Zinc in PDB 6kzn: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2, PDB code: 6kzn was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.61 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.960, 79.150, 77.740, 90.00, 138.40, 90.00
R / Rfree (%)	15.5 / 18.3

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2 (pdb code 6kzn). 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 in Complex with Inhibitor X2, PDB code: 6kzn:
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 in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:6.5 occ:1.00 NE2 A:HIS240 2.1 6.2 1.0 N2 A:E1C306 2.2 5.7 1.0 O3 A:E1C306 2.2 6.8 1.0 OD2 A:ASP118 2.3 6.7 1.0 SG A:CYS198 2.3 5.8 1.0 CD2 A:HIS240 3.0 5.8 1.0 C10 A:E1C306 3.1 7.4 1.0 CE1 A:HIS240 3.1 5.6 1.0 C2 A:E1C306 3.1 8.4 1.0 S1 A:E1C306 3.1 6.8 1.0 C3 A:E1C306 3.2 7.6 1.0 CG A:ASP118 3.3 6.0 1.0 CB A:CYS198 3.3 5.9 1.0 ZN A:ZN305 3.6 6.3 1.0 OD1 A:ASP118 3.7 6.3 1.0 O2 A:E1C306 3.8 6.9 1.0 NH2 A:ARG119 4.0 6.9 1.0 C1 A:E1C306 4.1 12.0 1.0 CG A:HIS240 4.2 6.1 1.0 ND1 A:HIS240 4.2 5.4 1.0 C4 A:E1C306 4.2 10.6 1.0 O A:HOH529 4.2 5.6 1.0 O1 A:E1C306 4.3 7.8 1.0 O4 A:E1C306 4.3 7.6 1.0 NE2 A:HIS179 4.3 5.8 1.0 CE1 A:HIS179 4.3 5.5 1.0 NE A:ARG119 4.4 6.5 1.0 CE1 A:HIS114 4.5 6.0 1.0 NE2 A:HIS114 4.5 6.4 1.0 CA A:CYS198 4.6 6.1 1.0 N1 A:E1C306 4.6 11.8 1.0 CB A:ASP118 4.6 6.4 1.0 CZ A:ARG119 4.7 7.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.7 occ:1.00 O2 A:FMT304 1.9 8.1 1.0 O2 A:FMT303 1.9 9.2 1.0 NE2 A:HIS153 2.0 8.5 1.0 C A:FMT303 2.7 9.3 1.0 C A:FMT304 2.8 10.8 1.0 O1 A:FMT303 2.9 9.5 1.0 CE1 A:HIS153 2.9 9.6 1.0 CD2 A:HIS153 3.1 8.9 1.0 O1 A:FMT304 3.1 9.8 1.0 ND1 A:HIS153 4.0 10.2 1.0 CG A:HIS153 4.2 8.3 1.0 CB A:ALA132 4.3 7.9 1.0 O A:HOH427 4.7 14.1 1.0 CA A:ALA132 4.8 8.1 1.0 CG2 A:THR152 4.8 10.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:6.3 occ:1.00 N2 A:E1C306 2.0 5.7 1.0 NE2 A:HIS179 2.0 5.8 1.0 NE2 A:HIS114 2.0 6.4 1.0 ND1 A:HIS116 2.0 6.8 1.0 O2 A:E1C306 2.8 6.9 1.0 S1 A:E1C306 2.9 6.8 1.0 CE1 A:HIS179 3.0 5.5 1.0 CD2 A:HIS114 3.0 6.0 1.0 CD2 A:HIS179 3.0 5.0 1.0 CE1 A:HIS116 3.0 6.6 1.0 CE1 A:HIS114 3.0 6.0 1.0 CG A:HIS116 3.0 6.4 1.0 CB A:HIS116 3.3 6.0 1.0 O1 A:E1C306 3.6 7.8 1.0 ZN A:ZN301 3.6 6.5 1.0 OD1 A:ASP118 4.0 6.3 1.0 O3 A:E1C306 4.0 6.8 1.0 CB A:CYS198 4.0 5.9 1.0 ND1 A:HIS179 4.1 5.3 1.0 ND1 A:HIS114 4.1 5.9 1.0 CG A:HIS179 4.1 5.4 1.0 SG A:CYS198 4.1 5.8 1.0 CG A:HIS114 4.1 5.6 1.0 NE2 A:HIS116 4.1 7.2 1.0 CD2 A:HIS116 4.2 7.0 1.0 C2 A:E1C306 4.3 8.4 1.0 OD2 A:ASP118 4.6 6.7 1.0 C10 A:E1C306 4.6 7.4 1.0 CG A:ASP118 4.7 6.0 1.0 CA A:HIS116 4.8 5.9 1.0 C3 A:E1C306 4.9 7.