Zinc in PDB 5yd7: Crystal Structure of Vim-2 Metallo-Beta-Lactamase

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

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase, PDB code: 5yd7 was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.25 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.800, 79.270, 67.390, 90.00, 130.15, 90.00
R / Rfree (%)	16.3 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase (pdb code 5yd7). 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 Metallo-Beta-Lactamase, PDB code: 5yd7:
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 Metallo-Beta-Lactamase


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.6 occ:1.00 SG A:CYS198 2.0 19.3 1.0 NE2 A:HIS240 2.3 19.5 1.0 O A:HOH424 2.5 11.8 1.0 OD2 A:ASP118 2.5 23.8 1.0 O A:HOH471 2.9 27.9 1.0 CB A:CYS198 3.1 14.0 1.0 CD2 A:HIS240 3.2 19.5 1.0 CE1 A:HIS240 3.3 17.5 1.0 CG A:ASP118 3.5 17.8 1.0 ZN A:ZN302 3.8 17.3 1.0 OD1 A:ASP118 3.9 19.7 1.0 NH2 A:ARG119 3.9 18.9 1.0 O A:HOH510 4.1 21.1 1.0 NE A:ARG119 4.2 15.8 1.0 CE1 A:HIS114 4.2 9.2 1.0 NE2 A:HIS179 4.3 9.5 1.0 CA A:CYS198 4.3 11.5 1.0 O A:HOH554 4.3 21.1 1.0 ND1 A:HIS240 4.4 17.0 1.0 CG A:HIS240 4.4 14.3 1.0 CE1 A:HIS179 4.4 11.6 1.0 O A:HOH422 4.5 26.2 1.0 NE2 A:HIS114 4.5 10.9 1.0 CZ A:ARG119 4.6 19.3 1.0 CB A:ASP118 4.8 22.4 1.0 N A:CYS198 4.9 10.4 1.0

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


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.3 occ:1.00 ND1 A:HIS116 2.0 16.8 1.0 O A:HOH424 2.0 11.8 1.0 NE2 A:HIS179 2.0 9.5 1.0 NE2 A:HIS114 2.1 10.9 1.0 O A:HOH422 2.8 26.2 1.0 CG A:HIS116 3.0 14.5 1.0 CE1 A:HIS179 3.0 11.6 1.0 CE1 A:HIS116 3.0 15.1 1.0 CD2 A:HIS179 3.0 9.9 1.0 CE1 A:HIS114 3.0 9.2 1.0 CD2 A:HIS114 3.1 10.7 1.0 CB A:HIS116 3.3 15.0 1.0 ZN A:ZN301 3.8 23.6 1.0 OD1 A:ASP118 4.1 19.7 1.0 ND1 A:HIS179 4.1 8.6 1.0 NE2 A:HIS116 4.1 16.4 1.0 CD2 A:HIS116 4.1 15.6 1.0 CG A:HIS179 4.1 9.4 1.0 ND1 A:HIS114 4.1 10.6 1.0 CG A:HIS114 4.2 8.7 1.0 SG A:CYS198 4.4 19.3 1.0 CB A:CYS198 4.4 14.0 1.0 OD2 A:ASP118 4.7 23.8 1.0 CA A:HIS116 4.8 16.2 1.0 CG A:ASP118 4.8 17.8 1.0

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


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:13.4 occ:1.00 O2 A:FMT305 1.5 22.5 1.0 O2 A:FMT304 1.9 22.2 1.0 NE2 A:HIS153 2.0 11.3 1.0 O1 A:FMT305 2.1 12.6 1.0 C A:FMT305 2.2 12.2 1.0 C A:FMT304 2.7 15.0 1.0 CE1 A:HIS153 2.9 12.4 1.0 O1 A:FMT304 2.9 29.2 1.0 CD2 A:HIS153 3.1 11.3 1.0 ND1 A:HIS153 4.1 11.7 1.0 O A:HOH401 4.1 30.9 1.0 CG A:HIS153 4.2 10.3 1.0 CB A:ALA132 4.3 10.0 1.0 CG2 A:THR152 4.7 12.1 1.0 O A:HOH549 4.9 19.5 1.0 CA A:ALA132 5.0 10.0 1.0

