Zinc in PDB 8pgq: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3225

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3225, PDB code: 8pgq 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)	29.06 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.52, 67.81, 40.23, 90, 93.58, 90
R / Rfree (%)	11.6 / 13.7

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3225 (pdb code 8pgq). 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 3225, PDB code: 8pgq:
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 3225


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 3225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.3 occ:0.82 O A:HOH522 1.9 4.1 0.5 NE2 A:HIS179 2.0 11.5 1.0 ND1 A:HIS116 2.0 11.4 1.0 NE2 A:HIS114 2.1 11.0 1.0 O38 A:YUC303 2.9 12.4 0.6 CE1 A:HIS179 3.0 11.4 1.0 CE1 A:HIS116 3.0 12.0 1.0 HB2 A:HIS116 3.0 11.5 1.0 O38 A:YUC303 3.0 13.9 0.4 CD2 A:HIS179 3.0 11.1 1.0 CE1 A:HIS114 3.0 9.8 1.0 CG A:HIS116 3.1 10.4 1.0 HE1 A:HIS116 3.1 14.4 1.0 CD2 A:HIS114 3.1 10.5 1.0 HE1 A:HIS179 3.1 13.7 1.0 HE1 A:HIS114 3.2 11.8 1.0 HD2 A:HIS179 3.2 13.3 1.0 H051 A:YUC303 3.2 14.4 0.6 H051 A:YUC303 3.2 16.8 0.4 HD2 A:HIS114 3.3 12.6 1.0 CB A:HIS116 3.4 9.6 1.0 H021 A:YUC303 3.5 16.9 0.4 H021 A:YUC303 3.5 15.4 0.6 ZN A:ZN302 3.6 9.8 0.8 HB3 A:HIS116 3.6 11.5 1.0 C37 A:YUC303 3.7 12.9 0.6 C37 A:YUC303 3.8 14.5 0.4 OD1 A:ASP118 3.9 12.0 1.0 HB2 A:CYS198 4.0 14.6 1.0 O09 A:YUC303 4.0 13.4 0.4 O09 A:YUC303 4.0 13.1 0.6 NE2 A:HIS116 4.1 11.7 1.0 ND1 A:HIS179 4.1 11.7 1.0 CG A:HIS179 4.1 11.1 1.0 CD2 A:HIS116 4.1 11.6 1.0 ND1 A:HIS114 4.2 10.1 1.0 N05 A:YUC303 4.2 12.0 0.6 HB3 A:CYS198 4.2 14.6 1.0 N05 A:YUC303 4.2 14.0 0.4 CG A:HIS114 4.3 10.1 1.0 N28 A:YUC303 4.4 13.1 0.6 C02 A:YUC303 4.4 14.1 0.4 C02 A:YUC303 4.4 12.8 0.6 N28 A:YUC303 4.4 14.6 0.4 CB A:CYS198 4.4 12.2 1.0 SG A:CYS198 4.5 11.3 1.0 OD2 A:ASP118 4.5 12.3 1.0 H A:HIS116 4.6 11.5 1.0 CG A:ASP118 4.6 11.1 1.0 O36 A:YUC303 4.7 13.7 0.6 HB3 A:SER180 4.7 13.2 1.0 O36 A:YUC303 4.8 15.6 0.4 HG2 A:ARG119 4.8 11.0 1.0 HE A:ARG119 4.8 11.5 1.0 C07 A:YUC303 4.8 12.8 0.6 CA A:HIS116 4.8 9.5 1.0 HE2 A:HIS116 4.9 14.0 1.0 O A:HOH557 4.9 12.4 0.8 HD1 A:HIS179 4.9 14.0 1.0 C07 A:YUC303 4.9 13.9 0.4 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 3225


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 3225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.8 occ:0.78 O A:HOH522 2.0 4.1 0.5 O09 A:YUC303 2.1 13.1 0.6 NE2 A:HIS240 2.1 11.7 1.0 O09 A:YUC303 2.2 13.4 0.4 SG A:CYS198 2.3 11.3 1.0 OD2 A:ASP118 2.4 12.3 1.0 H051 A:YUC303 2.6 14.4 0.6 H051 A:YUC303 2.7 16.8 0.4 CD2 A:HIS240 3.0 12.0 1.0 C07 A:YUC303 3.0 12.8 0.6 HB3 A:CYS198 3.0 14.6 1.0 C07 A:YUC303 3.1 13.9 0.4 HD2 A:HIS240 3.1 14.4 1.0 N05 A:YUC303 3.1 12.0 0.6 CE1 A:HIS240 3.2 12.3 1.0 N05 A:YUC303 3.2 14.0 0.4 CB A:CYS198 3.3 12.2 1.0 HH21 A:ARG119 3.3 13.4 1.0 C06 A:YUC303 3.4 12.3 0.6 C06 A:YUC303 3.4 14.0 0.4 HE1 A:HIS240 3.4 14.7 1.0 CG A:ASP118 3.4 11.1 1.0 HE1 A:HIS114 3.5 11.8 1.0 HE A:ARG119 3.5 11.5 1.0 ZN A:ZN301 3.6 10.3 0.8 HB2 A:CYS198 3.7 14.6 1.0 OD1 A:ASP118 3.8 12.0 1.0 NH2 A:ARG119 3.9 11.2 1.0 H021 A:YUC303 3.9 15.4 0.6 H021 A:YUC303 4.0 16.9 0.4 NE2 A:HIS179 4.1 11.5 1.0 CG A:HIS240 4.2 11.2 1.0 O08 A:YUC303 4.2 14.6 0.6 HE1 A:HIS179 4.2 13.7 1.0 NE A:ARG119 4.2 9.6 1.0 O08 A:YUC303 4.2 15.2 0.4 CE1 A:HIS114 4.2 9.8 1.0 ND1 A:HIS240 4.2 12.1 1.0 CE1 A:HIS179 4.3 11.4 1.0 C04 A:YUC303 4.3 12.7 0.6 O A:HOH513 4.3 8.2 0.5 C04 A:YUC303 4.3 14.2 0.4 NE2 A:HIS114 4.4 11.0 1.0 HH22 A:ARG119 4.4 13.4 1.0 HA A:CYS198 4.4 13.2 1.0 CZ A:ARG119 4.5 9.8 1.0 CA A:CYS198 4.5 11.0 1.0 C10 A:YUC303 4.6 12.6 0.6 HA3 A:GLY239 4.6 12.3 1.0 C10 A:YUC303 4.6 14.6 0.4 O38 A:YUC303 4.7 12.4 0.6 O38 A:YUC303 4.7 13.9 0.4 CB A:ASP118 4.8 10.2 1.0 H231 A:YUC303 4.8 23.0 0.6 HB2 A:ASP118 4.8 12.2 1.0 CD2 A:HIS179 4.9 11.1 1.0 C02 A:YUC303 4.9 12.8 0.6 C02 A:YUC303 5.0 14.1 0.4 H231 A:YUC303 5.0 24.6 0.4

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3225 To Be Published.