Zinc in PDB 8pgr: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3270

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3270, PDB code: 8pgr 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)	34.10 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.52, 67.86, 40.24, 90, 93.63, 90
R / Rfree (%)	11.1 / 13.3

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3270 (pdb code 8pgr). 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 3270, PDB code: 8pgr:
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 3270


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 3270 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.0 occ:0.77 O A:HOH514 1.9 4.4 0.5 NE2 A:HIS179 2.0 11.0 1.0 ND1 A:HIS116 2.0 10.7 1.0 NE2 A:HIS114 2.1 10.5 1.0 O26 A:YJZ304 2.9 12.0 1.0 HB2 A:HIS116 3.0 10.9 1.0 CE1 A:HIS179 3.0 10.2 1.0 CE1 A:HIS116 3.0 11.3 1.0 CD2 A:HIS179 3.0 10.4 1.0 CG A:HIS116 3.0 9.4 1.0 CE1 A:HIS114 3.1 8.9 1.0 CD2 A:HIS114 3.2 9.6 1.0 HE1 A:HIS116 3.2 13.5 1.0 HE1 A:HIS179 3.2 12.2 1.0 HE1 A:HIS114 3.2 10.7 1.0 HD2 A:HIS179 3.2 12.4 1.0 H111 A:YJZ304 3.3 14.5 1.0 HD2 A:HIS114 3.4 11.5 1.0 CB A:HIS116 3.4 9.1 1.0 H141 A:YJZ304 3.5 14.2 1.0 ZN A:ZN302 3.6 8.0 0.7 HB3 A:HIS116 3.6 10.9 1.0 C25 A:YJZ304 3.8 12.1 1.0 OD1 A:ASP118 3.8 11.1 1.0 HB2 A:CYS198 4.0 13.8 1.0 O09 A:YJZ304 4.0 11.7 1.0 NE2 A:HIS116 4.1 11.2 1.0 ND1 A:HIS179 4.1 10.7 1.0 CG A:HIS179 4.1 10.7 1.0 CD2 A:HIS116 4.1 11.6 1.0 ND1 A:HIS114 4.2 9.6 1.0 HB3 A:CYS198 4.2 13.8 1.0 N11 A:YJZ304 4.2 12.1 1.0 CG A:HIS114 4.3 9.4 1.0 N16 A:YJZ304 4.4 12.2 1.0 CB A:CYS198 4.4 11.5 1.0 C14 A:YJZ304 4.4 11.8 1.0 SG A:CYS198 4.5 10.8 1.0 OD2 A:ASP118 4.5 11.6 1.0 H A:HIS116 4.6 9.9 1.0 CG A:ASP118 4.6 10.2 1.0 O24 A:YJZ304 4.7 13.3 1.0 HB3 A:SER180 4.7 12.5 1.0 HG2 A:ARG119 4.8 10.3 1.0 C08 A:YJZ304 4.8 11.6 1.0 HE A:ARG119 4.8 10.9 1.0 CA A:HIS116 4.9 8.7 1.0 HE2 A:HIS116 4.9 13.4 1.0 HD1 A:HIS179 4.9 12.8 1.0 O A:HOH564 4.9 11.4 0.8 HD1 A:HIS114 5.0 11.5 1.0 H153 A:YJZ304 5.0 14.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3270


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 3270 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.0 occ:0.65 O A:HOH514 2.0 4.4 0.5 NE2 A:HIS240 2.1 10.8 1.0 O09 A:YJZ304 2.1 11.7 1.0 SG A:CYS198 2.3 10.8 1.0 OD2 A:ASP118 2.4 11.6 1.0 H111 A:YJZ304 2.6 14.5 1.0 CD2 A:HIS240 3.0 11.3 1.0 C08 A:YJZ304 3.1 11.6 1.0 HB3 A:CYS198 3.1 13.8 1.0 HD2 A:HIS240 3.1 13.6 1.0 N11 A:YJZ304 3.2 12.1 1.0 CE1 A:HIS240 3.2 11.2 1.0 HH21 A:ARG119 3.2 12.8 1.0 CB A:CYS198 3.3 11.5 1.0 C07 A:YJZ304 3.4 11.7 1.0 HE1 A:HIS240 3.4 13.5 1.0 CG A:ASP118 3.4 10.2 1.0 HE1 A:HIS114 3.5 10.7 1.0 HE A:ARG119 3.6 10.9 1.0 ZN A:ZN301 3.6 9.0 0.8 HB2 A:CYS198 3.7 13.8 1.0 OD1 A:ASP118 3.7 11.1 1.0 NH2 A:ARG119 3.9 10.7 1.0 H141 A:YJZ304 3.9 14.2 1.0 NE2 A:HIS179 4.1 11.0 1.0 CG A:HIS240 4.2 11.0 1.0 CE1 A:HIS114 4.2 8.9 1.0 NE A:ARG119 4.2 9.1 1.0 O10 A:YJZ304 4.2 13.3 1.0 HE1 A:HIS179 4.2 12.2 1.0 ND1 A:HIS240 4.2 11.4 1.0 CE1 A:HIS179 4.3 10.2 1.0 C12 A:YJZ304 4.3 12.3 1.0 O A:HOH533 4.3 9.0 0.6 HH22 A:ARG119 4.4 12.8 1.0 NE2 A:HIS114 4.4 10.5 1.0 HA A:CYS198 4.4 12.6 1.0 CZ A:ARG119 4.5 9.0 1.0 CA A:CYS198 4.5 10.5 1.0 C06 A:YJZ304 4.6 11.9 1.0 HA3 A:GLY239 4.6 12.1 1.0 O26 A:YJZ304 4.7 12.0 1.0 H311 A:YJZ304 4.7 17.6 1.0 CB A:ASP118 4.8 9.0 1.0 HB2 A:ASP118 4.8 10.8 1.0 CD2 A:HIS179 4.9 10.4 1.0 C14 A:YJZ304 4.9 11.8 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 3270 To Be Published.