Zinc in PDB 8pgj: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2985

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2985, PDB code: 8pgj 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)	34.05 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.404, 68.127, 40.283, 90, 93.77, 90
R / Rfree (%)	12 / 13.7

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2985 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 2985 (pdb code 8pgj). 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 2985, PDB code: 8pgj:
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 2985


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 2985 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.8 occ:0.79 O A:HOH482 1.9 3.5 0.5 NE2 A:HIS179 2.0 10.1 1.0 ND1 A:HIS116 2.0 10.6 1.0 NE2 A:HIS114 2.1 9.9 1.0 HB2 A:HIS116 2.9 10.8 1.0 CE1 A:HIS116 3.0 10.8 1.0 CE1 A:HIS179 3.0 10.8 1.0 CD2 A:HIS179 3.0 10.2 1.0 CE1 A:HIS114 3.0 9.3 1.0 CG A:HIS116 3.0 9.4 1.0 O38 A:YMB303 3.1 15.2 0.5 CD2 A:HIS114 3.1 9.5 1.0 HE1 A:HIS116 3.1 13.0 1.0 O38 A:YMB303 3.1 12.7 0.6 HE1 A:HIS179 3.1 13.0 1.0 HE1 A:HIS114 3.2 11.2 1.0 HD2 A:HIS179 3.2 12.2 1.0 H051 A:YMB303 3.2 13.3 0.5 H051 A:YMB303 3.3 11.3 0.6 HD2 A:HIS114 3.3 11.4 1.0 CB A:HIS116 3.4 9.0 1.0 H021 A:YMB303 3.5 13.8 0.6 H021 A:YMB303 3.5 15.6 0.5 ZN A:ZN302 3.6 8.3 0.8 HB3 A:HIS116 3.6 10.8 1.0 OD1 A:ASP118 3.8 10.9 1.0 C37 A:YMB303 3.8 15.0 0.5 C37 A:YMB303 3.9 13.7 0.6 O09 A:YMB303 4.0 13.7 0.5 O09 A:YMB303 4.0 7.3 0.6 HB2 A:CYS198 4.0 12.5 1.0 ND1 A:HIS179 4.1 11.2 1.0 NE2 A:HIS116 4.1 11.7 1.0 CG A:HIS179 4.1 10.8 1.0 ND1 A:HIS114 4.1 9.2 1.0 CD2 A:HIS116 4.2 11.4 1.0 HB3 A:CYS198 4.2 12.5 1.0 N05 A:YMB303 4.2 11.0 0.5 CG A:HIS114 4.2 8.9 1.0 N05 A:YMB303 4.3 9.4 0.6 CB A:CYS198 4.4 10.4 1.0 C02 A:YMB303 4.4 11.5 0.6 N27 A:YMB303 4.4 12.8 0.6 C02 A:YMB303 4.4 13.0 0.5 N27 A:YMB303 4.5 14.7 0.5 H A:HIS116 4.5 10.3 1.0 SG A:CYS198 4.5 10.2 1.0 OD2 A:ASP118 4.5 10.2 1.0 CG A:ASP118 4.6 10.1 1.0 HB3 A:SER180 4.7 13.2 1.0 O36 A:YMB303 4.7 16.3 0.5 HG2 A:ARG119 4.8 10.7 1.0 C07 A:YMB303 4.8 12.9 0.5 C07 A:YMB303 4.8 7.3 0.6 CA A:HIS116 4.8 8.4 1.0 HD1 A:HIS179 4.8 13.4 1.0 HE2 A:HIS116 4.9 14.0 1.0 O36 A:YMB303 4.9 16.9 0.6 O A:HOH547 4.9 11.7 0.8 HD1 A:HIS114 4.9 11.1 1.0 HE A:ARG119 4.9 10.7 1.0 C06 A:YMB303 5.0 11.7 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2985


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 2985 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.3 occ:0.75 O09 A:YMB303 1.8 13.7 0.5 O A:HOH482 2.0 3.5 0.5 NE2 A:HIS240 2.1 9.7 1.0 O09 A:YMB303 2.3 7.3 0.6 SG A:CYS198 2.3 10.2 1.0 OD2 A:ASP118 2.4 10.2 1.0 H051 A:YMB303 2.6 13.3 0.5 H051 A:YMB303 2.8 11.3 0.6 C07 A:YMB303 2.8 12.9 0.5 CD2 A:HIS240 3.0 10.0 1.0 HB3 A:CYS198 3.1 12.5 1.0 HD2 A:HIS240 3.1 12.0 1.0 N05 A:YMB303 3.1 11.0 0.5 CE1 A:HIS240 3.2 10.5 1.0 C07 A:YMB303 3.2 7.3 0.6 N05 A:YMB303 3.3 9.4 0.6 C06 A:YMB303 3.3 11.7 0.5 HH21 A:ARG119 3.3 12.8 1.0 CB A:CYS198 3.3 10.4 1.0 CG A:ASP118 3.4 10.1 1.0 HE1 A:HIS240 3.4 12.6 1.0 C06 A:YMB303 3.4 8.3 0.6 HE1 A:HIS114 3.5 11.2 1.0 ZN A:ZN301 3.6 8.8 0.8 HE A:ARG119 3.6 10.7 1.0 OD1 A:ASP118 3.7 10.9 1.0 HB2 A:CYS198 3.7 12.5 1.0 NH2 A:ARG119 3.9 10.6 1.0 H021 A:YMB303 4.0 13.8 0.6 O08 A:YMB303 4.0 13.1 0.5 H021 A:YMB303 4.1 15.6 0.5 NE2 A:HIS179 4.1 10.1 1.0 HE1 A:HIS179 4.2 13.0 1.0 CE1 A:HIS114 4.2 9.3 1.0 CG A:HIS240 4.2 10.2 1.0 NE A:ARG119 4.2 8.9 1.0 ND1 A:HIS240 4.2 10.6 1.0 O A:HOH499 4.3 9.3 0.6 CE1 A:HIS179 4.3 10.8 1.0 C04 A:YMB303 4.3 11.1 0.5 C04 A:YMB303 4.4 10.2 0.6 O08 A:YMB303 4.4 8.6 0.6 NE2 A:HIS114 4.4 9.9 1.0 HA A:CYS198 4.4 12.5 1.0 HH22 A:ARG119 4.4 12.8 1.0 H221 A:YMB303 4.5 15.8 0.5 CZ A:ARG119 4.5 9.3 1.0 H121 A:YMB303 4.5 14.8 0.6 CA A:CYS198 4.5 10.4 1.0 C10 A:YMB303 4.5 11.8 0.5 C10 A:YMB303 4.6 9.7 0.6 HA3 A:GLY239 4.6 11.9 1.0 O38 A:YMB303 4.6 15.2 0.5 CB A:ASP118 4.7 9.6 1.0 HB2 A:ASP118 4.8 11.6 1.0 O38 A:YMB303 4.9 12.7 0.6 CD2 A:HIS179 4.9 10.2 1.0 HB3 A:ASP118 5.0 11.6 1.0 C02 A:YMB303 5.0 11.5 0.6

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2985 To Be Published.