Zinc in PDB 8pg3: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729, PDB code: 8pg3 was solved by K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.63 / 1.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.52, 67.96, 40.34, 90, 93.78, 90
R / Rfree (%)	14.1 / 15.4

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729 (pdb code 8pg3). 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 2729, PDB code: 8pg3:
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 2729


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 2729 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.3 occ:0.83 O A:HOH466 1.9 6.4 0.6 NE2 A:HIS179 2.0 13.1 1.0 ND1 A:HIS116 2.1 13.1 1.0 NE2 A:HIS114 2.1 12.2 1.0 HB2 A:HIS116 2.9 13.1 1.0 CE1 A:HIS179 3.0 13.7 1.0 CE1 A:HIS116 3.0 13.8 1.0 CD2 A:HIS179 3.0 12.9 1.0 O35 A:YL9303 3.0 20.1 0.5 O35 A:YL9303 3.1 20.1 0.5 CG A:HIS116 3.1 12.0 1.0 CE1 A:HIS114 3.1 11.4 1.0 CD2 A:HIS114 3.1 12.2 1.0 HE1 A:HIS179 3.2 16.4 1.0 HE1 A:HIS116 3.2 16.6 1.0 H051 A:YL9303 3.2 24.1 0.5 H051 A:YL9303 3.2 24.1 0.5 HD2 A:HIS179 3.2 15.4 1.0 HE1 A:HIS114 3.3 13.7 1.0 HD2 A:HIS114 3.3 14.6 1.0 CB A:HIS116 3.4 10.9 1.0 H021 A:YL9303 3.5 24.1 0.5 H021 A:YL9303 3.5 24.1 0.5 ZN A:ZN302 3.5 12.3 0.8 HB3 A:HIS116 3.6 13.1 1.0 C34 A:YL9303 3.7 20.1 0.5 C34 A:YL9303 3.7 20.1 0.5 OD1 A:ASP118 3.8 13.6 1.0 O09 A:YL9303 4.0 20.1 0.5 HB2 A:CYS198 4.0 16.5 1.0 O09 A:YL9303 4.0 20.1 0.5 ND1 A:HIS179 4.1 14.4 1.0 NE2 A:HIS116 4.1 14.6 1.0 CG A:HIS179 4.1 13.6 1.0 CD2 A:HIS116 4.2 13.7 1.0 ND1 A:HIS114 4.2 11.0 1.0 N05 A:YL9303 4.2 20.1 0.5 HB3 A:CYS198 4.2 16.5 1.0 N05 A:YL9303 4.2 20.1 0.5 CG A:HIS114 4.2 11.1 1.0 N27 A:YL9303 4.3 20.1 0.5 N27 A:YL9303 4.3 20.1 0.5 C02 A:YL9303 4.4 20.1 0.5 C02 A:YL9303 4.4 20.1 0.5 CB A:CYS198 4.4 13.7 1.0 SG A:CYS198 4.5 12.9 1.0 OD2 A:ASP118 4.5 13.6 1.0 H A:HIS116 4.5 12.5 1.0 CG A:ASP118 4.6 12.2 1.0 O33 A:YL9303 4.6 20.1 0.5 O33 A:YL9303 4.6 20.1 0.5 HB3 A:SER180 4.7 16.5 1.0 C07 A:YL9303 4.8 20.1 0.5 HG2 A:ARG119 4.8 12.3 1.0 C07 A:YL9303 4.8 20.1 0.5 HE A:ARG119 4.8 13.1 1.0 CA A:HIS116 4.8 10.3 1.0 HD1 A:HIS179 4.9 17.3 1.0 O A:HOH553 4.9 10.4 0.6 HE2 A:HIS116 4.9 17.5 1.0 HG3 A:ARG119 4.9 12.3 1.0 HD1 A:HIS114 4.9 13.2 1.0 C06 A:YL9303 5.0 20.1 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729


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 2729 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.3 occ:0.79 O A:HOH466 2.0 6.4 0.6 O09 A:YL9303 2.1 20.1 0.5 O09 A:YL9303 2.1 20.1 0.5 NE2 A:HIS240 2.2 12.9 1.0 SG A:CYS198 2.3 12.9 1.0 OD2 A:ASP118 2.4 13.6 1.0 H051 A:YL9303 2.8 24.1 0.5 H051 A:YL9303 2.8 24.1 0.5 C07 A:YL9303 3.0 20.1 0.5 C07 A:YL9303 3.0 20.1 0.5 CD2 A:HIS240 3.0 12.5 1.0 HB3 A:CYS198 3.1 16.5 1.0 HD2 A:HIS240 3.1 15.0 1.0 CE1 A:HIS240 3.2 14.1 1.0 HH21 A:ARG119 3.2 15.2 1.0 N05 A:YL9303 3.2 20.1 0.5 N05 A:YL9303 3.2 20.1 0.5 CB A:CYS198 3.3 13.7 1.0 C06 A:YL9303 3.4 20.1 0.5 C06 A:YL9303 3.4 20.1 0.5 CG A:ASP118 3.4 12.2 1.0 HE1 A:HIS240 3.5 16.9 1.0 HE1 A:HIS114 3.5 13.7 1.0 ZN A:ZN301 3.5 12.3 0.8 HE A:ARG119 3.5 13.1 1.0 HB2 A:CYS198 3.7 16.5 1.0 OD1 A:ASP118 3.8 13.6 1.0 NH2 A:ARG119 3.9 12.7 1.0 H021 A:YL9303 4.0 24.1 0.5 H021 A:YL9303 4.0 24.1 0.5 NE2 A:HIS179 4.1 13.1 1.0 HE1 A:HIS179 4.1 16.4 1.0 O08 A:YL9303 4.2 20.1 0.5 CE1 A:HIS114 4.2 11.4 1.0 O08 A:YL9303 4.2 20.1 0.5 NE A:ARG119 4.2 10.9 1.0 CE1 A:HIS179 4.2 13.7 1.0 CG A:HIS240 4.2 12.9 1.0 O A:HOH497 4.3 7.7 0.4 ND1 A:HIS240 4.3 13.5 1.0 C04 A:YL9303 4.3 20.1 0.5 C04 A:YL9303 4.3 20.1 0.5 NE2 A:HIS114 4.3 12.2 1.0 HH22 A:ARG119 4.4 15.2 1.0 HA A:CYS198 4.4 15.6 1.0 CZ A:ARG119 4.5 10.9 1.0 H121 A:YL9303 4.5 24.1 0.5 H221 A:YL9303 4.5 24.1 0.5 CA A:CYS198 4.5 13.0 1.0 C10 A:YL9303 4.6 20.1 0.5 C10 A:YL9303 4.6 20.1 0.5 HA3 A:GLY239 4.6 13.8 1.0 O35 A:YL9303 4.6 20.1 0.5 O35 A:YL9303 4.7 20.1 0.5 HG A:SER69 4.8 15.8 0.3 CB A:ASP118 4.8 11.8 1.0 HB2 A:ASP118 4.8 14.2 1.0 CD2 A:HIS179 4.9 12.9 1.0 C02 A:YL9303 4.9 20.1 0.5 C02 A:YL9303 5.0 20.1 0.5 ND1 A:HIS179 5.0 14.4 1.0

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729 To Be Published.