Zinc in PDB 7a60: Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)

The structure of Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form), PDB code: 7a60 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.34 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.179, 79.38, 67.332, 90, 130.38, 90
R / Rfree (%)	16.3 / 18.9

The binding sites of Zinc atom in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) (pdb code 7a60). 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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form), PDB code: 7a60:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:18.1 occ:1.00 O08 A:QZH306 1.9 18.5 1.0 NE2 A:HIS179 2.0 15.9 1.0 ND1 A:HIS116 2.1 17.3 1.0 NE2 A:HIS114 2.1 14.4 1.0 C07 A:QZH306 2.6 23.6 1.0 O09 A:QZH306 2.7 21.7 1.0 HB2 A:HIS116 2.8 21.1 1.0 CE1 A:HIS179 3.0 17.0 1.0 CD2 A:HIS179 3.0 16.4 1.0 CE1 A:HIS114 3.0 16.1 1.0 CG A:HIS116 3.0 15.6 1.0 CE1 A:HIS116 3.1 17.8 1.0 CD2 A:HIS114 3.1 14.9 1.0 HE1 A:HIS114 3.2 19.3 1.0 HD2 A:HIS179 3.2 19.7 1.0 HE1 A:HIS179 3.2 20.5 1.0 HE1 A:HIS116 3.3 21.4 1.0 CB A:HIS116 3.3 17.6 1.0 HD2 A:HIS114 3.3 17.9 1.0 HB3 A:HIS116 3.5 21.1 1.0 HB2 A:CYS198 3.9 15.3 1.0 ND1 A:HIS179 4.1 15.5 1.0 ND1 A:HIS114 4.1 15.4 1.0 CG A:HIS179 4.1 13.9 1.0 C06 A:QZH306 4.1 22.8 1.0 OD1 A:ASP118 4.2 23.1 1.0 NE2 A:HIS116 4.2 22.7 1.0 CD2 A:HIS116 4.2 18.2 1.0 CG A:HIS114 4.2 14.1 1.0 HD22 A:ASN210 4.2 41.9 1.0 ZN A:ZN304 4.2 22.4 1.0 SG A:CYS198 4.2 18.0 1.0 HB3 A:CYS198 4.3 15.3 1.0 O12 A:QZH306 4.3 25.5 1.0 CB A:CYS198 4.3 12.8 1.0 H A:HIS116 4.5 17.8 1.0 H101 A:QZH306 4.6 42.0 1.0 N04 A:QZH306 4.6 21.8 1.0 C10 A:QZH306 4.6 25.6 1.0 HB3 A:SER180 4.6 16.8 1.0 CA A:HIS116 4.7 16.4 1.0 O20 A:QZH306 4.8 24.6 1.0 H061 A:QZH306 4.8 28.8 1.0 OD2 A:ASP118 4.8 21.7 1.0 HD1 A:HIS179 4.8 18.6 1.0 HD1 A:HIS114 4.9 18.5 1.0 ND2 A:ASN210 4.9 34.9 1.0 CG A:ASP118 4.9 19.3 1.0 C05 A:QZH306 4.9 19.3 1.0 HE2 A:HIS116 4.9 27.2 1.0 HG2 A:ARG119 5.0 21.3 1.0 C03 A:QZH306 5.0 21.8 1.0 N A:HIS116 5.0 14.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:22.4 occ:1.00 NE2 A:HIS240 2.1 16.7 1.0 N04 A:QZH306 2.1 21.8 1.0 OD2 A:ASP118 2.2 21.7 1.0 O20 A:QZH306 2.3 24.6 1.0 SG A:CYS198 2.3 18.0 1.0 C03 A:QZH306 2.7 21.8 1.0 C02 A:QZH306 2.9 21.8 1.0 HH21 A:ARG119 3.0 29.9 1.0 CE1 A:HIS240 3.1 17.1 1.0 CD2 A:HIS240 3.1 17.3 1.0 O08 A:QZH306 3.2 18.5 1.0 HE1 A:HIS240 3.2 20.6 1.0 HD2 A:HIS240 3.2 20.8 1.0 C05 A:QZH306 3.3 19.3 1.0 CG A:ASP118 3.3 19.3 1.0 HB3 A:CYS198 3.3 15.3 1.0 CB A:CYS198 3.5 12.8 1.0 H051 A:QZH306 3.6 31.6 1.0 C07 A:QZH306 3.7 23.6 1.0 OD1 A:ASP118 3.7 23.1 