Zinc in PDB 8pgm: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3062

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3062, PDB code: 8pgm 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)	28.90 / 1.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.42, 67.83, 40.08, 90, 93.28, 90
R / Rfree (%)	12.8 / 15.6

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3062 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 3062 (pdb code 8pgm). 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 3062, PDB code: 8pgm:
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 3062


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 3062 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.9 occ:0.93 O A:HOH439 1.9 12.4 0.9 ND1 A:HIS116 2.0 13.7 1.0 NE2 A:HIS179 2.0 13.1 1.0 NE2 A:HIS114 2.1 13.2 1.0 HB2 A:HIS116 2.9 15.0 1.0 CE1 A:HIS116 3.0 14.1 1.0 CD2 A:HIS179 3.0 13.5 1.0 CE1 A:HIS114 3.0 12.9 1.0 CE1 A:HIS179 3.0 13.6 1.0 CG A:HIS116 3.1 12.6 1.0 CD2 A:HIS114 3.1 12.3 1.0 HD2 A:HIS179 3.1 16.2 1.0 HE1 A:HIS116 3.1 17.0 1.0 H061 A:YU0303 3.2 15.4 0.4 H061 A:YU0303 3.2 17.6 0.6 HE1 A:HIS114 3.2 15.5 1.0 HE1 A:HIS179 3.3 16.3 1.0 HD2 A:HIS114 3.3 14.7 1.0 CB A:HIS116 3.4 12.5 1.0 ZN A:ZN302 3.5 13.0 0.9 HB3 A:HIS116 3.6 15.0 1.0 H021 A:YU0303 3.6 18.1 0.4 H021 A:YU0303 3.7 17.0 0.6 HB2 A:CYS198 3.8 17.0 1.0 OD1 A:ASP118 3.8 14.7 1.0 O09 A:YU0303 3.9 7.9 0.4 H032 A:YU0303 4.0 18.7 0.6 HB3 A:CYS198 4.1 17.0 1.0 NE2 A:HIS116 4.1 15.0 1.0 O09 A:YU0303 4.1 19.2 0.6 CG A:HIS179 4.1 13.8 1.0 ND1 A:HIS179 4.1 14.5 1.0 H032 A:YU0303 4.1 19.4 0.4 CD2 A:HIS116 4.1 14.9 1.0 ND1 A:HIS114 4.1 12.4 1.0 N06 A:YU0303 4.2 12.8 0.4 N06 A:YU0303 4.2 14.7 0.6 CG A:HIS114 4.2 12.1 1.0 CB A:CYS198 4.2 14.2 1.0 SG A:CYS198 4.3 13.3 1.0 H A:HIS116 4.5 15.0 1.0 OD2 A:ASP118 4.5 13.7 1.0 C02 A:YU0303 4.6 14.2 0.6 CG A:ASP118 4.6 12.8 1.0 C02 A:YU0303 4.6 15.1 0.4 C08 A:YU0303 4.6 9.6 0.4 C03 A:YU0303 4.7 15.6 0.6 HB3 A:SER180 4.7 18.4 1.0 HG2 A:ARG119 4.7 14.8 1.0 C08 A:YU0303 4.8 17.3 0.6 C03 A:YU0303 4.8 16.2 0.4 CA A:HIS116 4.8 11.7 1.0 H031 A:YU0303 4.8 18.7 0.6 HE A:ARG119 4.8 15.5 1.0 H031 A:YU0303 4.9 19.4 0.4 HE2 A:HIS116 4.9 18.0 1.0 C07 A:YU0303 4.9 11.8 0.4 HG3 A:ARG119 4.9 14.8 1.0 HD1 A:HIS114 4.9 14.9 1.0 HD1 A:HIS179 4.9 17.4 1.0 C07 A:YU0303 4.9 15.5 0.6 O A:HOH513 4.9 16.1 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3062


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 3062 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.0 occ:0.89 O09 A:YU0303 1.9 19.2 0.6 O A:HOH439 2.0 12.4 0.9 NE2 A:HIS240 2.1 13.3 1.0 O09 A:YU0303 2.2 7.9 0.4 SG A:CYS198 2.3 13.3 1.0 OD2 A:ASP118 2.3 13.7 1.0 H061 A:YU0303 2.7 17.6 0.6 C08 A:YU0303 2.9 17.3 0.6 H061 A:YU0303 3.0 15.4 0.4 HB3 A:CYS198 3.0 17.0 1.0 CD2 A:HIS240 3.0 12.9 1.0 C08 A:YU0303 3.1 9.6 0.4 HD2 A:HIS240 3.1 15.5 1.0 CE1 A:HIS240 3.2 14.1 1.0 N06 A:YU0303 3.2 14.7 0.6 CB A:CYS198 3.2 14.2 1.0 HH21 A:ARG119 3.2 16.2 1.0 CG A:ASP118 3.3 12.8 1.0 N06 A:YU0303 3.3 12.8 0.4 C07 A:YU0303 3.4 15.5 0.6 HE1 A:HIS240 3.4 17.0 1.0 C07 A:YU0303 3.4 11.8 0.4 HE A:ARG119 3.5 15.5 1.0 ZN A:ZN301 3.5 12.9 0.9 OD1 A:ASP118 3.6 14.7 1.0 HB2 A:CYS198 3.6 17.0 1.0 HE1 A:HIS114 3.7 15.5 1.0 NH2 A:ARG119 3.9 13.5 1.0 O10 A:YU0303 4.1 18.4 0.6 H021 A:YU0303 4.1 17.0 0.6 NE2 A:HIS179 4.1 13.1 1.0 HE1 A:HIS179 4.2 16.3 1.0 H021 A:YU0303 4.2 18.1 0.4 NE A:ARG119 4.2 12.9 1.0 CG A:HIS240 4.2 13.0 1.0 ND1 A:HIS240 4.3 13.4 1.0 O A:HOH496 4.3 15.4 0.9 CE1 A:HIS179 4.3 13.6 1.0 O10 A:YU0303 4.3 11.0 0.4 CE1 A:HIS114 4.3 12.9 1.0 C05 A:YU0303 4.3 14.7 0.6 C05 A:YU0303 4.4 14.1 0.4 H131 A:YU0303 4.4 19.2 0.4 H231 A:YU0303 4.4 21.6 0.6 NE2 A:HIS114 4.4 13.2 1.0 CZ A:ARG119 4.4 12.8 1.0 HA A:CYS198 4.4 16.2 1.0 HH22 A:ARG119 4.4 16.2 1.0 CA A:CYS198 4.5 13.5 1.0 C11 A:YU0303 4.5 13.1 0.4 C11 A:YU0303 4.6 15.0 0.6 HA3 A:GLY239 4.6 16.5 1.0 CB A:ASP118 4.6 13.4 1.0 HB2 A:ASP118 4.7 16.1 1.0 HB3 A:ASP118 4.9 16.1 1.0 CD2 A:HIS179 5.0 13.5 1.0 HG2 A:ARG119 5.0 14.8 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 3062 To Be Published.