Zinc in PDB 8pg8: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2816

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2816, PDB code: 8pg8 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)	27.41 / 1.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.52, 67.97, 40.34, 90, 93.28, 90
R / Rfree (%)	11.6 / 14.1

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2816 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 2816 (pdb code 8pg8). 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 2816, PDB code: 8pg8:
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 2816


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 2816 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.3 occ:0.83 O A:HOH474 1.9 8.6 0.7 ND1 A:HIS116 2.0 12.5 1.0 NE2 A:HIS179 2.0 11.9 1.0 NE2 A:HIS114 2.1 12.5 1.0 HB2 A:HIS116 2.9 11.7 1.0 CE1 A:HIS116 2.9 13.2 1.0 CE1 A:HIS179 3.0 12.4 1.0 CD2 A:HIS179 3.0 11.9 1.0 CG A:HIS116 3.0 10.5 1.0 CE1 A:HIS114 3.0 10.3 1.0 CD2 A:HIS114 3.1 10.5 1.0 O38 A:YVC303 3.1 17.3 0.4 HE1 A:HIS116 3.1 15.8 1.0 HE1 A:HIS179 3.1 14.9 1.0 O38 A:YVC303 3.2 16.0 0.6 H051 A:YVC303 3.2 16.7 0.6 HD2 A:HIS179 3.2 14.3 1.0 HE1 A:HIS114 3.2 12.3 1.0 H051 A:YVC303 3.2 18.1 0.4 HD2 A:HIS114 3.3 12.6 1.0 CB A:HIS116 3.4 9.8 1.0 H021 A:YVC303 3.4 15.5 0.6 ZN A:ZN302 3.5 11.8 0.8 HB3 A:HIS116 3.6 11.7 1.0 H021 A:YVC303 3.7 19.9 0.4 C37 A:YVC303 3.8 17.7 0.4 O08 A:YVC303 3.9 14.3 0.4 OD1 A:ASP118 3.9 13.3 1.0 C37 A:YVC303 3.9 16.3 0.6 O08 A:YVC303 4.0 14.0 0.6 HB2 A:CYS198 4.0 15.6 1.0 ND1 A:HIS179 4.1 12.5 1.0 NE2 A:HIS116 4.1 13.7 1.0 CG A:HIS179 4.1 12.8 1.0 CD2 A:HIS116 4.1 13.2 1.0 ND1 A:HIS114 4.1 10.7 1.0 N05 A:YVC303 4.2 13.9 0.6 HB3 A:CYS198 4.2 15.6 1.0 N05 A:YVC303 4.2 15.1 0.4 CG A:HIS114 4.2 9.9 1.0 CB A:CYS198 4.4 13.0 1.0 C02 A:YVC303 4.4 12.9 0.6 SG A:CYS198 4.4 12.3 1.0 H A:HIS116 4.5 10.8 1.0 OD2 A:ASP118 4.5 13.9 1.0 N27 A:YVC303 4.5 14.2 0.6 N27 A:YVC303 4.6 18.0 0.4 C02 A:YVC303 4.6 16.6 0.4 CG A:ASP118 4.6 12.1 1.0 HB3 A:SER180 4.7 16.1 1.0 C07 A:YVC303 4.7 14.7 0.4 O36 A:YVC303 4.7 17.6 0.4 HG2 A:ARG119 4.7 11.1 1.0 CA A:HIS116 4.8 9.5 1.0 HE A:ARG119 4.8 11.4 1.0 C07 A:YVC303 4.8 13.2 0.6 HD1 A:HIS179 4.8 15.0 1.0 HE2 A:HIS116 4.8 16.5 1.0 O A:HOH535 4.9 14.9 0.8 HD1 A:HIS114 4.9 12.8 1.0 O36 A:YVC303 4.9 18.6 0.6 C06 A:YVC303 5.0 14.7 0.4 HG3 A:ARG119 5.0 11.1 1.0 C06 A:YVC303 5.0 13.2 0.6 HD2 A:HIS116 5.0 15.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2816


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 2816 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.8 occ:0.79 O A:HOH474 2.0 8.6 0.7 O08 A:YVC303 2.0 14.0 0.6 O08 A:YVC303 2.1 14.3 0.4 NE2 A:HIS240 2.1 12.2 1.0 SG A:CYS198 2.3 12.3 1.0 OD2 A:ASP118 2.4 13.9 1.0 H051 A:YVC303 2.7 16.7 0.6 H051 A:YVC303 2.8 18.1 0.4 C07 A:YVC303 3.0 14.7 0.4 CD2 A:HIS240 3.0 11.7 1.0 C07 A:YVC303 3.0 13.2 0.6 HB3 A:CYS198 3.1 15.6 1.0 HD2 A:HIS240 3.1 14.1 1.0 CE1 A:HIS240 3.2 14.2 1.0 N05 A:YVC303 3.2 15.1 0.4 N05 A:YVC303 3.2 13.9 0.6 HH21 A:ARG119 3.2 15.2 1.0 CB A:CYS198 3.3 13.0 1.0 C06 A:YVC303 3.3 14.7 0.4 C06 A:YVC303 3.4 13.2 0.6 CG A:ASP118 3.4 12.1 1.0 HE1 A:HIS240 3.4 17.1 1.0 HE A:ARG119 3.5 11.4 1.0 HE1 A:HIS114 3.5 12.3 1.0 ZN A:ZN301 3.5 12.3 0.8 OD1 A:ASP118 3.7 13.3 1.0 HB2 A:CYS198 3.7 15.6 1.0 NH2 A:ARG119 3.9 12.6 1.0 H021 A:YVC303 4.0 19.9 0.4 H021 A:YVC303 4.1 15.5 0.6 NE2 A:HIS179 4.1 11.9 1.0 O09 A:YVC303 4.1 16.6 0.4 NE A:ARG119 4.2 9.5 1.0 CE1 A:HIS114 4.2 10.3 1.0 O09 A:YVC303 4.2 14.4 0.6 CG A:HIS240 4.2 12.5 1.0 HE1 A:HIS179 4.2 14.9 1.0 ND1 A:HIS240 4.3 13.8 1.0 O A:HOH480 4.3 11.9 0.5 CE1 A:HIS179 4.3 12.4 1.0 C04 A:YVC303 4.3 15.5 0.4 NE2 A:HIS114 4.3 12.5 1.0 C04 A:YVC303 4.4 14.0 0.6 HH22 A:ARG119 4.4 15.2 1.0 HA A:CYS198 4.4 14.4 1.0 CZ A:ARG119 4.5 10.1 1.0 H221 A:YVC303 4.5 20.3 0.6 H121 A:YVC303 4.5 20.2 0.4 C10 A:YVC303 4.5 15.0 0.4 CA A:CYS198 4.5 12.0 1.0 C10 A:YVC303 4.6 13.4 0.6 HA3 A:GLY239 4.6 13.2 1.0 O38 A:YVC303 4.7 17.3 0.4 CB A:ASP118 4.7 10.7 1.0 HB2 A:ASP118 4.8 12.9 1.0 CD2 A:HIS179 4.9 11.9 1.0 O38 A:YVC303 4.9 16.0 0.6 H013 A:YVC303 5.0 14.9 0.6 C02 A:YVC303 5.0 12.9 0.6 HB3 A:ASP118 5.0 12.9 1.0 C02 A:YVC303 5.0 16.6 0.4

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2816 To Be Published.