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:6.6 occ:1.00 NE2 B:HIS240 2.1 6.3 1.0 N2 B:E1C306 2.2 6.2 1.0 O4 B:E1C306 2.2 7.2 1.0 OD2 B:ASP118 2.3 6.4 1.0 SG B:CYS198 2.3 6.0 1.0 CD2 B:HIS240 3.0 6.3 1.0 C2 B:E1C306 3.1 8.0 1.0 C10 B:E1C306 3.1 7.8 1.0 CE1 B:HIS240 3.1 6.9 1.0 S1 B:E1C306 3.1 6.7 1.0 C3 B:E1C306 3.2 8.0 1.0 CG B:ASP118 3.3 6.2 1.0 CB B:CYS198 3.4 5.6 1.0 ZN B:ZN303 3.6 6.0 1.0 OD1 B:ASP118 3.7 7.0 1.0 O2 B:E1C306 3.9 6.4 1.0 NH2 B:ARG119 4.0 8.0 1.0 C1 B:E1C306 4.0 11.4 1.0 C4 B:E1C306 4.1 10.8 1.0 O B:HOH503 4.2 6.9 1.0 CG B:HIS240 4.2 6.9 1.0 ND1 B:HIS240 4.2 6.4 1.0 O1 B:E1C306 4.3 8.3 1.0 NE2 B:HIS179 4.3 6.1 1.0 O3 B:E1C306 4.3 9.8 1.0 NE B:ARG119 4.4 7.4 1.0 CE1 B:HIS179 4.4 6.4 1.0 CE1 B:HIS114 4.4 6.5 1.0 N1 B:E1C306 4.5 12.4 1.0 NE2 B:HIS114 4.5 6.0 1.0 CA B:CYS198 4.6 5.8 1.0 CB B:ASP118 4.6 6.8 1.0 CZ B:ARG119 4.6 7.5 1.0 C6 B:E1C306 4.9 13.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.9 occ:1.00 O2 B:FMT305 1.9 15.4 1.0 O2 B:FMT304 1.9 13.1 1.0 NE2 B:HIS153 2.0 8.0 1.0 C B:FMT304 2.7 11.7 1.0 O1 B:FMT304 2.9 14.6 1.0 CE1 B:HIS153 2.9 9.8 1.0 CD2 B:HIS153 3.1 9.1 1.0 C B:FMT305 3.1 25.8 1.0 O1 B:FMT305 3.9 20.3 1.0 ND1 B:HIS153 4.0 10.2 1.0 CG B:HIS153 4.1 8.5 1.0 CB B:ALA132 4.3 8.3 1.0 O B:HOH418 4.4 17.3 1.0 CG2 B:THR152 4.6 11.1 1.0 CA B:ALA132 4.9 7.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:6.0 occ:1.00 N2 B:E1C306 2.0 6.2 1.0 NE2 B:HIS179 2.0 6.1 1.0 NE2 B:HIS114 2.1 6.0 1.0 ND1 B:HIS116 2.1 6.3 1.0 O2 B:E1C306 2.9 6.4 1.0 S1 B:E1C306 2.9 6.7 1.0 CE1 B:HIS179 3.0 6.4 1.0 CD2 B:HIS179 3.0 5.6 1.0 CD2 B:HIS114 3.0 6.1 1.0 CE1 B:HIS114 3.0 6.5 1.0 CE1 B:HIS116 3.0 6.0 1.0 CG B:HIS116 3.1 5.8 1.0 CB B:HIS116 3.4 5.5 1.0 O1 B:E1C306 3.6 8.3 1.0 ZN B:ZN301 3.6 6.6 1.0 OD1 B:ASP118 4.0 7.0 1.0 O4 B:E1C306 4.0 7.2 1.0 CB B:CYS198 4.1 5.6 1.0 ND1 B:HIS179 4.1 6.1 1.0 ND1 B:HIS114 4.1 5.8 1.0 CG B:HIS179 4.1 5.5 1.0 CG B:HIS114 4.1 6.0 1.0 NE2 B:HIS116 4.2 6.2 1.0 CD2 B:HIS116 4.2 6.0 1.0 SG B:CYS198 4.2 6.0 1.0 C2 B:E1C306 4.4 8.0 1.0 OD2 B:ASP118 4.6 6.4 1.0 C10 B:E1C306 4.7 7.8 1.0 CG B:ASP118 4.7 6.2 1.0 CA B:HIS116 4.8 5.5 1.0 C3 B:E1C306 5.0 8.0 1.0

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