Zinc in PDB 8pga: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2818

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2818, PDB code: 8pga 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)	34.60 / 1.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.42, 67.93, 40.3, 90, 94.02, 90
R / Rfree (%)	12.7 / 14.6

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2818 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 2818 (pdb code 8pga). 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 2818, PDB code: 8pga:
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 2818


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 2818 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.2 occ:0.84 O A:HOH525 1.9 8.5 0.8 NE2 A:HIS179 2.0 10.3 1.0 ND1 A:HIS116 2.0 10.9 1.0 NE2 A:HIS114 2.1 9.8 1.0 O36 A:YLH303 2.8 11.3 0.8 O36 A:YLH303 2.8 18.5 0.2 CE1 A:HIS116 2.9 10.9 1.0 HB2 A:HIS116 3.0 10.6 1.0 CE1 A:HIS179 3.0 10.7 1.0 CD2 A:HIS179 3.0 10.4 1.0 CE1 A:HIS114 3.0 9.8 1.0 CG A:HIS116 3.1 9.7 1.0 HE1 A:HIS116 3.1 13.0 1.0 CD2 A:HIS114 3.1 9.9 1.0 HE1 A:HIS179 3.2 12.8 1.0 HE1 A:HIS114 3.2 11.8 1.0 HD2 A:HIS179 3.2 12.5 1.0 H051 A:YLH303 3.2 13.4 0.8 H051 A:YLH303 3.3 22.4 0.2 HD2 A:HIS114 3.3 11.8 1.0 CB A:HIS116 3.4 8.8 1.0 H021 A:YLH303 3.5 13.8 0.8 H021 A:YLH303 3.5 22.5 0.2 ZN A:ZN302 3.6 9.8 0.7 C35 A:YLH303 3.6 11.7 0.8 HB3 A:HIS116 3.7 10.6 1.0 C35 A:YLH303 3.7 18.6 0.2 OD1 A:ASP118 3.9 12.0 1.0 O09 A:YLH303 4.0 11.7 0.8 NE2 A:HIS116 4.1 11.1 1.0 HB2 A:CYS198 4.1 15.3 1.0 ND1 A:HIS179 4.1 11.4 1.0 CG A:HIS179 4.1 11.2 1.0 CD2 A:HIS116 4.1 10.6 1.0 ND1 A:HIS114 4.2 9.1 1.0 N05 A:YLH303 4.2 11.1 0.8 CG A:HIS114 4.2 8.7 1.0 N05 A:YLH303 4.2 18.6 0.2 O09 A:YLH303 4.2 18.1 0.2 HB3 A:CYS198 4.3 15.3 1.0 N27 A:YLH303 4.4 11.5 0.8 C02 A:YLH303 4.4 11.5 0.8 N27 A:YLH303 4.4 18.8 0.2 C02 A:YLH303 4.4 18.8 0.2 CB A:CYS198 4.5 12.8 1.0 SG A:CYS198 4.5 11.1 1.0 O34 A:YLH303 4.5 12.3 0.8 OD2 A:ASP118 4.5 12.4 1.0 H A:HIS116 4.6 10.4 1.0 O34 A:YLH303 4.6 18.7 0.2 CG A:ASP118 4.6 11.1 1.0 HB3 A:SER180 4.7 13.1 1.0 C07 A:YLH303 4.8 11.8 0.8 HG2 A:ARG119 4.8 10.6 1.0 O A:HOH553 4.8 12.5 0.9 HE2 A:HIS116 4.8 13.3 1.0 CA A:HIS116 4.8 9.0 1.0 HE A:ARG119 4.9 10.6 1.0 HD1 A:HIS179 4.9 13.7 1.0 HD1 A:HIS114 4.9 10.9 1.0 H012 A:YLH303 5.0 13.3 0.8 H012 A:YLH303 5.0 22.3 0.2 C07 A:YLH303 5.0 18.1 0.2 HD2 A:HIS116 5.0 12.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2818


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 2818 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.8 occ:0.68 O A:HOH525 2.0 8.5 0.8 O09 A:YLH303 2.0 11.7 0.8 NE2 A:HIS240 2.1 11.9 1.0 SG A:CYS198 2.3 11.1 1.0 O09 A:YLH303 2.3 18.1 0.2 OD2 A:ASP118 2.5 12.4 1.0 H051 A:YLH303 2.7 13.4 0.8 H051 A:YLH303 2.8 22.4 0.2 HB3 A:CYS198 3.0 15.3 1.0 C07 A:YLH303 3.0 11.8 0.8 CD2 A:HIS240 3.0 11.9 1.0 HD2 A:HIS240 3.1 14.2 1.0 C07 A:YLH303 3.2 18.1 0.2 N05 A:YLH303 3.2 11.1 0.8 CE1 A:HIS240 3.2 12.6 1.0 CB A:CYS198 3.2 12.8 1.0 N05 A:YLH303 3.2 18.6 0.2 HH21 A:ARG119 3.2 13.5 1.0 C06 A:YLH303 3.4 11.2 0.8 C06 A:YLH303 3.4 18.4 0.2 HE1 A:HIS114 3.4 11.8 1.0 HE1 A:HIS240 3.5 15.2 1.0 CG A:ASP118 3.5 11.1 1.0 HE A:ARG119 3.5 10.6 1.0 ZN A:ZN301 3.6 9.2 0.8 HB2 A:CYS198 3.6 15.3 1.0 OD1 A:ASP118 3.8 12.0 1.0 NH2 A:ARG119 3.9 11.2 1.0 H021 A:YLH303 3.9 22.5 0.2 H021 A:YLH303 3.9 13.8 0.8 NE2 A:HIS179 4.1 10.3 1.0 CE1 A:HIS114 4.2 9.8 1.0 HE1 A:HIS179 4.2 12.8 1.0 NE A:ARG119 4.2 8.8 1.0 O08 A:YLH303 4.2 12.7 0.8 O A:HOH456 4.2 10.6 0.6 CG A:HIS240 4.2 11.8 1.0 CE1 A:HIS179 4.3 10.7 1.0 ND1 A:HIS240 4.3 12.4 1.0 C04 A:YLH303 4.3 18.6 0.2 C04 A:YLH303 4.3 10.2 0.8 O08 A:YLH303 4.3 18.0 0.2 NE2 A:HIS114 4.4 9.8 1.0 H221 A:YLH303 4.4 22.2 0.2 HA A:CYS198 4.4 13.8 1.0 HH22 A:ARG119 4.5 13.5 1.0 H121 A:YLH303 4.5 17.4 0.8 CZ A:ARG119 4.5 9.3 1.0 CA A:CYS198 4.5 11.5 1.0 O36 A:YLH303 4.6 11.3 0.8 C10 A:YLH303 4.6 18.3 0.2 C10 A:YLH303 4.6 10.8 0.8 O36 A:YLH303 4.6 18.5 0.2 HA3 A:GLY239 4.6 11.9 1.0 CB A:ASP118 4.8 10.5 1.0 CD2 A:HIS179 4.8 10.4 1.0 HB2 A:ASP118 4.9 12.5 1.0 C02 A:YLH303 4.9 18.8 0.2 C02 A:YLH303 4.9 11.5 0.8

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2818 To Be Published.