Zinc in PDB 8pgx: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3461

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3461, PDB code: 8pgx 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)	40.27 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.38, 67.99, 40.35, 90, 93.67, 90
R / Rfree (%)	12.5 / 13.9

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3461 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3461 (pdb code 8pgx). 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 3461, PDB code: 8pgx:
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 3461


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 3461 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.1 occ:0.84 O A:HOH497 1.9 6.0 0.7 NE2 A:HIS179 2.0 9.8 1.0 ND1 A:HIS116 2.0 10.1 1.0 NE2 A:HIS114 2.1 9.5 1.0 CE1 A:HIS179 2.9 10.0 1.0 HB2 A:HIS116 3.0 9.8 1.0 O33 A:YKO303 3.0 12.4 1.0 CE1 A:HIS116 3.0 9.9 1.0 CD2 A:HIS179 3.0 9.4 1.0 CE1 A:HIS114 3.0 8.2 1.0 CG A:HIS116 3.1 8.8 1.0 CD2 A:HIS114 3.1 9.4 1.0 HE1 A:HIS116 3.1 11.9 1.0 HE1 A:HIS179 3.1 12.0 1.0 HE1 A:HIS114 3.2 9.8 1.0 HD2 A:HIS179 3.2 11.2 1.0 H211 A:YKO303 3.2 14.8 1.0 HD2 A:HIS114 3.3 11.2 1.0 CB A:HIS116 3.4 8.2 1.0 H021 A:YKO303 3.5 14.6 1.0 ZN A:ZN302 3.6 7.9 0.6 HB3 A:HIS116 3.6 9.8 1.0 C32 A:YKO303 3.7 12.0 1.0 OD1 A:ASP118 3.9 11.1 1.0 HB2 A:CYS198 4.0 13.6 1.0 ND1 A:HIS179 4.0 10.6 1.0 O19 A:YKO303 4.1 12.4 1.0 NE2 A:HIS116 4.1 10.6 1.0 O A:HOH433 4.1 39.7 0.6 CG A:HIS179 4.1 10.0 1.0 CD2 A:HIS116 4.2 10.2 1.0 ND1 A:HIS114 4.2 8.9 1.0 N21 A:YKO303 4.2 12.3 1.0 CG A:HIS114 4.2 8.4 1.0 HB3 A:CYS198 4.3 13.6 1.0 N23 A:YKO303 4.4 12.4 1.0 C02 A:YKO303 4.4 12.2 1.0 CB A:CYS198 4.4 11.3 1.0 SG A:CYS198 4.5 10.2 1.0 OD2 A:ASP118 4.5 10.9 1.0 H A:HIS116 4.6 9.0 1.0 CG A:ASP118 4.6 9.9 1.0 O31 A:YKO303 4.7 12.9 1.0 HB3 A:SER180 4.7 11.9 1.0 HE A:ARG119 4.8 10.6 1.0 HD1 A:HIS179 4.8 12.7 1.0 HE2 A:HIS116 4.8 12.7 1.0 HG2 A:ARG119 4.8 9.7 1.0 CA A:HIS116 4.8 7.7 1.0 C18 A:YKO303 4.9 12.2 1.0 O A:HOH548 4.9 12.8 0.8 H011 A:YKO303 4.9 14.3 1.0 HD1 A:HIS114 4.9 10.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3461


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 3461 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.9 occ:0.64 O A:HOH497 2.0 6.0 0.7 NE2 A:HIS240 2.1 10.0 1.0 O19 A:YKO303 2.1 12.4 1.0 SG A:CYS198 2.3 10.2 1.0 OD2 A:ASP118 2.4 10.9 1.0 H211 A:YKO303 2.7 14.8 1.0 CD2 A:HIS240 3.0 10.8 1.0 HB3 A:CYS198 3.1 13.6 1.0 C18 A:YKO303 3.1 12.2 1.0 HD2 A:HIS240 3.1 12.9 1.0 CE1 A:HIS240 3.2 11.1 1.0 N21 A:YKO303 3.2 12.3 1.0 HH21 A:ARG119 3.2 13.2 1.0 CB A:CYS198 3.3 11.3 1.0 CG A:ASP118 3.4 9.9 1.0 C17 A:YKO303 3.4 11.6 1.0 HE1 A:HIS240 3.4 13.3 1.0 HE1 A:HIS114 3.5 9.8 1.0 O A:HOH433 3.5 39.7 0.6 HE A:ARG119 3.6 10.6 1.0 ZN A:ZN301 3.6 9.1 0.8 HB2 A:CYS198 3.7 13.6 1.0 OD1 A:ASP118 3.8 11.1 1.0 NH2 A:ARG119 3.9 11.0 1.0 H021 A:YKO303 3.9 14.6 1.0 NE2 A:HIS179 4.1 9.8 1.0 CE1 A:HIS114 4.2 8.2 1.0 HE1 A:HIS179 4.2 12.0 1.0 CG A:HIS240 4.2 10.9 1.0 NE A:ARG119 4.2 8.8 1.0 ND1 A:HIS240 4.2 11.6 1.0 O20 A:YKO303 4.2 14.1 1.0 CE1 A:HIS179 4.3 10.0 1.0 C22 A:YKO303 4.3 11.8 1.0 O A:HOH507 4.3 13.0 0.8 HH22 A:ARG119 4.4 13.2 1.0 NE2 A:HIS114 4.4 9.5 1.0 CZ A:ARG119 4.4 9.1 1.0 HA A:CYS198 4.5 12.5 1.0 CA A:CYS198 4.5 10.4 1.0 HA3 A:GLY239 4.6 11.6 1.0 C08 A:YKO303 4.6 11.8 1.0 O33 A:YKO303 4.7 12.4 1.0 H161 A:YKO303 4.7 18.2 1.0 CB A:ASP118 4.7 8.7 1.0 HB2 A:ASP118 4.8 10.4 1.0 CD2 A:HIS179 4.9 9.4 1.0 C02 A:YKO303 4.9 12.2 1.0 HB3 A:ASP118 5.0 10.4 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 3461 To Be Published.