Zinc in PDB 8pg7: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755, PDB code: 8pg7 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)	34.48 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.302, 67.869, 40.101, 90, 93.53, 90
R / Rfree (%)	12.5 / 14.1

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755 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 2755 (pdb code 8pg7). 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 2755, PDB code: 8pg7:
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 2755


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 2755 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.6 occ:0.95 O A:HOH482 1.9 3.9 0.5 NE2 A:HIS179 2.0 10.2 1.0 ND1 A:HIS116 2.0 10.3 1.0 NE2 A:HIS114 2.1 9.6 1.0 HB2 A:HIS116 2.9 10.6 1.0 CE1 A:HIS116 3.0 10.0 1.0 CE1 A:HIS179 3.0 10.5 1.0 CD2 A:HIS179 3.0 9.5 1.0 CE1 A:HIS114 3.0 8.1 1.0 CG A:HIS116 3.0 9.2 1.0 CD2 A:HIS114 3.1 9.1 1.0 O29 A:YV3303 3.1 13.2 0.5 HE1 A:HIS116 3.1 12.0 1.0 HE1 A:HIS179 3.2 12.6 1.0 HD2 A:HIS179 3.2 11.4 1.0 HE1 A:HIS114 3.2 9.7 1.0 O29 A:YV3303 3.2 12.6 0.5 H051 A:YV3303 3.2 11.9 0.5 HD2 A:HIS114 3.3 10.9 1.0 H051 A:YV3303 3.3 13.8 0.5 CB A:HIS116 3.4 8.8 1.0 H021 A:YV3303 3.5 14.5 0.5 ZN A:ZN302 3.5 8.5 0.8 H021 A:YV3303 3.6 13.7 0.5 HB3 A:HIS116 3.6 10.6 1.0 OD1 A:ASP118 3.8 10.9 1.0 HB2 A:CYS198 3.9 12.6 1.0 O08 A:YV3303 4.0 7.8 0.5 C28 A:YV3303 4.0 13.6 0.5 C28 A:YV3303 4.0 13.7 0.5 O08 A:YV3303 4.0 12.4 0.5 NE2 A:HIS116 4.1 11.1 1.0 ND1 A:HIS179 4.1 10.6 1.0 CG A:HIS179 4.1 10.3 1.0 ND1 A:HIS114 4.1 8.4 1.0 HB3 A:CYS198 4.1 12.6 1.0 CD2 A:HIS116 4.2 10.8 1.0 CG A:HIS114 4.2 8.6 1.0 N05 A:YV3303 4.2 10.0 0.5 N05 A:YV3303 4.3 11.5 0.5 CB A:CYS198 4.3 10.5 1.0 SG A:CYS198 4.4 9.4 1.0 OD2 A:ASP118 4.5 10.4 1.0 C02 A:YV3303 4.5 12.1 0.5 H A:HIS116 4.5 9.9 1.0 C02 A:YV3303 4.5 11.4 0.5 CG A:ASP118 4.6 9.8 1.0 N27 A:YV3303 4.6 13.2 0.5 HB3 A:SER180 4.6 11.9 1.0 N27 A:YV3303 4.6 12.6 0.5 HG2 A:ARG119 4.7 9.8 1.0 HE A:ARG119 4.8 9.9 1.0 C07 A:YV3303 4.8 12.3 0.5 CA A:HIS116 4.8 8.1 1.0 H013 A:YV3303 4.8 14.0 0.5 H301 A:YV3303 4.8 18.8 0.5 H301 A:YV3303 4.8 19.0 0.5 C07 A:YV3303 4.8 9.6 0.5 HE2 A:HIS116 4.9 13.3 1.0 H013 A:YV3303 4.9 13.2 0.5 HD1 A:HIS179 4.9 12.7 1.0 HD1 A:HIS114 4.9 10.1 1.0 O A:HOH537 4.9 12.0 0.9 HG3 A:ARG119 5.0 9.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755


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 2755 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.5 occ:0.81 O08 A:YV3303 2.0 12.4 0.5 O A:HOH482 2.0 3.9 0.5 NE2 A:HIS240 2.1 9.7 1.0 O08 A:YV3303 2.3 7.8 0.5 SG A:CYS198 2.3 9.4 1.0 OD2 A:ASP118 2.4 10.4 1.0 H051 A:YV3303 2.6 11.9 0.5 H051 A:YV3303 2.8 13.8 0.5 C07 A:YV3303 2.9 12.3 0.5 CD2 A:HIS240 3.0 9.4 1.0 HB3 A:CYS198 3.1 12.6 1.0 HD2 A:HIS240 3.1 11.2 1.0 N05 A:YV3303 3.1 10.0 0.5 C07 A:YV3303 3.2 9.6 0.5 CE1 A:HIS240 3.2 10.1 1.0 CB A:CYS198 3.3 10.5 1.0 N05 A:YV3303 3.3 11.5 0.5 HH21 A:ARG119 3.3 11.5 1.0 C06 A:YV3303 3.3 10.6 0.5 CG A:ASP118 3.4 9.8 1.0 HE1 A:HIS240 3.4 12.1 1.0 C06 A:YV3303 3.4 10.3 0.5 ZN A:ZN301 3.5 9.6 0.9 HE1 A:HIS114 3.5 9.7 1.0 HE A:ARG119 3.5 9.9 1.0 HB2 A:CYS198 3.7 12.6 1.0 OD1 A:ASP118 3.7 10.9 1.0 NH2 A:ARG119 3.9 9.6 1.0 H021 A:YV3303 4.0 14.5 0.5 H021 A:YV3303 4.1 13.7 0.5 NE2 A:HIS179 4.1 10.2 1.0 O09 A:YV3303 4.1 13.4 0.5 HE1 A:HIS179 4.2 12.6 1.0 NE A:ARG119 4.2 8.2 1.0 CE1 A:HIS114 4.2 8.1 1.0 CG A:HIS240 4.2 9.9 1.0 O A:HOH520 4.2 9.2 0.7 CE1 A:HIS179 4.3 10.5 1.0 ND1 A:HIS240 4.3 9.9 1.0 C04 A:YV3303 4.3 9.8 0.5 O09 A:YV3303 4.4 11.4 0.5 NE2 A:HIS114 4.4 9.6 1.0 C04 A:YV3303 4.4 11.1 0.5 HA A:CYS198 4.4 12.1 1.0 HH22 A:ARG119 4.4 11.5 1.0 CZ A:ARG119 4.4 8.2 1.0 H221 A:YV3303 4.5 13.3 0.5 H121 A:YV3303 4.5 15.7 0.5 CA A:CYS198 4.5 10.1 1.0 C10 A:YV3303 4.5 10.0 0.5 HA3 A:GLY239 4.6 10.9 1.0 C10 A:YV3303 4.6 10.8 0.5 CB A:ASP118 4.7 9.5 1.0 HB2 A:ASP118 4.8 11.4 1.0 O29 A:YV3303 4.8 13.2 0.5 O29 A:YV3303 4.9 12.6 0.5 CD2 A:HIS179 4.9 9.5 1.0 HB3 A:ASP118 4.9 11.4 1.0 C02 A:YV3303 5.0 12.1 0.5

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755 To Be Published.