0 OD2 B:ASP118 5.0 10.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:12.8 occ:1.00 NE2 B:HIS240 2.0 10.8 1.0 O16 B:OK3600 2.0 10.5 1.0 O26 B:OK3600 2.2 12.8 1.0 SG B:CYS198 2.3 11.4 1.0 OD2 B:ASP118 2.3 10.8 1.0 CE1 B:HIS240 3.0 11.5 1.0 CD2 B:HIS240 3.0 11.0 1.0 C15 B:OK3600 3.0 12.1 1.0 C24 B:OK3600 3.1 14.6 1.0 B17 B:OK3600 3.1 19.9 1.0 O18 B:OK3600 3.1 12.9 1.0 C20 B:OK3600 3.4 14.7 1.0 CG B:ASP118 3.4 11.3 1.0 CB B:CYS198 3.4 11.2 1.0 OD1 B:ASP118 3.8 11.6 1.0 NH2 B:ARG119 4.0 12.4 1.0 O19 B:OK3600 4.0 9.9 1.0 C14 B:OK3600 4.1 15.0 1.0 ND1 B:HIS240 4.1 11.9 1.0 CG B:HIS240 4.1 11.5 1.0 O B:HOH2168 4.2 11.5 1.0 O25 B:OK3600 4.3 14.1 1.0 C12 B:OK3600 4.4 11.9 1.0 ZN B:ZN500 4.4 12.2 1.0 CE1 B:HIS179 4.4 9.8 1.0 C13 B:OK3600 4.4 14.9 1.0 CA B:CYS198 4.5 10.7 1.0 NE B:ARG119 4.6 11.8 1.0 NE2 B:HIS179 4.6 9.4 1.0 CB B:ASP118 4.6 11.9 1.0 C21 B:OK3600 4.7 14.5 1.0 CZ B:ARG119 4.8 11.9 1.0 CE1 B:HIS114 4.8 10.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with 2C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:14.3 occ:1.00 O2 B:FMT400 1.9 16.7 1.0 NE2 B:HIS153 2.0 15.3 1.0 O1 B:FMT401 2.1 17.1 1.0 C B:FMT400 2.6 17.8 1.0 O1 B:FMT400 2.6 18.4 1.0 CE1 B:HIS153 2.9 15.8 1.0 C B:FMT401 3.0 17.9 1.0 CD2 B:HIS153 3.1 14.6 1.0 O2 B:FMT401 3.2 18.2 1.0 ND1 B:HIS153 4.1 15.1 1.0 CB B:ALA132 4.2 14.6 1.0 CG B:HIS153 4.2 14.3 1.0 CA B:ALA132 4.8 14.3 1.0 O B:HOH2104 4.8 19.2 1.0

J.Brem, R.Cain, S.Cahill, M.A.Mcdonough, I.J.Clifton, J.C.Jimenez-Castellanos, M.B.Avison, J.Spencer, C.W.Fishwick, C.J.Schofield. Structural Basis of Metallo-Beta-Lactamase, Serine-Beta-Lactamase and Penicillin-Binding Protein Inhibition By Cyclic Boronates. Nat Commun V. 7 12406 2016.
ISSN: ESSN 2041-1723
PubMed: 27499424
DOI: 10.1038/NCOMMS12406