Zinc in PDB 8pgv: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3396

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3396, PDB code: 8pgv 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)	29.14 / 1.23
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.53, 68.05, 40.3, 90, 93.81, 90
R / Rfree (%)	11.8 / 14

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3396 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 3396 (pdb code 8pgv). 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 3396, PDB code: 8pgv:
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 3396


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 3396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.0 occ:0.90 O A:HOH495 1.8 7.8 0.7 NE2 A:HIS179 2.0 11.5 1.0 ND1 A:HIS116 2.0 11.2 1.0 NE2 A:HIS114 2.1 10.9 1.0 O40 A:YRT303 2.9 15.8 0.4 O40 A:YRT303 2.9 11.7 0.6 HB2 A:HIS116 3.0 12.1 1.0 CE1 A:HIS116 3.0 11.3 1.0 CE1 A:HIS179 3.0 11.7 1.0 CD2 A:HIS179 3.0 11.4 1.0 CE1 A:HIS114 3.0 10.0 1.0 CG A:HIS116 3.0 10.1 1.0 CD2 A:HIS114 3.1 10.2 1.0 HE1 A:HIS116 3.1 13.5 1.0 HE1 A:HIS179 3.2 14.0 1.0 HE1 A:HIS114 3.2 12.0 1.0 HD2 A:HIS179 3.2 13.7 1.0 HD2 A:HIS114 3.3 12.2 1.0 CB A:HIS116 3.4 10.1 1.0 H281 A:YRT303 3.4 17.6 0.4 H281 A:YRT303 3.4 14.8 0.6 H021 A:YRT303 3.5 13.5 0.6 H021 A:YRT303 3.6 18.3 0.4 ZN A:ZN302 3.6 10.1 0.7 HB3 A:HIS116 3.6 12.1 1.0 C39 A:YRT303 3.7 15.8 0.4 C39 A:YRT303 3.7 12.2 0.6 OD1 A:ASP118 3.8 11.8 1.0 O27 A:YRT303 3.9 12.3 0.4 HB2 A:CYS198 4.0 14.5 1.0 O27 A:YRT303 4.1 13.0 0.6 ND1 A:HIS179 4.1 12.2 1.0 NE2 A:HIS116 4.1 11.6 1.0 CG A:HIS179 4.1 11.6 1.0 CD2 A:HIS116 4.1 11.8 1.0 ND1 A:HIS114 4.2 10.3 1.0 N28 A:YRT303 4.2 14.7 0.4 N28 A:YRT303 4.2 12.3 0.6 CG A:HIS114 4.2 10.1 1.0 HB3 A:CYS198 4.2 14.5 1.0 C02 A:YRT303 4.4 11.2 0.6 CB A:CYS198 4.4 12.1 1.0 N30 A:YRT303 4.4 11.8 0.6 SG A:CYS198 4.5 10.9 1.0 C02 A:YRT303 4.5 15.2 0.4 OD2 A:ASP118 4.5 12.2 1.0 N30 A:YRT303 4.5 16.0 0.4 H A:HIS116 4.6 11.5 1.0 CG A:ASP118 4.6 11.0 1.0 O38 A:YRT303 4.6 16.1 0.4 HB3 A:SER180 4.7 14.1 1.0 O38 A:YRT303 4.7 13.0 0.6 HG2 A:ARG119 4.8 11.6 1.0 C25 A:YRT303 4.8 12.7 0.6 CA A:HIS116 4.8 9.6 1.0 HD1 A:HIS179 4.8 14.6 1.0 HE A:ARG119 4.9 12.6 1.0 HE2 A:HIS116 4.9 14.0 1.0 O A:HOH549 4.9 13.2 0.8 HD1 A:HIS114 4.9 12.4 1.0 C25 A:YRT303 4.9 13.5 0.4 H013 A:YRT303 5.0 14.6 0.6 H013 A:YRT303 5.0 18.5 0.4 C24 A:YRT303 5.0 12.0 0.6 HG3 A:ARG119 5.0 11.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3396


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 3396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.1 occ:0.73 O A:HOH495 2.0 7.8 0.7 O27 A:YRT303 2.0 13.0 0.6 NE2 A:HIS240 2.1 11.8 1.0 O27 A:YRT303 2.2 12.3 0.4 SG A:CYS198 2.3 10.9 1.0 OD2 A:ASP118 2.4 12.2 1.0 H281 A:YRT303 2.7 17.6 0.4 H281 A:YRT303 2.8 14.8 0.6 CD2 A:HIS240 3.0 11.4 1.0 HB3 A:CYS198 3.1 14.5 1.0 C25 A:YRT303 3.1 12.7 0.6 HD2 A:HIS240 3.1 13.7 1.0 N28 A:YRT303 3.2 14.7 0.4 CE1 A:HIS240 3.2 12.3 1.0 C25 A:YRT303 3.2 13.5 0.4 N28 A:YRT303 3.2 12.3 0.6 HH21 A:ARG119 3.2 14.0 1.0 CB A:CYS198 3.3 12.1 1.0 C24 A:YRT303 3.4 12.0 0.6 CG A:ASP118 3.4 11.0 1.0 HE1 A:HIS240 3.4 14.7 1.0 C24 A:YRT303 3.4 14.2 0.4 HE1 A:HIS114 3.5 12.0 1.0 HE A:ARG119 3.6 12.6 1.0 ZN A:ZN301 3.6 11.0 0.9 HB2 A:CYS198 3.7 14.5 1.0 OD1 A:ASP118 3.7 11.8 1.0 H021 A:YRT303 3.8 13.5 0.6 H021 A:YRT303 3.8 18.3 0.4 NH2 A:ARG119 3.9 11.7 1.0 NE2 A:HIS179 4.2 11.5 1.0 CE1 A:HIS114 4.2 10.0 1.0 NE A:ARG119 4.2 10.5 1.0 CG A:HIS240 4.2 10.7 1.0 O26 A:YRT303 4.2 13.5 0.6 HE1 A:HIS179 4.2 14.0 1.0 ND1 A:HIS240 4.2 12.2 1.0 C29 A:YRT303 4.3 14.7 0.4 O26 A:YRT303 4.3 14.1 0.4 CE1 A:HIS179 4.3 11.7 1.0 C29 A:YRT303 4.3 11.9 0.6 O A:HOH499 4.4 12.2 0.7 NE2 A:HIS114 4.4 10.9 1.0 HH22 A:ARG119 4.4 14.0 1.0 CZ A:ARG119 4.5 10.8 1.0 HA A:CYS198 4.5 13.2 1.0 H231 A:YRT303 4.5 18.0 0.6 CA A:CYS198 4.5 11.0 1.0 O40 A:YRT303 4.6 15.8 0.4 HA3 A:GLY239 4.6 13.2 1.0 H231 A:YRT303 4.6 21.6 0.4 C08 A:YRT303 4.7 11.0 0.6 O40 A:YRT303 4.7 11.7 0.6 CB A:ASP118 4.7 10.4 1.0 C08 A:YRT303 4.7 14.8 0.4 HB2 A:ASP118 4.8 12.5 1.0 C02 A:YRT303 4.9 15.2 0.4 C02 A:YRT303 4.9 11.2 0.6 CD2 A:HIS179 4.9 11.4 1.0 HB3 A:ASP118 5.0 12.5 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 3396 To Be Published.