1.0 NH2 A:ARG119 3.8 24.9 1.0 HE A:ARG119 3.8 23.0 1.0 HB2 A:CYS198 4.1 15.3 1.0 HE1 A:HIS114 4.1 19.3 1.0 C14 A:QZH306 4.1 21.2 1.0 C06 A:QZH306 4.1 22.8 1.0 ND1 A:HIS240 4.2 15.5 1.0 O01 A:QZH306 4.2 25.8 1.0 CG A:HIS240 4.2 15.2 1.0 HE1 A:HIS179 4.2 20.5 1.0 ZN A:ZN303 4.2 18.1 1.0 HH22 A:ARG119 4.3 29.9 1.0 O A:HOH425 4.3 18.0 1.0 O09 A:QZH306 4.4 21.7 1.0 HA A:CYS198 4.4 17.1 1.0 CE1 A:HIS179 4.5 17.0 1.0 NE A:ARG119 4.5 19.2 1.0 CB A:ASP118 4.5 16.5 1.0 S13 A:QZH306 4.5 24.4 1.0 CA A:CYS198 4.6 14.2 1.0 NE2 A:HIS179 4.6 15.9 1.0 O12 A:QZH306 4.6 25.5 1.0 H121 A:QZH306 4.6 29.9 1.0 CZ A:ARG119 4.6 19.7 1.0 HB3 A:ASP118 4.7 19.8 1.0 HB2 A:ASP118 4.7 19.8 1.0 HA3 A:GLY239 4.8 19.6 1.0 CE1 A:HIS114 4.8 16.1 1.0 H061 A:QZH306 4.9 28.8 1.0 HD1 A:HIS240 4.9 18.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:23.6 occ:1.00 O2 A:FMT302 1.9 31.9 1.0 NE2 A:HIS153 2.0 20.5 1.0 O1 A:FMT301 2.1 25.7 1.0 C A:FMT302 2.6 26.8 1.0 O1 A:FMT302 2.7 32.2 1.0 CE1 A:HIS153 2.8 21.8 1.0 HE1 A:HIS153 2.9 26.2 1.0 C A:FMT301 3.1 31.9 1.0 CD2 A:HIS153 3.1 18.7 1.0 O2 A:FMT301 3.3 25.1 1.0 HD2 A:HIS153 3.4 22.4 1.0 H A:FMT302 3.6 32.2 1.0 HB1 A:ALA132 3.7 20.7 1.0 HB2 A:ALA132 4.0 20.7 1.0 ND1 A:HIS153 4.0 20.6 1.0 H A:FMT301 4.1 38.3 1.0 CG A:HIS153 4.2 18.7 1.0 HG22 A:THR152 4.3 23.9 1.0 CB A:ALA132 4.3 17.3 1.0 HG21 A:THR152 4.4 23.9 1.0 HA A:ALA132 4.4 21.2 1.0 HD1 A:HIS153 4.8 24.7 1.0 CG2 A:THR152 4.8 19.9 1.0 CA A:ALA132 4.9 17.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:17.8 occ:1.00 ND1 B:HIS116 2.0 18.8 1.0 O08 B:QZH306 2.0 17.0 1.0 NE2 B:HIS179 2.0 14.6 1.0 NE2 B:HIS114 2.0 13.6 1.0 C07 B:QZH306 2.6 18.4 1.0 O09 B:QZH306 2.7 20.3 1.0 HB2 B:HIS116 2.8 20.7 1.0 CE1 B:HIS116 2.9 17.8 1.0 CE1 B:HIS179 3.0 13.7 1.0 CG B:HIS116 3.0 17.4 1.0 CE1 B:HIS114 3.0 15.9 1.0 CD2 B:HIS179 3.0 15.8 1.0 CD2 B:HIS114 3.1 14.7 1.0 HE1 B:HIS114 3.1 19.1 1.0 HE1 B:HIS116 3.1 21.3 1.0 HE1 B:HIS179 3.1 16.4 1.0 HD2 B:HIS179 3.2 18.9 1.0 HD2 B:HIS114 3.3 17.6 1.0 CB B:HIS116 3.3 17.3 1.0 HB3 B:HIS116 3.6 20.7 1.0 HB2 B:CYS198 3.9 13.3 1.0 NE2 B:HIS116 4.1 21.8 1.0 ND1 B:HIS179 4.1 14.3 1.0 ND1 B:HIS114 4.1 14.4 1.0 CD2 B:HIS116 4.1 20.0 1.0 C06 B:QZH306 4.1 20.4 1.0 CG B:HIS179 4.1 15.7 1.0 OD1 B:ASP118 4.1 18.9 1.0 CG B:HIS114 4.1 13.1 1.0 SG B:CYS198 4.2 18.2 1.0 ZN B:ZN304 4.2 19.6 1.0 HB3 B:CYS198 4.2 13.3 1.0 HD22 B:ASN210 4.2 28.5 1.0 O12 B:QZH306 4.3 22.2 1.0 CB B:CYS198 4.3 11.1 1.0 H101 B:QZH306 4.4 28.7 1.0 H B:HIS116 4.5 19.0 1.0 C10 B:QZH306 4.5 25.3 1.0 N04 B:QZH306 4.5 17.2 1.0 H121 B:QZH306 4.5 19.8 1.0 HB3 B:SER180 4.6 17.8 1.0 CA B:HIS116 4.7 15.4 1.0 H061 B:QZH306 4.8 23.6 1.0 OD2 B:ASP118 4.8 19.3 1.0 O20 B:QZH306 4.8 18.6 1.0 HE2 B:HIS116 4.8 26.2 1.0 HD1 B:HIS179 4.8 17.2 1.0 HD1 B:HIS114 4.8 17.2 1.0 C05 B:QZH306 4.9 19.9 1.0 CG B:ASP118 4.9 17.4 1.0 ND2 B:ASN210 4.9 23.8 1.0 HD2 B:HIS116 4.9 24.0 1.0 HG2 B:ARG119 5.0 18.6 1.0 N B:HIS116 5.0 15.