Zinc in PDB 7cjl: Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide

The structure of Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide, PDB code: 7cjl was solved by Y.-H.Yan, J.Chen, Z.Zhan, Z.-J.Yu, G.Li, G.-B.Li, L.Guo, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.07 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.356, 90.132, 125.849, 90, 90, 90
R / Rfree (%)	20.5 / 24.6

The binding sites of Zinc atom in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide (pdb code 7cjl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide, PDB code: 7cjl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.7 occ:1.00 ND1 B:HIS116 1.8 15.6 1.0 NE2 B:HIS179 2.0 27.4 1.0 NE2 B:HIS114 2.1 20.0 1.0 S17 B:G0O304 2.4 29.0 1.0 CE1 B:HIS116 2.6 24.1 1.0 CG B:HIS116 2.9 20.9 1.0 CD2 B:HIS179 3.0 20.5 1.0 CD2 B:HIS114 3.0 19.7 1.0 CE1 B:HIS179 3.0 23.0 1.0 C16 B:G0O304 3.0 29.3 1.0 CE1 B:HIS114 3.1 22.4 1.0 CB B:HIS116 3.5 19.2 1.0 ZN B:ZN302 3.6 23.6 1.0 NE2 B:HIS116 3.7 25.2 1.0 CD2 B:HIS116 3.9 25.1 1.0 OD1 B:ASP118 4.1 20.9 1.0 ND1 B:HIS179 4.1 28.3 1.0 ND1 B:HIS114 4.1 17.1 1.0 CG B:HIS179 4.1 23.5 1.0 CG B:HIS114 4.1 20.6 1.0 CB B:CYS198 4.2 20.3 1.0 O B:HOH481 4.2 33.8 1.0 SG B:CYS198 4.2 21.3 1.0 C15 B:G0O304 4.6 27.9 1.0 OD2 B:ASP118 4.6 15.0 1.0 CG B:ASP118 4.8 15.8 1.0 CA B:HIS116 4.9 20.8 1.0

Zinc binding site 2 out of 4 in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:23.6 occ:1.00 NE2 B:HIS240 2.1 15.3 1.0 OD2 B:ASP118 2.1 15.0 1.0 S17 B:G0O304 2.2 29.0 1.0 SG B:CYS198 2.4 21.3 1.0 O B:HOH481 2.7 33.8 1.0 CE1 B:HIS240 2.9 19.4 1.0 CG B:ASP118 3.2 15.8 1.0 CD2 B:HIS240 3.2 22.6 1.0 C16 B:G0O304 3.4 29.3 1.0 CB B:CYS198 3.5 20.3 1.0 OD1 B:ASP118 3.6 20.9 1.0 NH2 B:ARG119 3.6 23.2 1.0 ZN B:ZN301 3.6 21.7 1.0 C15 B:G0O304 3.9 27.9 1.0 N12 B:G0O304 4.0 32.9 1.0 ND1 B:HIS240 4.1 15.8 1.0 NE B:ARG119 4.2 18.6 1.0 C13 B:G0O304 4.2 31.7 1.0 CG B:HIS240 4.2 17.9 1.0 NE2 B:HIS179 4.3 27.4 1.0 CE1 B:HIS114 4.4 22.4 1.0 CZ B:ARG119 4.4 15.0 1.0 NE2 B:HIS114 4.4 20.0 1.0 CB B:ASP118 4.5 10.1 1.0 O B:HOH505 4.6 31.5 1.0 CE1 B:HIS179 4.6 23.0 1.0 O B:HOH460 4.7 28.2 1.0 CA B:CYS198 4.8 25.8 1.0 C04 B:G0O304 4.9 29.4 1.0 C03 B:G0O304 5.0 30.6 1.0

Zinc binding site 3 out of 4 in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:27.2 occ:1.00 NE2 A:HIS179 1.9 23.2 1.0 ND1 A:HIS116 2.0 25.6 1.0 NE2 A:HIS114 2.0 23.8 1.0 S17 A:G0O303 2.4 35.1 1.0 CE1 A:HIS179 2.7 24.5 1.0 CE1 A:HIS116 2.8 30.4 1.0 CE1 A:HIS114 2.9 26.7 1.0 CD2 A:HIS114 3.0 22.1 1.0 CD2 A:HIS179 3.0 23.4 1.0 CG A:HIS116 3.0 24.2 1.0 C16 A:G0O303 3.2 28.0 1.0 CB A:HIS116 3.5 19.7 1.0 ZN A:ZN302 3.7 28.5 1.0 ND1 A:HIS179 3.9 28.3 1.0 NE2 A:HIS116 4.0 28.8 1.0 ND1 A:HIS114 4.0 19.9 1.0 CB A:CYS198 4.0 25.5 1.0 CG A:HIS179 4.1 29.8 1.0 OD1 A:ASP118 4.1 21.1 1.0 CG A:HIS114 4.1 17.8 1.0 CD2 A:HIS116 4.1 31.6 1.0 SG A:CYS198 4.1 27.2 1.0 O A:HOH485 4.4 33.0 1.0 OD2 A:ASP118 4.6 17.9 1.0 C15 A:G0O303 4.7 32.2 1.0 CG A:ASP118 4.8 21.1 1.0 CA A:HIS116 4.8 18.7 1.0

Zinc binding site 4 out of 4 in the Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase Vim-2 in Complex with (S)-N-(3-(2H-Tetrazol-5- Yl)Phenyl)-3-Mercapto-2-Methylpropanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.5 occ:1.00 SG A:CYS198 2.0 27.2 1.0 OD2 A:ASP118 2.1 17.9 1.0 NE2 A:HIS240 2.1 25.9 1.0 S17 A:G0O303 2.2 35.1 1.0 O A:HOH485 2.7 33.0 1.0 CE1 A:HIS240 3.0 21.7 1.0 CD2 A:HIS240 3.1 23.0 1.0 CG A:ASP118 3.1 21.1 1.0 CB A:CYS198 3.4 25.5 1.0 C16 A:G0O303 3.5 28.0 1.0 OD1 A:ASP118 3.6 21.1 1.0 ZN A:ZN301 3.7 27.2 1.0 NH2 A:ARG119 3.8 22.8 1.0 C15 A:G0O303 4.0 32.2 1.0 NE A:ARG119 4.1 22.4 1.0 ND1 A:HIS240 4.2 19.8 1.0 N12 A:G0O303 4.2 42.9 1.0 CG A:HIS240 4.2 24.6 1.0 CE1 A:HIS114 4.3 26.7 1.0 CB A:ASP118 4.4 14.6 1.0 C13 A:G0O303 4.4 44.3 1.0 CZ A:ARG119 4.4 20.2 1.0 NE2 A:HIS179 4.4 23.2 1.0 NE2 A:HIS114 4.4 23.8 1.0 O A:HOH464 4.5 33.2 1.0 CE1 A:HIS179 4.6 24.5 1.0 CA A:CYS198 4.6 32.0 1.0 O A:HOH504 4.8 38.6 1.0

Y.-L.Wang, S.Liu, Y.-H.Yan, Y.Wu, Q.Chen, Y.Wu, G.-B.Li. Metallo-Beta-Lactamase Inhibitor ZZS01 To Be Published.