Zinc in PDB 6kxo: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9, PDB code: 6kxo was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.49 / 1.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.501, 79.210, 67.660, 90.00, 130.13, 90.00
R / Rfree (%)	14.6 / 16.9

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 (pdb code 6kxo). 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 NO9, PDB code: 6kxo:
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 NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.9 occ:1.00 NE2 A:HIS240 2.1 6.7 1.0 O5 A:NO9306 2.1 8.9 1.0 OD2 A:ASP118 2.3 7.6 1.0 SG A:CYS198 2.3 7.2 1.0 N1 A:NO9306 2.3 6.4 1.0 C5 A:NO9306 3.0 11.7 1.0 CD2 A:HIS240 3.0 6.6 1.0 CE1 A:HIS240 3.1 7.4 1.0 C2 A:NO9306 3.1 11.4 1.0 C1 A:NO9306 3.1 10.7 1.0 S A:NO9306 3.2 8.4 1.0 CG A:ASP118 3.3 7.2 1.0 CB A:CYS198 3.3 6.2 1.0 ZN A:ZN302 3.6 7.3 1.0 OD1 A:ASP118 3.7 7.2 1.0 O2 A:NO9306 3.9 8.0 1.0 NH2 A:ARG119 3.9 10.2 1.0 C4 A:NO9306 4.1 13.0 1.0 C3 A:NO9306 4.1 14.3 1.0 ND1 A:HIS240 4.2 7.0 1.0 CG A:HIS240 4.2 7.1 1.0 O4 A:NO9306 4.2 13.4 1.0 O A:HOH569 4.2 8.6 1.0 NE A:ARG119 4.3 8.2 1.0 O3 A:NO9306 4.3 9.3 1.0 NE2 A:HIS179 4.3 6.2 1.0 CE1 A:HIS114 4.4 7.2 1.0 CE1 A:HIS179 4.4 6.9 1.0 O1 A:NO9306 4.5 14.0 1.0 CA A:CYS198 4.5 5.9 1.0 NE2 A:HIS114 4.5 6.8 1.0 CZ A:ARG119 4.6 9.4 1.0 CB A:ASP118 4.6 9.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.3 occ:1.00 N1 A:NO9306 1.9 6.4 1.0 NE2 A:HIS179 2.0 6.2 1.0 NE2 A:HIS114 2.0 6.8 1.0 ND1 A:HIS116 2.0 7.9 1.0 O2 A:NO9306 2.9 8.0 1.0 S A:NO9306 2.9 8.4 1.0 CE1 A:HIS114 3.0 7.2 1.0 CE1 A:HIS179 3.0 6.9 1.0 CD2 A:HIS179 3.0 6.5 1.0 CE1 A:HIS116 3.0 7.1 1.0 CD2 A:HIS114 3.0 6.4 1.0 CG A:HIS116 3.0 7.4 1.0 CB A:HIS116 3.3 6.9 1.0 O3 A:NO9306 3.6 9.3 1.0 ZN A:ZN301 3.6 7.9 1.0 O5 A:NO9306 4.0 8.9 1.0 OD1 A:ASP118 4.0 7.2 1.0 ND1 A:HIS114 4.1 6.5 1.0 CB A:CYS198 4.1 6.2 1.0 ND1 A:HIS179 4.1 6.7 1.0 CG A:HIS179 4.1 6.4 1.0 CG A:HIS114 4.1 6.7 1.0 NE2 A:HIS116 4.1 7.7 1.0 CD2 A:HIS116 4.2 7.3 1.0 SG A:CYS198 4.2 7.2 1.0 C1 A:NO9306 4.4 10.7 1.0 OD2 A:ASP118 4.6 7.6 1.0 C5 A:NO9306 4.7 11.7 1.0 CG A:ASP118 4.7 7.2 1.0 CA A:HIS116 4.8 7.0 1.0 C2 A:NO9306 5.0 11.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:10.7 occ:1.00 O2 A:FMT309 1.9 14.8 1.0 O2 A:FMT308 2.0 12.5 1.0 NE2 A:HIS153 2.0 7.6 1.0 C A:FMT308 2.7 8.6 1.0 CE1 A:HIS153 2.9 8.7 1.0 O1 A:FMT308 2.9 13.7 1.0 C A:FMT309 3.1 22.4 1.0 CD2 A:HIS153 3.1 8.0 1.0 O1 A:FMT309 4.0 18.8 1.0 ND1 A:HIS153 4.0 8.8 1.0 CG A:HIS153 4.2 7.5 1.0 CB A:ALA132 4.3 8.6 1.0 O A:HOH422 4.4 15.1 1.0 CG2 A:THR152 4.6 10.0 1.0 CA A:ALA132 4.9 8.