Zinc in PDB 8pg9: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2817

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2817, PDB code: 8pg9 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)	40.21 / 1.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.5, 67.96, 40.29, 90, 93.53, 90
R / Rfree (%)	13.5 / 16

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2817 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 2817 (pdb code 8pg9). 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 2817, PDB code: 8pg9:
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 2817


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 2817 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.9 occ:0.99 O A:HOH488 1.9 7.9 0.8 NE2 A:HIS179 2.0 11.5 1.0 ND1 A:HIS116 2.1 11.4 1.0 NE2 A:HIS114 2.2 11.2 1.0 HB2 A:HIS116 2.9 11.4 1.0 O36 A:YV8303 2.9 15.9 0.3 O36 A:YV8303 3.0 12.6 0.7 CE1 A:HIS179 3.0 11.3 1.0 CE1 A:HIS116 3.0 11.2 1.0 CD2 A:HIS179 3.0 10.8 1.0 CG A:HIS116 3.1 10.0 1.0 CE1 A:HIS114 3.1 10.1 1.0 CD2 A:HIS114 3.1 9.9 1.0 HE1 A:HIS179 3.2 13.4 1.0 HE1 A:HIS116 3.2 13.4 1.0 H051 A:YV8303 3.2 18.0 0.3 H051 A:YV8303 3.2 13.6 0.7 HD2 A:HIS179 3.2 12.8 1.0 HE1 A:HIS114 3.3 12.0 1.0 HD2 A:HIS114 3.3 11.7 1.0 CB A:HIS116 3.4 9.6 1.0 H021 A:YV8303 3.5 14.1 0.7 H021 A:YV8303 3.5 18.5 0.3 ZN A:ZN302 3.6 12.5 1.0 HB3 A:HIS116 3.6 11.4 1.0 C35 A:YV8303 3.7 16.3 0.3 C35 A:YV8303 3.7 12.8 0.7 OD1 A:ASP118 3.9 11.8 1.0 O09 A:YV8303 4.0 12.5 0.7 HB2 A:CYS198 4.0 14.2 1.0 O09 A:YV8303 4.1 15.9 0.3 ND1 A:HIS179 4.1 12.0 1.0 NE2 A:HIS116 4.1 11.8 1.0 CG A:HIS179 4.2 11.4 1.0 HB3 A:CYS198 4.2 14.2 1.0 CD2 A:HIS116 4.2 11.8 1.0 ND1 A:HIS114 4.2 9.5 1.0 N05 A:YV8303 4.2 15.1 0.3 N05 A:YV8303 4.2 11.5 0.7 CG A:HIS114 4.2 9.3 1.0 CB A:CYS198 4.4 11.9 1.0 N27 A:YV8303 4.4 16.1 0.3 C02 A:YV8303 4.4 11.8 0.7 N27 A:YV8303 4.4 12.1 0.7 C02 A:YV8303 4.4 15.5 0.3 SG A:CYS198 4.5 10.8 1.0 H A:HIS116 4.5 11.0 1.0 O34 A:YV8303 4.5 17.0 0.3 O34 A:YV8303 4.5 13.4 0.7 OD2 A:ASP118 4.5 12.3 1.0 CG A:ASP118 4.6 10.4 1.0 HB3 A:SER180 4.7 13.8 1.0 HG2 A:ARG119 4.8 10.9 1.0 C07 A:YV8303 4.8 11.3 0.7 C07 A:YV8303 4.8 15.3 0.3 CA A:HIS116 4.8 9.8 1.0 HE A:ARG119 4.8 10.9 1.0 O A:HOH525 4.8 15.0 1.0 HD1 A:HIS179 4.9 14.3 1.0 HE2 A:HIS116 4.9 14.0 1.0 HG3 A:ARG119 5.0 10.9 1.0 HD1 A:HIS114 5.0 11.2 1.0 C06 A:YV8303 5.0 15.0 0.3 C06 A:YV8303 5.0 11.3 0.7

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2817


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 2817 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.5 occ:0.99 O A:HOH488 2.0 7.9 0.8 O09 A:YV8303 2.0 15.9 0.3 O09 A:YV8303 2.0 12.5 0.7 NE2 A:HIS240 2.2 11.1 1.0 SG A:CYS198 2.3 10.8 1.0 OD2 A:ASP118 2.4 12.3 1.0 H051 A:YV8303 2.7 13.6 0.7 H051 A:YV8303 2.8 18.0 0.3 C07 A:YV8303 3.0 15.3 0.3 C07 A:YV8303 3.0 11.3 0.7 CD2 A:HIS240 3.0 10.9 1.0 HB3 A:CYS198 3.1 14.2 1.0 HD2 A:HIS240 3.1 13.0 1.0 N05 A:YV8303 3.2 11.5 0.7 N05 A:YV8303 3.2 15.1 0.3 CE1 A:HIS240 3.2 11.2 1.0 CB A:CYS198 3.3 11.9 1.0 HH21 A:ARG119 3.3 13.2 1.0 C06 A:YV8303 3.4 15.0 0.3 C06 A:YV8303 3.4 11.3 0.7 CG A:ASP118 3.4 10.4 1.0 HE1 A:HIS240 3.5 13.3 1.0 HE1 A:HIS114 3.5 12.0 1.0 HE A:ARG119 3.5 10.9 1.0 ZN A:ZN301 3.6 11.9 1.0 HB2 A:CYS198 3.7 14.2 1.0 OD1 A:ASP118 3.7 11.8 1.0 NH2 A:ARG119 3.9 11.1 1.0 H021 A:YV8303 3.9 14.1 0.7 H021 A:YV8303 4.0 18.5 0.3 O08 A:YV8303 4.1 15.7 0.3 NE2 A:HIS179 4.2 11.5 1.0 O08 A:YV8303 4.2 12.8 0.7 NE A:ARG119 4.2 9.2 1.0 O A:HOH509 4.2 12.5 0.8 CE1 A:HIS114 4.2 10.1 1.0 CG A:HIS240 4.2 10.7 1.0 HE1 A:HIS179 4.2 13.4 1.0 ND1 A:HIS240 4.3 11.4 1.0 CE1 A:HIS179 4.3 11.3 1.0 C04 A:YV8303 4.3 15.1 0.3 C04 A:YV8303 4.3 11.8 0.7 NE2 A:HIS114 4.4 11.2 1.0 HA A:CYS198 4.4 13.4 1.0 H121 A:YV8303 4.4 18.7 0.7 HH22 A:ARG119 4.4 13.2 1.0 CZ A:ARG119 4.5 9.6 1.0 H221 A:YV8303 4.5 19.3 0.3 CA A:CYS198 4.5 11.3 1.0 C10 A:YV8303 4.5 15.1 0.3 C10 A:YV8303 4.6 12.0 0.7 HA3 A:GLY239 4.6 12.5 1.0 HG A:SER69 4.6 15.9 0.2 O36 A:YV8303 4.7 12.6 0.7 O36 A:YV8303 4.7 15.9 0.3 CB A:ASP118 4.8 10.3 1.0 HB2 A:ASP118 4.8 12.2 1.0 CD2 A:HIS179 4.9 10.8 1.0 C02 A:YV8303 4.9 11.8 0.7 C02 A:YV8303 4.9 15.5 0.3

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2817 To Be Published.