Zinc in PDB 8pgg: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2954

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2954, PDB code: 8pgg 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)	39.82 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.67, 67.15, 39.82, 90, 90.29, 90
R / Rfree (%)	12.1 / 15.2

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2954 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 2954 (pdb code 8pgg). 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 2954, PDB code: 8pgg:
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 2954


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 2954 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.5 occ:1.00 O A:HOH491 1.9 10.2 0.9 NE2 A:HIS179 2.0 11.0 1.0 ND1 A:HIS116 2.1 11.8 1.0 NE2 A:HIS114 2.1 11.0 1.0 HB2 A:HIS116 2.9 13.6 1.0 CD2 A:HIS179 3.0 10.5 1.0 CE1 A:HIS114 3.0 10.8 1.0 CE1 A:HIS179 3.0 10.9 1.0 CE1 A:HIS116 3.0 13.2 1.0 CG A:HIS116 3.1 11.4 1.0 CD2 A:HIS114 3.1 10.3 1.0 HD2 A:HIS179 3.2 12.6 1.0 HE1 A:HIS114 3.2 12.9 1.0 H121 A:YU3303 3.2 22.7 0.2 HE1 A:HIS116 3.2 15.8 1.0 HE1 A:HIS179 3.2 13.1 1.0 H121 A:YU3303 3.2 13.1 0.8 HD2 A:HIS114 3.3 12.3 1.0 H041 A:YU3303 3.3 31.5 0.2 CB A:HIS116 3.4 11.3 1.0 O09 A:YU3303 3.4 30.5 0.8 ZN A:ZN302 3.5 11.8 0.9 H021 A:YU3303 3.5 27.2 0.2 H021 A:YU3303 3.6 15.6 0.8 HB3 A:HIS116 3.6 13.6 1.0 C04 A:YU3303 3.8 26.3 0.2 HB2 A:CYS198 3.9 14.4 1.0 OD1 A:ASP118 3.9 12.7 1.0 O16 A:YU3303 3.9 10.7 0.8 C08 A:YU3303 3.9 22.7 0.8 O16 A:YU3303 4.0 17.5 0.2 ND1 A:HIS179 4.1 11.1 1.0 ND1 A:HIS114 4.1 10.3 1.0 CG A:HIS179 4.1 10.1 1.0 HB3 A:CYS198 4.1 14.4 1.0 NE2 A:HIS116 4.1 13.9 1.0 N12 A:YU3303 4.2 18.9 0.2 CG A:HIS114 4.2 9.8 1.0 CD2 A:HIS116 4.2 13.1 1.0 N12 A:YU3303 4.2 10.9 0.8 CB A:CYS198 4.3 12.0 1.0 SG A:CYS198 4.4 10.9 1.0 H A:HIS116 4.5 12.5 1.0 C03 A:YU3303 4.5 25.3 0.2 OD2 A:ASP118 4.5 12.6 1.0 C02 A:YU3303 4.5 22.6 0.2 C03 A:YU3303 4.5 18.1 0.8 C02 A:YU3303 4.5 13.0 0.8 C05 A:YU3303 4.6 27.8 0.2 CG A:ASP118 4.6 11.9 1.0 H051 A:YU3303 4.6 33.3 0.2 HB3 A:SER180 4.6 13.6 1.0 N07 A:YU3303 4.7 24.8 0.8 C14 A:YU3303 4.7 11.2 0.8 HG2 A:ARG119 4.7 13.1 1.0 HE A:ARG119 4.8 12.7 1.0 C14 A:YU3303 4.8 18.0 0.2 H071 A:YU3303 4.8 29.7 0.8 CA A:HIS116 4.8 10.9 1.0 HD1 A:HIS179 4.9 13.3 1.0 HD1 A:HIS114 4.9 12.3 1.0 HE2 A:HIS116 4.9 16.7 1.0 O A:HOH538 4.9 11.6 0.8 C13 A:YU3303 4.9 18.4 0.2 C13 A:YU3303 5.0 11.3 0.8 HG3 A:ARG119 5.0 13.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2954


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 2954 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.8 occ:0.94 O A:HOH491 2.0 10.2 0.9 O16 A:YU3303 2.1 10.7 0.8 O16 A:YU3303 2.1 17.5 0.2 NE2 A:HIS240 2.1 12.4 1.0 OD2 A:ASP118 2.3 12.6 1.0 SG A:CYS198 2.3 10.9 1.0 H121 A:YU3303 2.7 13.1 0.8 H121 A:YU3303 2.7 22.7 0.2 C14 A:YU3303 3.0 11.2 0.8 C14 A:YU3303 3.0 18.0 0.2 CD2 A:HIS240 3.0 11.9 1.0 HB3 A:CYS198 3.1 14.4 1.0 HD2 A:HIS240 3.1 14.3 1.0 N12 A:YU3303 3.2 18.9 0.2 N12 A:YU3303 3.2 10.9 0.8 CE1 A:HIS240 3.2 12.9 1.0 HH21 A:ARG119 3.2 15.0 1.0 CB A:CYS198 3.3 12.0 1.0 C13 A:YU3303 3.3 18.4 0.2 CG A:ASP118 3.3 11.9 1.0 C13 A:YU3303 3.4 11.3 0.8 HE1 A:HIS240 3.4 15.5 1.0 ZN A:ZN301 3.5 11.5 1.0 HE A:ARG119 3.5 12.7 1.0 HE1 A:HIS114 3.6 12.9 1.0 OD1 A:ASP118 3.7 12.7 1.0 HB2 A:CYS198 3.7 14.4 1.0 H021 A:YU3303 3.9 15.6 0.8 NH2 A:ARG119 3.9 12.5 1.0 H021 A:YU3303 3.9 27.2 0.2 NE2 A:HIS179 4.1 11.0 1.0 O15 A:YU3303 4.2 17.9 0.2 HE1 A:HIS179 4.2 13.1 1.0 NE A:ARG119 4.2 10.6 1.0 CG A:HIS240 4.2 11.9 1.0 C11 A:YU3303 4.2 19.6 0.2 O15 A:YU3303 4.2 11.4 0.8 CE1 A:HIS114 4.3 10.8 1.0 ND1 A:HIS240 4.3 12.1 1.0 C11 A:YU3303 4.3 11.5 0.8 CE1 A:HIS179 4.3 10.9 1.0 O A:HOH523 4.3 10.7 0.7 NE2 A:HIS114 4.4 11.0 1.0 H291 A:YU3303 4.4 16.8 0.8 HA A:CYS198 4.4 13.2 1.0 HH22 A:ARG119 4.5 15.0 1.0 H191 A:YU3303 4.5 21.4 0.2 C17 A:YU3303 4.5 18.4 0.2 CZ A:ARG119 4.5 10.8 1.0 CA A:CYS198 4.5 11.0 1.0 C17 A:YU3303 4.5 11.7 0.8 HA3 A:GLY239 4.6 14.4 1.0 H041 A:YU3303 4.6 31.5 0.2 CB A:ASP118 4.7 12.7 1.0 O09 A:YU3303 4.7 30.5 0.8 HB2 A:ASP118 4.7 15.2 1.0 C02 A:YU3303 4.9 13.0 0.8 C02 A:YU3303 4.9 22.6 0.2 HB3 A:ASP118 4.9 15.2 1.0 CD2 A:HIS179 4.9 10.5 1.0 C30 A:YU3303 4.9 19.3 0.2

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2954 To Be Published.