Zinc in PDB 8pgn: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3169

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3169, PDB code: 8pgn 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)	40.18 / 1.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.43, 67.95, 40.25, 90, 93.4, 90
R / Rfree (%)	12.1 / 14

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3169 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 3169 (pdb code 8pgn). 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 3169, PDB code: 8pgn:
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 3169


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 3169 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.3 occ:0.68 O A:HOH488 1.9 7.5 0.6 NE2 A:HIS179 2.0 12.5 1.0 ND1 A:HIS116 2.0 11.6 1.0 NE2 A:HIS114 2.1 11.2 1.0 HB2 A:HIS116 2.9 11.5 1.0 CE1 A:HIS116 2.9 12.3 1.0 CE1 A:HIS179 3.0 12.4 1.0 CD2 A:HIS179 3.0 11.6 1.0 O38 A:YRF303 3.0 15.7 1.0 CE1 A:HIS114 3.0 10.1 1.0 CG A:HIS116 3.1 10.9 1.0 HE1 A:HIS116 3.1 14.8 1.0 CD2 A:HIS114 3.1 10.5 1.0 HE1 A:HIS179 3.2 14.9 1.0 HD2 A:HIS179 3.2 13.9 1.0 HE1 A:HIS114 3.2 12.1 1.0 H051 A:YRF303 3.2 15.2 1.0 HD2 A:HIS114 3.3 12.6 1.0 CB A:HIS116 3.4 9.6 1.0 H021 A:YRF303 3.5 16.2 1.0 ZN A:ZN302 3.6 8.4 0.6 HB3 A:HIS116 3.7 11.5 1.0 C37 A:YRF303 3.8 14.3 1.0 OD1 A:ASP118 3.8 11.9 1.0 HB2 A:CYS198 4.0 15.1 1.0 O08 A:YRF303 4.0 12.8 1.0 ND1 A:HIS179 4.1 12.6 1.0 NE2 A:HIS116 4.1 13.1 1.0 CG A:HIS179 4.1 11.7 1.0 CD2 A:HIS116 4.2 12.9 1.0 ND1 A:HIS114 4.2 10.2 1.0 N05 A:YRF303 4.2 12.6 1.0 HB3 A:CYS198 4.2 15.1 1.0 CG A:HIS114 4.2 9.9 1.0 C02 A:YRF303 4.4 13.5 1.0 N27 A:YRF303 4.4 15.0 1.0 CB A:CYS198 4.4 12.6 1.0 SG A:CYS198 4.5 11.1 1.0 OD2 A:ASP118 4.5 12.4 1.0 H A:HIS116 4.6 10.2 1.0 CG A:ASP118 4.6 10.9 1.0 HB3 A:SER180 4.7 14.4 1.0 O36 A:YRF303 4.7 17.9 1.0 HG2 A:ARG119 4.8 10.7 1.0 C07 A:YRF303 4.8 13.2 1.0 HE A:ARG119 4.8 11.0 1.0 HD1 A:HIS179 4.8 15.1 1.0 CA A:HIS116 4.8 9.2 1.0 HE2 A:HIS116 4.9 15.7 1.0 O A:HOH549 4.9 13.3 0.7 HD1 A:HIS114 4.9 12.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3169


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 3169 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.4 occ:0.59 O A:HOH488 2.0 7.5 0.6 NE2 A:HIS240 2.1 11.4 1.0 O08 A:YRF303 2.1 12.8 1.0 SG A:CYS198 2.3 11.1 1.0 OD2 A:ASP118 2.4 12.4 1.0 H051 A:YRF303 2.6 15.2 1.0 CD2 A:HIS240 3.0 11.9 1.0 C07 A:YRF303 3.1 13.2 1.0 HB3 A:CYS198 3.1 15.1 1.0 HD2 A:HIS240 3.1 14.2 1.0 CE1 A:HIS240 3.2 12.0 1.0 N05 A:YRF303 3.2 12.6 1.0 HH21 A:ARG119 3.2 13.3 1.0 CB A:CYS198 3.3 12.6 1.0 C06 A:YRF303 3.4 12.6 1.0 HE1 A:HIS240 3.4 14.4 1.0 CG A:ASP118 3.4 10.9 1.0 HE1 A:HIS114 3.5 12.1 1.0 HE A:ARG119 3.5 11.0 1.0 ZN A:ZN301 3.6 9.3 0.7 OD1 A:ASP118 3.7 11.9 1.0 HB2 A:CYS198 3.7 15.1 1.0 NH2 A:ARG119 3.9 11.1 1.0 H021 A:YRF303 4.0 16.2 1.0 NE2 A:HIS179 4.2 12.5 1.0 HE1 A:HIS179 4.2 14.9 1.0 O09 A:YRF303 4.2 14.8 1.0 CG A:HIS240 4.2 11.5 1.0 NE A:ARG119 4.2 9.2 1.0 CE1 A:HIS114 4.2 10.1 1.0 ND1 A:HIS240 4.2 12.2 1.0 O A:HOH547 4.3 10.9 0.6 CE1 A:HIS179 4.3 12.4 1.0 H121 A:YRF303 4.3 22.9 1.0 C04 A:YRF303 4.3 13.2 1.0 NE2 A:HIS114 4.4 11.2 1.0 HH22 A:ARG119 4.4 13.3 1.0 HA A:CYS198 4.5 13.7 1.0 CZ A:ARG119 4.5 9.3 1.0 CA A:CYS198 4.5 11.4 1.0 C10 A:YRF303 4.6 13.2 1.0 HA3 A:GLY239 4.6 13.1 1.0 O38 A:YRF303 4.7 15.7 1.0 CB A:ASP118 4.7 10.2 1.0 HB2 A:ASP118 4.8 12.2 1.0 CD2 A:HIS179 4.9 11.6 1.0 C02 A:YRF303 5.0 13.5 1.0 HB3 A:ASP118 5.0 12.2 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 3169 To Be Published.