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


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.0 occ:1.00 SG B:CYS198 2.1 18.4 1.0 O2 B:FMT306 2.2 17.2 1.0 NE2 B:HIS240 2.3 17.5 1.0 O B:HOH427 2.3 18.8 1.0 OD2 B:ASP118 2.4 25.3 1.0 CB B:CYS198 3.1 14.0 1.0 CD2 B:HIS240 3.2 15.3 1.0 O B:HOH547 3.2 28.1 1.0 CE1 B:HIS240 3.3 18.0 1.0 C B:FMT306 3.4 29.5 1.0 CG B:ASP118 3.4 16.4 1.0 ZN B:ZN302 3.7 18.9 1.0 OD1 B:ASP118 3.9 18.6 1.0 NH2 B:ARG119 3.9 16.5 1.0 NE B:ARG119 4.2 12.8 1.0 NE2 B:HIS179 4.2 11.6 1.0 CE1 B:HIS114 4.2 12.2 1.0 O B:HOH522 4.3 18.2 1.0 CA B:CYS198 4.3 12.2 1.0 ND1 B:HIS240 4.3 15.8 1.0 CG B:HIS240 4.4 14.8 1.0 CE1 B:HIS179 4.4 13.0 1.0 O1 B:FMT306 4.4 23.3 1.0 NE2 B:HIS114 4.5 11.4 1.0 CZ B:ARG119 4.5 16.5 1.0 CB B:ASP118 4.7 17.5 1.0 O B:HOH412 4.7 31.5 1.0 N B:CYS198 5.0 12.3 1.0

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


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.9 occ:1.00 ND1 B:HIS116 1.9 16.8 1.0 NE2 B:HIS114 2.0 11.4 1.0 NE2 B:HIS179 2.0 11.6 1.0 O B:HOH427 2.1 18.8 1.0 O B:HOH412 2.8 31.5 1.0 CE1 B:HIS116 2.9 18.1 1.0 CG B:HIS116 2.9 16.7 1.0 CD2 B:HIS179 2.9 12.8 1.0 CE1 B:HIS114 2.9 12.2 1.0 CD2 B:HIS114 3.0 12.9 1.0 CE1 B:HIS179 3.1 13.0 1.0 CB B:HIS116 3.3 17.6 1.0 ZN B:ZN301 3.7 23.0 1.0 NE2 B:HIS116 4.0 20.9 1.0 CD2 B:HIS116 4.0 19.3 1.0 OD1 B:ASP118 4.0 18.6 1.0 ND1 B:HIS114 4.1 12.8 1.0 CG B:HIS179 4.1 9.8 1.0 CG B:HIS114 4.1 10.8 1.0 ND1 B:HIS179 4.1 10.8 1.0 O2 B:FMT306 4.2 17.2 1.0 CB B:CYS198 4.3 14.0 1.0 SG B:CYS198 4.4 18.4 1.0 OD2 B:ASP118 4.5 25.3 1.0 CG B:ASP118 4.7 16.4 1.0 CA B:HIS116 4.7 18.0 1.0 C B:FMT306 5.0 29.5 1.0

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


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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:15.2 occ:1.00 O2 B:FMT305 1.8 22.0 1.0 O2 B:FMT304 1.9 23.8 1.0 NE2 B:HIS153 2.0 14.2 1.0 C B:FMT305 2.6 15.0 1.0 O1 B:FMT305 2.7 13.5 1.0 CE1 B:HIS153 2.8 12.4 1.0 C B:FMT304 3.0 26.6 1.0 CD2 B:HIS153 3.2 15.2 1.0 O1 B:FMT304 3.2 25.8 1.0 ND1 B:HIS153 4.0 13.2 1.0 CB B:ALA132 4.2 12.3 1.0 CG B:HIS153 4.2 12.2 1.0 O B:HOH401 4.6 31.0 1.0 CA B:ALA132 4.9 11.4 1.0 CG2 B:THR152 5.0 14.3 1.0

J.Wachino, J.Wachino. N/A N/A.