Zinc in PDB 7yrp: Crystal Structure of Vim-28 Metallo-Beta-Lactamase

The structure of Crystal Structure of Vim-28 Metallo-Beta-Lactamase, PDB code: 7yrp was solved by A.Shimizu-Ibuka, H.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.48 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.36, 45.91, 103.26, 90, 103.59, 90
R / Rfree (%)	17.2 / 20.4

The binding sites of Zinc atom in the Crystal Structure of Vim-28 Metallo-Beta-Lactamase (pdb code 7yrp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Vim-28 Metallo-Beta-Lactamase, PDB code: 7yrp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vim-28 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-28 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.3 occ:0.70 OB1 A:FLC301 1.9 27.4 1.0 ND1 A:HIS116 2.0 19.0 1.0 NE2 A:HIS179 2.1 17.3 1.0 NE2 A:HIS114 2.1 20.8 1.0 CBC A:FLC301 2.6 29.1 1.0 OB2 A:FLC301 2.8 29.6 1.0 CE1 A:HIS116 2.9 21.7 1.0 CD2 A:HIS179 3.0 18.6 1.0 CE1 A:HIS114 3.0 22.6 1.0 CG A:HIS116 3.1 21.6 1.0 CE1 A:HIS179 3.1 19.4 1.0 CD2 A:HIS114 3.1 21.4 1.0 CB A:HIS116 3.4 19.4 1.0 ZN A:ZN303 3.9 17.7 0.5 OD1 A:ASP118 4.0 27.6 1.0 NE2 A:HIS116 4.0 18.5 1.0 CB A:FLC301 4.1 31.5 1.0 CG A:HIS179 4.1 18.6 1.0 CD2 A:HIS116 4.1 21.3 1.0 ND1 A:HIS179 4.2 19.2 1.0 ND1 A:HIS114 4.2 21.4 1.0 SG A:CYS198 4.2 23.1 1.0 CG A:HIS114 4.2 19.2 1.0 CB A:CYS198 4.3 23.1 1.0 OA1 A:FLC301 4.3 28.6 1.0 OG1 A:FLC301 4.4 35.8 1.0 OHB A:FLC301 4.5 27.7 1.0 CG A:ASP118 4.8 27.2 1.0 CA A:HIS116 4.8 19.9 1.0 CGC A:FLC301 4.8 36.2 1.0 OD2 A:ASP118 4.9 28.6 1.0 CG A:FLC301 4.9 32.1 1.0 CAC A:FLC301 5.0 35.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vim-28 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-28 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:17.7 occ:0.50 NE2 A:HIS240 2.1 21.2 1.0 OHB A:FLC301 2.2 27.7 1.0 OD2 A:ASP118 2.3 28.6 1.0 OA1 A:FLC301 2.3 28.6 1.0 SG A:CYS198 2.4 23.1 1.0 OB1 A:FLC301 2.4 27.4 1.0 CB A:FLC301 3.0 31.5 1.0 CBC A:FLC301 3.0 29.1 1.0 CE1 A:HIS240 3.1 20.5 1.0 CD2 A:HIS240 3.1 23.1 1.0 CAC A:FLC301 3.2 35.1 1.0 CG A:ASP118 3.2 27.2 1.0 CA A:FLC301 3.5 32.1 1.0 OD1 A:ASP118 3.6 27.6 1.0 CB A:CYS198 3.7 23.1 1.0 ZN A:ZN302 3.9 15.3 0.7 NH2 A:ARG119 4.1 25.7 1.0 ND1 A:HIS240 4.2 20.7 1.0 OB2 A:FLC301 4.2 29.6 1.0 CG A:HIS240 4.2 20.6 1.0 OG1 A:FLC301 4.3 35.8 1.0 CG A:FLC301 4.4 32.1 1.0 OA2 A:FLC301 4.4 42.8 1.0 O A:HOH530 4.4 23.9 1.0 CB A:ASP118 4.5 24.9 1.0 NE2 A:HIS179 4.5 17.3 1.0 CE1 A:HIS179 4.6 19.4 1.0 NE A:ARG119 4.7 20.9 1.0 CE1 A:HIS114 4.7 22.6 1.0 CZ A:ARG119 4.8 24.6 1.0 NE2 A:HIS114 4.8 20.8 1.0 CA A:CYS198 4.9 21.6 1.0 CGC A:FLC301 4.9 36.