Zinc in PDB 8pgi: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2984

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2984, PDB code: 8pgi 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)	40.12 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.318, 67.975, 40.204, 90, 93.78, 90
R / Rfree (%)	15.4 / 19.3

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2984 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 2984 (pdb code 8pgi). 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 2984, PDB code: 8pgi:
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 2984


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 2984 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.2 occ:0.80 O A:HOH447 1.8 34.3 1.0 NE2 A:HIS179 2.2 16.8 1.0 ND1 A:HIS116 2.2 17.0 1.0 NE2 A:HIS114 2.3 17.4 1.0 HB2 A:HIS116 2.9 16.7 1.0 O39 A:YRX303 3.0 18.2 0.4 O39 A:YRX303 3.0 20.5 0.6 CD2 A:HIS179 3.0 16.7 1.0 HD2 A:HIS179 3.1 20.1 1.0 CE1 A:HIS114 3.2 16.1 1.0 CG A:HIS116 3.2 15.1 1.0 H051 A:YRX303 3.2 21.5 0.6 H051 A:YRX303 3.2 20.3 0.4 CD2 A:HIS114 3.2 16.7 1.0 CE1 A:HIS116 3.2 16.6 1.0 CE1 A:HIS179 3.2 17.1 1.0 HE1 A:HIS114 3.3 19.3 1.0 HD2 A:HIS114 3.4 20.0 1.0 HE1 A:HIS116 3.4 19.9 1.0 CB A:HIS116 3.4 13.9 1.0 HE1 A:HIS179 3.5 20.5 1.0 ZN A:ZN302 3.5 18.8 1.0 H021 A:YRX303 3.6 23.4 0.6 H021 A:YRX303 3.7 21.5 0.4 HB3 A:HIS116 3.7 16.7 1.0 C38 A:YRX303 3.8 18.7 0.4 OD1 A:ASP118 3.8 17.3 1.0 C38 A:YRX303 3.9 21.0 0.6 O08 A:YRX303 4.0 15.5 0.6 HB2 A:CYS198 4.0 20.9 1.0 N05 A:YRX303 4.2 16.9 0.4 N05 A:YRX303 4.2 17.9 0.6 HB3 A:CYS198 4.2 20.9 1.0 CG A:HIS179 4.2 16.7 1.0 O08 A:YRX303 4.2 18.4 0.4 ND1 A:HIS114 4.2 15.5 1.0 ND1 A:HIS179 4.3 17.3 1.0 CG A:HIS114 4.3 15.2 1.0 NE2 A:HIS116 4.3 19.2 1.0 CD2 A:HIS116 4.3 17.2 1.0 CB A:CYS198 4.4 17.4 1.0 SG A:CYS198 4.4 17.3 1.0 C02 A:YRX303 4.5 19.5 0.6 OD2 A:ASP118 4.5 16.1 1.0 N27 A:YRX303 4.5 18.8 0.4 N27 A:YRX303 4.5 20.9 0.6 H A:HIS116 4.5 18.2 1.0 C02 A:YRX303 4.5 17.9 0.4 CG A:ASP118 4.6 14.5 1.0 HG2 A:ARG119 4.7 17.5 1.0 HB3 A:SER180 4.7 20.5 1.0 C07 A:YRX303 4.7 17.9 0.4 C07 A:YRX303 4.8 17.2 0.6 O37 A:YRX303 4.8 19.8 0.4 CA A:HIS116 4.8 14.3 1.0 HE A:ARG119 4.9 18.7 1.0 O A:HOH545 4.9 15.1 0.8 C06 A:YRX303 4.9 16.6 0.4 C06 A:YRX303 5.0 17.1 0.6 O37 A:YRX303 5.0 22.3 0.6

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2984


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 2984 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.8 occ:0.99 O08 A:YRX303 2.0 18.4 0.4 O A:HOH447 2.1 34.3 1.0 O08 A:YRX303 2.2 15.5 0.6 NE2 A:HIS240 2.3 17.8 1.0 SG A:CYS198 2.3 17.3 1.0 OD2 A:ASP118 2.3 16.1 1.0 H051 A:YRX303 2.8 20.3 0.4 H051 A:YRX303 2.9 21.5 0.6 C07 A:YRX303 3.0 17.9 0.4 HB3 A:CYS198 3.1 20.9 1.0 CD2 A:HIS240 3.1 16.9 1.0 C07 A:YRX303 3.1 17.2 0.6 HH21 A:ARG119 3.2 20.4 1.0 HD2 A:HIS240 3.2 20.3 1.0 N05 A:YRX303 3.3 16.9 0.4 CB A:CYS198 3.3 17.4 1.0 N05 A:YRX303 3.3 17.9 0.6 CE1 A:HIS240 3.3 17.8 1.0 C06 A:YRX303 3.4 16.6 0.4 CG A:ASP118 3.4 14.5 1.0 C06 A:YRX303 3.4 17.1 0.6 ZN A:ZN301 3.5 16.2 0.8 HE A:ARG119 3.6 18.7 1.0 HE1 A:HIS240 3.6 21.4 1.0 HE1 A:HIS114 3.6 19.3 1.0 OD1 A:ASP118 3.7 17.3 1.0 HB2 A:CYS198 3.7 20.9 1.0 NH2 A:ARG119 3.9 17.0 1.0 H021 A:YRX303 4.1 21.5 0.4 H021 A:YRX303 4.1 23.4 0.6 O09 A:YRX303 4.1 17.7 0.4 NE2 A:HIS179 4.2 16.8 1.0 NE A:ARG119 4.2 15.6 1.0 O A:HOH474 4.3 19.1 0.7 CE1 A:HIS114 4.3 16.1 1.0 O09 A:YRX303 4.3 18.1 0.6 HE1 A:HIS179 4.3 20.5 1.0 CG A:HIS240 4.3 18.0 1.0 C04 A:YRX303 4.3 18.1 0.6 C04 A:YRX303 4.4 16.5 0.4 HH22 A:ARG119 4.4 20.4 1.0 CE1 A:HIS179 4.4 17.1 1.0 ND1 A:HIS240 4.4 17.4 1.0 NE2 A:HIS114 4.4 17.4 1.0 HA A:CYS198 4.4 20.1 1.0 CZ A:ARG119 4.4 15.8 1.0 H121 A:YRX303 4.5 20.6 0.4 H221 A:YRX303 4.5 23.7 0.6 CA A:CYS198 4.5 16.7 1.0 C10 A:YRX303 4.5 16.3 0.4 C10 A:YRX303 4.6 17.8 0.6 HA3 A:GLY239 4.6 18.4 1.0 CB A:ASP118 4.7 15.3 1.0 HB2 A:ASP118 4.7 18.3 1.0 O39 A:YRX303 4.8 20.5 0.6 O39 A:YRX303 4.8 18.2 0.4 CD2 A:HIS179 4.9 16.7 1.0 HB3 A:ASP118 5.0 18.3 1.0 HG2 A:ARG119 5.0 17.5 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 2984 To Be Published.