Zinc in PDB 8pg2: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2728

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2728, PDB code: 8pg2 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)	29.09 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.548, 67.957, 40.341, 90, 93.52, 90
R / Rfree (%)	11.2 / 13.1

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2728 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 2728 (pdb code 8pg2). 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 2728, PDB code: 8pg2:
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 2728


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 2728 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.6 occ:0.86 O A:HOH482 1.9 7.2 0.6 NE2 A:HIS179 2.0 12.5 1.0 ND1 A:HIS116 2.0 12.0 1.0 NE2 A:HIS114 2.1 11.5 1.0 HB2 A:HIS116 2.9 12.0 1.0 CE1 A:HIS179 3.0 12.5 1.0 O36 A:YLH303 3.0 14.1 0.7 CE1 A:HIS116 3.0 12.7 1.0 CG A:HIS116 3.0 10.9 1.0 CD2 A:HIS179 3.0 11.7 1.0 CE1 A:HIS114 3.1 10.4 1.0 O36 A:YLH303 3.1 17.6 0.4 CD2 A:HIS114 3.1 11.4 1.0 HE1 A:HIS179 3.2 15.0 1.0 HE1 A:HIS116 3.2 15.2 1.0 H051 A:YLH303 3.2 15.2 0.7 HD2 A:HIS179 3.2 14.0 1.0 HE1 A:HIS114 3.2 12.4 1.0 H051 A:YLH303 3.3 18.4 0.4 HD2 A:HIS114 3.3 13.7 1.0 CB A:HIS116 3.4 10.0 1.0 H021 A:YLH303 3.4 15.2 0.7 H021 A:YLH303 3.5 20.1 0.4 ZN A:ZN302 3.6 11.4 0.8 HB3 A:HIS116 3.6 12.0 1.0 C35 A:YLH303 3.7 17.6 0.4 C35 A:YLH303 3.8 14.5 0.7 OD1 A:ASP118 3.9 12.7 1.0 O09 A:YLH303 4.0 12.3 0.7 HB2 A:CYS198 4.1 15.4 1.0 ND1 A:HIS179 4.1 13.4 1.0 O09 A:YLH303 4.1 16.5 0.4 NE2 A:HIS116 4.1 14.1 1.0 CG A:HIS179 4.1 12.5 1.0 CD2 A:HIS116 4.1 13.0 1.0 ND1 A:HIS114 4.2 10.2 1.0 N05 A:YLH303 4.2 12.7 0.7 HB3 A:CYS198 4.2 15.4 1.0 N05 A:YLH303 4.2 15.3 0.4 CG A:HIS114 4.2 10.4 1.0 N27 A:YLH303 4.4 17.5 0.4 C02 A:YLH303 4.4 12.6 0.7 N27 A:YLH303 4.4 13.0 0.7 C02 A:YLH303 4.4 16.8 0.4 CB A:CYS198 4.4 12.9 1.0 H A:HIS116 4.5 11.4 1.0 SG A:CYS198 4.5 11.9 1.0 OD2 A:ASP118 4.5 12.7 1.0 CG A:ASP118 4.6 11.2 1.0 O34 A:YLH303 4.6 17.7 0.4 O34 A:YLH303 4.7 15.2 0.7 HB3 A:SER180 4.7 15.4 1.0 C07 A:YLH303 4.8 12.6 0.7 C07 A:YLH303 4.8 16.2 0.4 CA A:HIS116 4.8 9.3 1.0 O A:HOH548 4.8 15.1 0.9 HG2 A:ARG119 4.8 11.3 1.0 HD1 A:HIS179 4.9 16.1 1.0 HE A:ARG119 4.9 12.0 1.0 HE2 A:HIS116 4.9 16.9 1.0 HD1 A:HIS114 4.9 12.2 1.0 HD2 A:HIS116 5.0 15.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2728


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 2728 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.4 occ:0.81 O09 A:YLH303 2.0 16.5 0.4 O A:HOH482 2.0 7.2 0.6 NE2 A:HIS240 2.1 11.9 1.0 O09 A:YLH303 2.1 12.3 0.7 SG A:CYS198 2.3 11.9 1.0 OD2 A:ASP118 2.4 12.7 1.0 H051 A:YLH303 2.6 15.2 0.7 H051 A:YLH303 2.7 18.4 0.4 CD2 A:HIS240 3.0 11.4 1.0 C07 A:YLH303 3.0 16.2 0.4 C07 A:YLH303 3.1 12.6 0.7 HB3 A:CYS198 3.1 15.4 1.0 HD2 A:HIS240 3.1 13.7 1.0 N05 A:YLH303 3.2 12.7 0.7 N05 A:YLH303 3.2 15.3 0.4 CE1 A:HIS240 3.2 13.6 1.0 CB A:CYS198 3.3 12.9 1.0 HH21 A:ARG119 3.3 14.2 1.0 C06 A:YLH303 3.3 15.4 0.4 C06 A:YLH303 3.4 12.2 0.7 CG A:ASP118 3.4 11.2 1.0 HE1 A:HIS240 3.4 16.3 1.0 HE1 A:HIS114 3.5 12.4 1.0 HE A:ARG119 3.6 12.0 1.0 ZN A:ZN301 3.6 11.6 0.9 HB2 A:CYS198 3.7 15.4 1.0 OD1 A:ASP118 3.7 12.7 1.0 H021 A:YLH303 3.9 20.1 0.4 NH2 A:ARG119 3.9 11.8 1.0 H021 A:YLH303 4.0 15.2 0.7 NE2 A:HIS179 4.1 12.5 1.0 CE1 A:HIS114 4.2 10.4 1.0 HE1 A:HIS179 4.2 15.0 1.0 O08 A:YLH303 4.2 16.7 0.4 CG A:HIS240 4.2 12.1 1.0 NE A:ARG119 4.2 10.0 1.0 O A:HOH504 4.3 12.4 0.7 ND1 A:HIS240 4.3 12.4 1.0 O08 A:YLH303 4.3 13.7 0.7 CE1 A:HIS179 4.3 12.5 1.0 C04 A:YLH303 4.3 15.5 0.4 C04 A:YLH303 4.3 12.7 0.7 NE2 A:HIS114 4.4 11.5 1.0 HA A:CYS198 4.4 14.4 1.0 HH22 A:ARG119 4.5 14.2 1.0 CZ A:ARG119 4.5 9.8 1.0 H121 A:YLH303 4.5 19.0 0.7 H221 A:YLH303 4.5 19.1 0.4 C10 A:YLH303 4.5 15.5 0.4 CA A:CYS198 4.5 12.0 1.0 C10 A:YLH303 4.6 13.2 0.7 O36 A:YLH303 4.6 17.6 0.4 HA3 A:GLY239 4.6 12.8 1.0 CB A:ASP118 4.7 10.8 1.0 O36 A:YLH303 4.7 14.1 0.7 HB2 A:ASP118 4.8 13.0 1.0 CD2 A:HIS179 4.9 11.7 1.0 C02 A:YLH303 4.9 16.8 0.4 C02 A:YLH303 4.9 12.6 0.7 HB3 A:ASP118 5.0 13.0 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 2728 To Be Published.