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vim-28 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-28 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:28.6 occ:0.70 OB2 B:FLC301 1.9 40.2 1.0 ND1 B:HIS116 2.0 35.6 1.0 NE2 B:HIS179 2.1 35.3 1.0 NE2 B:HIS114 2.3 34.9 1.0 CBC B:FLC301 2.7 44.0 1.0 OB1 B:FLC301 2.8 38.4 1.0 CE1 B:HIS116 2.9 38.6 1.0 CD2 B:HIS179 3.0 36.6 1.0 CG B:HIS116 3.0 35.7 1.0 CE1 B:HIS179 3.1 38.0 1.0 CD2 B:HIS114 3.2 35.9 1.0 CE1 B:HIS114 3.2 36.3 1.0 CB B:HIS116 3.3 34.4 1.0 OD1 B:ASP118 3.9 36.8 1.0 ZN B:ZN303 3.9 26.0 0.5 NE2 B:HIS116 4.1 37.4 1.0 CD2 B:HIS116 4.1 35.0 1.0 CG B:HIS179 4.2 35.7 1.0 CB B:FLC301 4.2 41.2 1.0 ND1 B:HIS179 4.2 35.6 1.0 CB B:CYS198 4.3 38.2 1.0 SG B:CYS198 4.3 35.0 1.0 ND1 B:HIS114 4.3 36.5 1.0 CG B:HIS114 4.3 33.8 1.0 OG2 B:FLC301 4.4 41.6 1.0 OA2 B:FLC301 4.5 44.1 1.0 OHB B:FLC301 4.5 36.7 1.0 CG B:ASP118 4.6 34.9 1.0 OD2 B:ASP118 4.7 33.9 1.0 CGC B:FLC301 4.8 42.8 1.0 CA B:HIS116 4.8 32.9 1.0 CG B:FLC301 4.9 42.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vim-28 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-28 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:26.0 occ:0.50 NE2 B:HIS240 2.1 24.3 1.0 OHB B:FLC301 2.2 36.7 1.0 OD2 B:ASP118 2.2 33.9 1.0 OA2 B:FLC301 2.4 44.1 1.0 OB2 B:FLC301 2.4 40.2 1.0 SG B:CYS198 2.5 35.0 1.0 CBC B:FLC301 2.9 44.0 1.0 CB B:FLC301 2.9 41.2 1.0 CE1 B:HIS240 3.1 24.8 1.0 CD2 B:HIS240 3.1 26.5 1.0 CG B:ASP118 3.2 34.9 1.0 CAC B:FLC301 3.3 47.8 1.0 CA B:FLC301 3.5 42.3 1.0 OD1 B:ASP118 3.7 36.8 1.0 CB B:CYS198 3.8 38.2 1.0 ZN B:ZN302 3.9 28.6 0.7 NH2 B:ARG119 4.0 31.6 1.0 OB1 B:FLC301 4.0 38.4 1.0 ND1 B:HIS240 4.2 24.1 1.0 CG B:HIS240 4.2 26.7 1.0 OG2 B:FLC301 4.3 41.6 1.0 CG B:FLC301 4.3 42.3 1.0 CB B:ASP118 4.4 33.4 1.0 OA1 B:FLC301 4.4 50.9 1.0 NE2 B:HIS179 4.4 35.3 1.0 O B:HOH459 4.5 42.2 1.0 CE1 B:HIS179 4.6 38.0 1.0 NE B:ARG119 4.7 33.6 1.0 CE1 B:HIS114 4.8 36.3 1.0 CZ B:ARG119 4.8 33.7 1.0 CGC B:FLC301 4.8 42.8 1.0 NE2 B:HIS114 4.9 34.9 1.0 CA B:CYS198 4.9 38.6 1.0

A.Shimizu-Ibuka, H.Sato. Crystal Structure of Vim-28 Metallo-Beta-Lactamase To Be Published.