Zinc in PDB 7afy: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306, PDB code: 7afy was solved by J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.18 / 1.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.648, 68.015, 40.236, 90, 92.94, 90
R / Rfree (%)	12.6 / 14.5

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306 (pdb code 7afy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306, PDB code: 7afy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306


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 the Metallo-Beta-Lactamase VIM1 with 1306 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:8.7 occ:1.00 O A:HOH479 2.0 8.0 1.0 NE2 A:HIS240 2.1 8.8 1.0 O09 A:RBW301 2.1 9.9 0.7 O09 A:RBW301 2.2 6.8 0.3 SG A:CYS198 2.3 8.2 1.0 OD2 A:ASP118 2.3 8.0 1.0 H061 A:RBW301 2.9 10.9 0.7 H061 A:RBW301 2.9 11.9 0.3 CD2 A:HIS240 3.0 8.3 1.0 C08 A:RBW301 3.1 9.3 0.7 HB3 A:CYS198 3.1 11.3 1.0 HD2 A:HIS240 3.1 9.9 1.0 C08 A:RBW301 3.1 7.4 0.3 CE1 A:HIS240 3.1 9.5 1.0 N06 A:RBW301 3.3 9.1 0.7 CB A:CYS198 3.3 9.5 1.0 HH21 A:ARG119 3.3 10.8 1.0 N06 A:RBW301 3.3 9.9 0.3 CG A:ASP118 3.3 8.0 1.0 HE1 A:HIS240 3.4 11.3 1.0 C07 A:RBW301 3.4 8.9 0.7 C07 A:RBW301 3.4 9.1 0.3 ZN A:ZN305 3.5 8.7 1.0 HE A:ARG119 3.6 9.8 1.0 HE1 A:HIS114 3.6 9.3 1.0 OD1 A:ASP118 3.6 8.8 1.0 HB2 A:CYS198 3.7 11.3 1.0 NH2 A:ARG119 3.9 9.0 1.0 NE2 A:HIS179 4.2 9.9 1.0 CG A:HIS240 4.2 8.5 1.0 NE A:ARG119 4.2 8.1 1.0 HE1 A:HIS179 4.2 11.3 1.0 ND1 A:HIS240 4.2 9.0 1.0 H021 A:RBW301 4.2 12.0 0.7 H021 A:RBW301 4.2 12.4 0.3 O10 A:RBW301 4.2 11.4 0.7 O10 A:RBW301 4.3 9.0 0.3 CE1 A:HIS114 4.3 7.7 1.0 CE1 A:HIS179 4.3 9.4 1.0 O A:HOH522 4.3 11.6 1.0 C05 A:RBW301 4.4 10.1 0.3 C05 A:RBW301 4.4 9.3 0.7 NE2 A:HIS114 4.4 8.1 1.0 CZ A:ARG119 4.4 8.0 1.0 HH22 A:ARG119 4.5 10.8 1.0 HA A:CYS198 4.5 11.0 1.0 CA A:CYS198 4.5 9.2 1.0 HA3 A:GLY239 4.6 10.8 1.0 H171 A:RBW301 4.6 14.1 0.7 C11 A:RBW301 4.6 10.0 0.7 C11 A:RBW301 4.6 10.8 0.3 CB A:ASP118 4.6 8.5 1.0 H271 A:RBW301 4.7 17.5 0.3 HB2 A:ASP118 4.7 10.2 1.0 HB3 A:ASP118 4.9 10.2 1.0 HG2 A:ARG119 5.0 8.7 1.0 CD2 A:HIS179 5.0 8.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306


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 the Metallo-Beta-Lactamase VIM1 with 1306 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:8.7 occ:1.00 O A:HOH479 1.9 8.0 1.0 ND1 A:HIS116 2.0 8.7 1.0 NE2 A:HIS179 2.0 9.9 1.0 NE2 A:HIS114 2.0 8.1 1.0 HB2 A:HIS116 2.9 10.3 1.0 CE1 A:HIS116 3.0 9.4 1.0 CE1 A:HIS114 3.0 7.7 1.0 CD2 A:HIS179 3.0 8.7 1.0 CE1 A:HIS179 3.0 9.4 1.0 CG A:HIS116 3.0 8.8 1.0 CD2 A:HIS114 3.0 8.1 1.0 HE1 A:HIS116 3.1 11.3 1.0 HE1 A:HIS114 3.2 9.3 1.0 HD2 A:HIS179 3.2 10.4 1.0 HE1 A:HIS179 3.2 11.3 1.0 HD2 A:HIS114 3.2 9.7 1.0 H061 A:RBW301 3.3 11.9 0.3 H061 A:RBW301 3.3 10.9 0.7 CB A:HIS116 3.4 8.6 1.0 ZN A:ZN304 3.5 8.7 1.0 HB3 A:HIS116 3.6 10.3 1.0 HB2 A:CYS198 3.8 11.3 1.0 H021 A:RBW301 3.8 12.4 0.3 H021 A:RBW301 3.8 12.0 0.7 OD1 A:ASP118 3.8 8.8 1.0 O09 A:RBW301 3.9 6.8 0.3 O09 A:RBW301 3.9 9.9 0.7 ND1 A:HIS179 4.1 9.7 1.0 ND1 A:HIS114 4.1 7.9 1.0 NE2 A:HIS116 4.1 10.8 1.0 H033 A:RBW301 4.1 14.1 0.7 CG A:HIS179 4.1 9.3 1.0 CD2 A:HIS116 4.2 10.2 1.0 HB3 A:CYS198 4.2 11.3 1.0 CG A:HIS114 4.2 7.8 1.0 N06 A:RBW301 4.2 9.9 0.3 H033 A:RBW301 4.2 13.3 0.3 N06 A:RBW301 4.2 9.1 0.7 CB A:CYS198 4.3 9.5 1.0 SG A:CYS198 4.3 8.2 1.0 H A:HIS116 4.4 8.8 1.0 OD2 A:ASP118 4.5 8.0 1.0 H032 A:RBW301 4.6 14.1 0.7 CG A:ASP118 4.6 8.0 1.0 C02 A:RBW301 4.7 10.4 0.3 C02 A:RBW301 4.7 10.0 0.7 C03 A:RBW301 4.7 11.7 0.7 HG2 A:ARG119 4.7 8.7 1.0 HB3 A:SER180 4.7 11.4 1.0 C08 A:RBW301 4.7 7.4 0.3 C08 A:RBW301 4.7 9.3 0.7 H032 A:RBW301 4.7 13.3 0.3 C03 A:RBW301 4.7 11.1 0.3 CA A:HIS116 4.8 8.1 1.0 HE A:ARG119 4.8 9.8 1.0 HD1 A:HIS114 4.9 9.5 1.0 HE2 A:HIS116 4.9 12.9 1.0 HD1 A:HIS179 4.9 11.7 1.0 HG3 A:ARG119 4.9 8.7 1.0 C07 A:RBW301 4.9 9.1 0.3 C07 A:RBW301 4.9 8.9 0.7 NA A:NA303 5.0 17.9 1.0

J.Brem, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 To Be Published.