Zinc in PDB 8pgc: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2868

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2868, PDB code: 8pgc 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)	34.65 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.531, 68.282, 40.302, 90, 93.96, 90
R / Rfree (%)	13.1 / 14.6

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2868 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 2868 (pdb code 8pgc). 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 2868, PDB code: 8pgc:
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 2868


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 2868 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.9 occ:0.83 O20 A:YSB303 1.8 16.1 0.5 O A:HOH485 2.0 7.1 0.5 NE2 A:HIS240 2.1 14.0 1.0 O20 A:YSB303 2.2 10.2 0.5 SG A:CYS198 2.3 13.3 1.0 OD2 A:ASP118 2.4 15.1 1.0 C19 A:YSB303 2.9 16.2 0.5 H171 A:YSB303 3.0 17.0 0.5 CD2 A:HIS240 3.0 13.3 1.0 HB3 A:CYS198 3.1 17.6 1.0 H171 A:YSB303 3.1 17.4 0.5 HD2 A:HIS240 3.1 15.9 1.0 C19 A:YSB303 3.2 11.5 0.5 N17 A:YSB303 3.2 14.2 0.5 CE1 A:HIS240 3.2 15.1 1.0 CB A:CYS198 3.3 14.7 1.0 N17 A:YSB303 3.3 14.5 0.5 HH21 A:ARG119 3.3 16.9 1.0 C18 A:YSB303 3.3 15.2 0.5 CG A:ASP118 3.4 13.9 1.0 C18 A:YSB303 3.4 14.4 0.5 HE1 A:HIS240 3.4 18.1 1.0 HE1 A:HIS114 3.5 14.2 1.0 HE A:ARG119 3.5 15.4 1.0 ZN A:ZN302 3.5 12.6 0.8 HB2 A:CYS198 3.7 17.6 1.0 OD1 A:ASP118 3.7 14.2 1.0 NH2 A:ARG119 3.9 14.1 1.0 H131 A:YSB303 3.9 18.7 0.5 O21 A:YSB303 4.0 17.7 0.5 H131 A:YSB303 4.1 16.0 0.5 NE2 A:HIS179 4.1 13.3 1.0 NE A:ARG119 4.2 12.9 1.0 CE1 A:HIS114 4.2 11.8 1.0 HE1 A:HIS179 4.2 15.8 1.0 CG A:HIS240 4.2 13.7 1.0 ND1 A:HIS240 4.3 14.0 1.0 CE1 A:HIS179 4.3 13.1 1.0 O A:HOH476 4.3 7.2 0.3 O21 A:YSB303 4.3 13.0 0.5 C16 A:YSB303 4.3 15.3 0.5 C16 A:YSB303 4.4 13.5 0.5 NE2 A:HIS114 4.4 13.6 1.0 HA A:CYS198 4.4 16.0 1.0 HH22 A:ARG119 4.4 16.9 1.0 H241 A:YSB303 4.4 18.9 0.5 CZ A:ARG119 4.4 11.7 1.0 C22 A:YSB303 4.5 14.7 0.5 H291 A:YSB303 4.5 23.0 0.5 CA A:CYS198 4.5 13.3 1.0 C22 A:YSB303 4.5 16.0 0.5 HA3 A:GLY239 4.6 15.4 1.0 O10 A:YSB303 4.7 14.7 0.5 O10 A:YSB303 4.7 15.3 0.5 CB A:ASP118 4.7 12.6 1.0 HB2 A:ASP118 4.8 15.1 1.0 CD2 A:HIS179 4.8 12.6 1.0 C13 A:YSB303 4.9 15.6 0.5 HG2 A:ARG119 5.0 12.1 1.0 HB3 A:ASP118 5.0 15.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2868


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 2868 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.6 occ:0.81 O A:HOH485 1.9 7.1 0.5 NE2 A:HIS179 2.0 13.3 1.0 ND1 A:HIS116 2.1 14.0 1.0 NE2 A:HIS114 2.1 13.6 1.0 HB2 A:HIS116 2.9 14.7 1.0 O10 A:YSB303 2.9 14.7 0.5 CE1 A:HIS179 3.0 13.1 1.0 CD2 A:HIS179 3.0 12.6 1.0 CE1 A:HIS116 3.0 15.2 1.0 CE1 A:HIS114 3.0 11.8 1.0 CG A:HIS116 3.1 12.4 1.0 CD2 A:HIS114 3.1 12.8 1.0 HE1 A:HIS179 3.2 15.8 1.0 O10 A:YSB303 3.2 15.3 0.5 HE1 A:HIS116 3.2 18.2 1.0 HD2 A:HIS179 3.2 15.1 1.0 HE1 A:HIS114 3.2 14.2 1.0 H171 A:YSB303 3.2 17.0 0.5 H171 A:YSB303 3.3 17.4 0.5 HD2 A:HIS114 3.3 15.4 1.0 CB A:HIS116 3.4 12.3 1.0 H131 A:YSB303 3.5 18.7 0.5 H131 A:YSB303 3.5 16.0 0.5 ZN A:ZN301 3.5 12.9 0.8 HB3 A:HIS116 3.6 14.7 1.0 C09 A:YSB303 3.7 16.3 0.5 C09 A:YSB303 3.8 15.9 0.5 OD1 A:ASP118 3.9 14.2 1.0 O20 A:YSB303 3.9 10.2 0.5 HB2 A:CYS198 4.0 17.6 1.0 ND1 A:HIS179 4.1 14.1 1.0 CG A:HIS179 4.1 13.5 1.0 O20 A:YSB303 4.1 16.1 0.5 NE2 A:HIS116 4.1 15.3 1.0 ND1 A:HIS114 4.2 12.6 1.0 HB3 A:CYS198 4.2 17.6 1.0 CD2 A:HIS116 4.2 14.7 1.0 N17 A:YSB303 4.2 14.2 0.5 N17 A:YSB303 4.2 14.5 0.5 CG A:HIS114 4.2 12.0 1.0 N12 A:YSB303 4.4 13.6 0.5 CB A:CYS198 4.4 14.7 1.0 N12 A:YSB303 4.4 16.6 0.5 C13 A:YSB303 4.5 15.6 0.5 C13 A:YSB303 4.5 13.3 0.5 H A:HIS116 4.5 13.7 1.0 SG A:CYS198 4.5 13.3 1.0 OD2 A:ASP118 4.5 15.1 1.0 CG A:ASP118 4.6 13.9 1.0 O08 A:YSB303 4.7 17.7 0.5 O08 A:YSB303 4.7 16.4 0.5 C19 A:YSB303 4.7 16.2 0.5 HB3 A:SER180 4.7 18.1 1.0 C19 A:YSB303 4.7 11.5 0.5 HG2 A:ARG119 4.7 12.1 1.0 CA A:HIS116 4.8 11.3 1.0 HE A:ARG119 4.8 15.4 1.0 HD1 A:HIS179 4.9 16.9 1.0 O A:HOH544 4.9 14.4 0.7 HE2 A:HIS116 4.9 18.3 1.0 C18 A:YSB303 4.9 15.2 0.5 HD1 A:HIS114 4.9 15.2 1.0 C18 A:YSB303 4.9 14.4 0.5 HG3 A:ARG119 5.0 12.1 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 2868 To Be Published.