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:6.9 occ:1.00 ND1 B:HIS116 2.0 7.3 1.0 NE2 B:HIS179 2.0 5.6 1.0 N1 B:NO9306 2.0 8.1 1.0 NE2 B:HIS114 2.1 5.5 1.0 O3 B:NO9306 2.8 9.1 1.0 S B:NO9306 2.9 8.8 1.0 CE1 B:HIS116 3.0 7.5 1.0 CD2 B:HIS179 3.0 5.7 1.0 CG B:HIS116 3.0 6.8 1.0 CE1 B:HIS179 3.0 6.0 1.0 CD2 B:HIS114 3.0 5.8 1.0 CE1 B:HIS114 3.0 6.4 1.0 CB B:HIS116 3.4 6.4 1.0 O2 B:NO9306 3.5 9.7 1.0 ZN B:ZN302 3.6 7.8 1.0 O5 B:NO9306 3.9 8.9 1.0 OD1 B:ASP118 4.0 7.7 1.0 CB B:CYS198 4.1 6.4 1.0 NE2 B:HIS116 4.1 8.0 1.0 CG B:HIS179 4.1 5.6 1.0 ND1 B:HIS179 4.1 6.0 1.0 ND1 B:HIS114 4.1 5.6 1.0 CD2 B:HIS116 4.1 7.4 1.0 CG B:HIS114 4.2 5.5 1.0 SG B:CYS198 4.2 6.8 1.0 C1 B:NO9306 4.3 9.5 1.0 OD2 B:ASP118 4.5 7.9 1.0 C5 B:NO9306 4.6 11.2 1.0 CG B:ASP118 4.7 7.1 1.0 CA B:HIS116 4.8 6.3 1.0 C2 B:NO9306 4.9 10.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:7.8 occ:1.00 NE2 B:HIS240 2.1 6.6 1.0 O5 B:NO9306 2.1 8.9 1.0 N1 B:NO9306 2.2 8.1 1.0 OD2 B:ASP118 2.2 7.9 1.0 SG B:CYS198 2.3 6.8 1.0 C5 B:NO9306 3.0 11.2 1.0 CD2 B:HIS240 3.0 6.4 1.0 CE1 B:HIS240 3.1 6.6 1.0 C2 B:NO9306 3.2 10.1 1.0 C1 B:NO9306 3.2 9.5 1.0 S B:NO9306 3.2 8.8 1.0 CG B:ASP118 3.3 7.1 1.0 CB B:CYS198 3.3 6.4 1.0 ZN B:ZN301 3.6 6.9 1.0 OD1 B:ASP118 3.7 7.7 1.0 O3 B:NO9306 3.9 9.1 1.0 NH2 B:ARG119 4.0 7.8 1.0 C4 B:NO9306 4.2 13.7 1.0 ND1 B:HIS240 4.2 6.2 1.0 CG B:HIS240 4.2 6.4 1.0 O4 B:NO9306 4.2 11.4 1.0 NE2 B:HIS179 4.3 5.6 1.0 C3 B:NO9306 4.3 13.0 1.0 O B:HOH525 4.3 7.5 1.0 NE B:ARG119 4.3 6.8 1.0 O2 B:NO9306 4.4 9.7 1.0 CE1 B:HIS179 4.4 6.0 1.0 CE1 B:HIS114 4.4 6.4 1.0 NE2 B:HIS114 4.5 5.5 1.0 CA B:CYS198 4.5 6.0 1.0 CB B:ASP118 4.6 7.2 1.0 CZ B:ARG119 4.6 7.2 1.0 O1 B:NO9306 4.7 14.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:8.1 occ:1.00 O2 B:FMT307 1.9 10.7 1.0 O2 B:FMT308 2.0 9.3 1.0 NE2 B:HIS153 2.0 8.1 1.0 C B:FMT308 2.7 8.1 1.0 O1 B:FMT308 2.8 8.4 1.0 CE1 B:HIS153 2.9 9.2 1.0 C B:FMT307 2.9 14.3 1.0 CD2 B:HIS153 3.1 8.5 1.0 O1 B:FMT307 3.2 13.5 1.0 ND1 B:HIS153 4.1 9.8 1.0 CG B:HIS153 4.2 8.0 1.0 CB B:ALA132 4.2 8.2 1.0 CA B:ALA132 4.8 7.9 1.0 O B:HOH459 4.8 14.7 1.0 CG2 B:THR152 4.9 9.6 1.0

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