Zinc in PDB 7a5z: Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product

The structure of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product, PDB code: 7a5z was solved by A.Lucic, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 1.29
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.647, 74.68, 78.766, 90, 90, 90
R / Rfree (%)	14 / 15.8

The structure of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product (pdb code 7a5z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product, PDB code: 7a5z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.9 occ:0.82 NE2 A:HIS153 2.1 15.7 1.0 CL A:CL305 2.2 17.4 1.0 CL A:CL306 2.2 17.5 1.0 CE1 A:HIS153 2.9 16.2 1.0 HE1 A:HIS153 2.9 19.5 1.0 CD2 A:HIS153 3.2 14.4 1.0 HB1 A:ALA132 3.5 16.0 1.0 HD2 A:HIS153 3.5 17.3 1.0 HB2 A:ALA132 3.6 16.0 1.0 CB A:ALA132 4.0 13.3 1.0 ND1 A:HIS153 4.1 16.8 1.0 CG A:HIS153 4.3 13.7 1.0 HA A:ALA132 4.4 14.8 1.0 O A:HOH434 4.6 23.4 1.0 HG22 A:THR152 4.6 19.4 1.0 HG21 A:THR152 4.7 19.4 1.0 HB3 A:ALA132 4.7 16.0 1.0 CA A:ALA132 4.8 12.3 1.0 HD1 A:HIS153 4.8 20.1 1.0

Zinc binding site 2 out of 3 in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:11.9 occ:1.00 O09 A:QZH301 1.9 12.2 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 11.8 1.0 C07 A:QZH301 2.6 12.2 1.0 O08 A:QZH301 2.8 12.7 1.0 HB2 A:HIS116 2.8 12.8 1.0 CD2 A:HIS179 3.0 10.1 1.0 CG A:HIS116 3.0 11.1 1.0 CE1 A:HIS116 3.0 13.8 1.0 CE1 A:HIS114 3.0 9.9 1.0 CE1 A:HIS179 3.0 10.9 1.0 CD2 A:HIS114 3.0 10.8 1.0 HD2 A:HIS179 3.2 12.1 1.0 HE1 A:HIS114 3.2 11.8 1.0 HE1 A:HIS116 3.2 16.5 1.0 HE1 A:HIS179 3.2 13.1 1.0 HD2 A:HIS114 3.2 12.9 1.0 CB A:HIS116 3.3 10.7 1.0 HB3 A:HIS116 3.5 12.8 1.0 HB2 A:CYS198 3.9 12.0 1.0 ND1 A:HIS114 4.1 10.6 1.0 C06 A:QZH301 4.1 12.5 1.0 NE2 A:HIS116 4.1 13.9 1.0 ND1 A:HIS179 4.1 11.3 1.0 CD2 A:HIS116 4.1 13.3 1.0 CG A:HIS179 4.1 10.4 1.0 OD1 A:ASP118 4.1 11.5 1.0 CG A:HIS114 4.2 9.8 1.0 SG A:CYS198 4.2 12.1 1.0 HD22 A:ASN210 4.2 25.2 1.0 HB3 A:CYS198 4.3 12.0 1.0 ZN A:ZN304 4.3 10.4 0.8 CB A:CYS198 4.3 10.0 1.0 O12 A:QZH301 4.3 12.8 1.0 H101 A:QZH301 4.3 14.8 1.0 N04 A:QZH301 4.4 12.4 1.0 H A:HIS116 4.4 11.6 1.0 HB3 A:SER180 4.5 14.4 1.0 H121 A:QZH301 4.5 15.4 1.0 C10 A:QZH301 4.5 12.3 1.0 CA A:HIS116 4.7 9.9 1.0 H061 A:QZH301 4.8 15.0 1.0 O20 A:QZH301 4.8 12.3 1.0 OD2 A:ASP118 4.9 11.2 1.0 HD1 A:HIS114 4.9 12.7 1.0 HD1 A:HIS179 4.9 13.5 1.0 HE2 A:HIS116 4.9 16.7 1.0 HG2 A:ARG119 4.9 12.5 1.0 CG A:ASP118 4.9 10.7 1.0 C05 A:QZH301 4.9 13.0 1.0 O A:HOH492 4.9 16.4 1.0 ND2 A:ASN210 5.0 21.0 1.0 N A:HIS116 5.0 9.7 1.0 HD2 A:HIS116 5.0 16.0 1.0

Zinc binding site 3 out of 3 in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:10.4 occ:0.85 NE2 A:HIS240 2.1 10.4 1.0 OD2 A:ASP118 2.1 11.2 1.0 N04 A:QZH301 2.1 12.4 1.0 O20 A:QZH301 2.3 12.3 1.0 SG A:CYS198 2.3 12.1 1.0 C03 A:QZH301 2.9 13.2 1.0 C02 A:QZH301 3.0 13.2 1.0 CE1 A:HIS240 3.0 8.8 1.0 HH21 A:ARG119 3.1 18.4 1.0 CD2 A:HIS240 3.1 10.5 1.0 HE1 A:HIS240 3.2 10.5 1.0 C05 A:QZH301 3.2 13.0 1.0 CG A:ASP118 3.2 10.7 1.0 O09 A:QZH301 3.2 12.2 1.0 H051 A:QZH301 3.2 15.6 1.0 HB3 A:CYS198 3.3 12.0 1.0 HD2 A:HIS240 3.3 12.7 1.0 CB A:CYS198 3.5 10.0 1.0 C07 A:QZH301 3.6 12.2 1.0 OD1 A:ASP118 3.6 11.5 1.0 HE A:ARG119 3.8 14.1 1.0 NH2 A:ARG119 3.9 15.4 1.0 C06 A:QZH301 4.0 12.5 1.0 HB2 A:CYS198 4.0 12.0 1.0 HE1 A:HIS114 4.1 11.8 1.0 ND1 A:HIS240 4.2 10.4 1.0 C14 A:QZH301 4.2 15.2 1.0 HE1 A:HIS179 4.2 13.1 1.0 CG A:HIS240 4.2 9.7 1.0 O01 A:QZH301 4.2 14.5 1.0 ZN A:ZN303 4.3 11.9 1.0 O08 A:QZH301 4.3 12.7 1.0 HA A:CYS198 4.3 13.0 1.0 HH22 A:ARG119 4.4 18.4 1.0 O A:HOH444 4.4 12.6 1.0 CE1 A:HIS179 4.5 10.9 1.0 CB A:ASP118 4.5 11.3 1.0 O12 A:QZH301 4.5 12.8 1.0 NE A:ARG119 4.5 11.8 1.0 CA A:CYS198 4.5 10.8 1.0 NE2 A:HIS179 4.6 9.9 1.0 S13 A:QZH301 4.6 14.6 1.0 HB3 A:ASP118 4.6 13.6 1.0 HB2 A:ASP118 4.6 13.6 1.0 CZ A:ARG119 4.6 13.8 1.0 HA3 A:GLY239 4.8 13.2 1.0 H061 A:QZH301 4.8 15.0 1.0 CE1 A:HIS114 4.9 9.9 1.0 C10 A:QZH301 4.9 12.3 1.0 HD1 A:HIS240 4.9 12.5 1.0

A.Lucic, P.Hinchliffe, T.R.Malla, C.L.Tooke, J.Brem, K.Calvopina, C.T.Lohans, P.Rabe, M.A.Mcdonough, T.Armistead, A.M.Orville, J.Spencer, C.J.Schofield. Faropenem Reacts with Serine and Metallo-Beta-Lactamases to Give Multiple Products Eur.J.Med.Chem. 2021.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2021.113257