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:19.6 occ:1.00 NE2 B:HIS240 2.1 13.8 1.0 N04 B:QZH306 2.1 17.2 1.0 OD2 B:ASP118 2.1 19.3 1.0 SG B:CYS198 2.3 18.2 1.0 O20 B:QZH306 2.3 18.6 1.0 C03 B:QZH306 2.8 17.6 1.0 C02 B:QZH306 2.9 18.2 1.0 CE1 B:HIS240 3.0 16.9 1.0 HH21 B:ARG119 3.0 33.5 1.0 O08 B:QZH306 3.1 17.0 1.0 CD2 B:HIS240 3.1 16.8 1.0 HE1 B:HIS240 3.1 20.3 1.0 CG B:ASP118 3.2 17.4 1.0 C05 B:QZH306 3.3 19.9 1.0 HD2 B:HIS240 3.3 20.2 1.0 HB3 B:CYS198 3.4 13.3 1.0 H051 B:QZH306 3.5 25.0 1.0 CB B:CYS198 3.5 11.1 1.0 C07 B:QZH306 3.6 18.4 1.0 OD1 B:ASP118 3.7 18.9 1.0 HE B:ARG119 3.8 20.6 1.0 NH2 B:ARG119 3.8 27.9 1.0 HE1 B:HIS114 4.1 19.1 1.0 C06 B:QZH306 4.1 20.4 1.0 HB2 B:CYS198 4.1 13.3 1.0 ND1 B:HIS240 4.1 17.4 1.0 C14 B:QZH306 4.1 18.7 1.0 O01 B:QZH306 4.2 25.7 1.0 HE1 B:HIS179 4.2 16.4 1.0 ZN B:ZN303 4.2 17.8 1.0 CG B:HIS240 4.2 14.8 1.0 HH22 B:ARG119 4.3 33.5 1.0 O B:HOH419 4.3 16.5 1.0 O09 B:QZH306 4.3 20.3 1.0 HA B:CYS198 4.4 14.8 1.0 CE1 B:HIS179 4.5 13.7 1.0 O12 B:QZH306 4.5 22.2 1.0 CB B:ASP118 4.5 15.7 1.0 NE B:ARG119 4.5 17.2 1.0 S13 B:QZH306 4.6 23.0 1.0 CA B:CYS198 4.6 12.3 1.0 NE2 B:HIS179 4.6 14.6 1.0 HB3 B:ASP118 4.6 18.9 1.0 CZ B:ARG119 4.6 23.8 1.0 HB2 B:ASP118 4.6 18.9 1.0 CE1 B:HIS114 4.8 15.9 1.0 HA3 B:GLY239 4.8 15.3 1.0 HD1 B:HIS240 4.9 20.8 1.0 H061 B:QZH306 4.9 23.6 1.0 C10 B:QZH306 5.0 25.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 with Hydrolyzed Faropenem (Ring-Open Form)


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 Vim-2 with Hydrolyzed Faropenem (Ring-Open Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:39.6 occ:1.00 O1 B:FMT301 1.7 34.7 1.0 O2 B:FMT302 2.1 48.3 1.0 NE2 B:HIS153 2.2 23.3 1.0 C B:FMT301 2.3 40.5 1.0 O2 B:FMT301 2.3 48.6 1.0 HE1 B:HIS153 2.7 30.1 1.0 CE1 B:HIS153 2.8 25.0 1.0 C B:FMT302 3.1 48.0 1.0 H B:FMT301 3.4 48.7 1.0 O1 B:FMT302 3.5 38.5 1.0 CD2 B:HIS153 3.5 19.9 1.0 HB1 B:ALA132 3.8 24.9 1.0 HB2 B:ALA132 3.8 24.9 1.0 HD2 B:HIS153 3.9 23.9 1.0 ND1 B:HIS153 4.0 24.1 1.0 H B:FMT302 4.1 57.6 1.0 CB B:ALA132 4.3 20.8 1.0 O B:HOH403 4.3 34.1 1.0 CG B:HIS153 4.4 22.6 1.0 HA B:ALA132 4.5 26.3 1.0 HG22 B:THR152 4.7 30.4 1.0 HD1 B:HIS153 4.7 28.9 1.0 HG21 B:THR152 4.8 30.4 1.0 CA B:ALA132 5.0 21.9 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