Zinc in PDB 8pgu: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3394

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3394, PDB code: 8pgu 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)	34.58 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.42, 67.88, 40.26, 90, 93.54, 90
R / Rfree (%)	16.1 / 18.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3394 (pdb code 8pgu). 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 3394, PDB code: 8pgu:
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 3394


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 3394 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.1 occ:0.86 O A:HOH447 1.9 9.0 0.8 NE2 A:HIS179 2.2 14.5 1.0 ND1 A:HIS116 2.3 15.4 1.0 NE2 A:HIS114 2.3 13.8 1.0 O32 A:YUH303 2.8 19.9 1.0 HB2 A:HIS116 2.9 16.7 1.0 CD2 A:HIS179 3.1 14.4 1.0 CE1 A:HIS114 3.2 13.6 1.0 CG A:HIS116 3.2 15.1 1.0 HD2 A:HIS179 3.2 17.3 1.0 CE1 A:HIS116 3.2 16.3 1.0 H201 A:YUH303 3.2 24.0 1.0 CE1 A:HIS179 3.3 15.0 1.0 CD2 A:HIS114 3.3 13.5 1.0 HE1 A:HIS114 3.3 16.3 1.0 HE1 A:HIS116 3.4 19.5 1.0 CB A:HIS116 3.4 13.9 1.0 HD2 A:HIS114 3.5 16.2 1.0 HE1 A:HIS179 3.5 18.0 1.0 ZN A:ZN302 3.5 13.6 0.8 H021 A:YUH303 3.5 23.9 1.0 HB3 A:HIS116 3.6 16.7 1.0 C31 A:YUH303 3.7 20.0 1.0 OD1 A:ASP118 3.9 15.4 1.0 HB2 A:CYS198 4.1 18.5 1.0 HB3 A:CYS198 4.2 18.5 1.0 O19 A:YUH303 4.2 19.9 1.0 N20 A:YUH303 4.2 20.0 1.0 CG A:HIS179 4.3 14.4 1.0 ND1 A:HIS114 4.3 13.4 1.0 NE2 A:HIS116 4.3 16.2 1.0 CD2 A:HIS116 4.3 15.9 1.0 ND1 A:HIS179 4.3 14.9 1.0 CG A:HIS114 4.4 13.1 1.0 N22 A:YUH303 4.4 19.9 1.0 C02 A:YUH303 4.4 20.0 1.0 CB A:CYS198 4.4 15.4 1.0 SG A:CYS198 4.4 14.9 1.0 OD2 A:ASP118 4.5 15.7 1.0 CG A:ASP118 4.6 14.9 1.0 H A:HIS116 4.6 15.2 1.0 O30 A:YUH303 4.7 20.0 1.0 HG2 A:ARG119 4.8 15.3 1.0 HB3 A:SER180 4.8 16.7 1.0 HE A:ARG119 4.8 16.3 1.0 CA A:HIS116 4.9 13.1 1.0 O A:HOH548 4.9 10.2 0.6 C17 A:YUH303 4.9 20.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3394


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 3394 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.6 occ:0.82 O A:HOH447 2.1 9.0 0.8 O19 A:YUH303 2.2 19.9 1.0 NE2 A:HIS240 2.3 13.6 1.0 SG A:CYS198 2.3 14.9 1.0 OD2 A:ASP118 2.5 15.7 1.0 H201 A:YUH303 2.8 24.0 1.0 HB3 A:CYS198 3.1 18.5 1.0 CD2 A:HIS240 3.1 13.6 1.0 C17 A:YUH303 3.1 20.0 1.0 HD2 A:HIS240 3.2 16.3 1.0 HH21 A:ARG119 3.2 18.1 1.0 N20 A:YUH303 3.3 20.0 1.0 CB A:CYS198 3.3 15.4 1.0 CE1 A:HIS240 3.4 13.8 1.0 C16 A:YUH303 3.5 20.0 1.0 CG A:ASP118 3.5 14.9 1.0 ZN A:ZN301 3.5 14.1 0.9 HE A:ARG119 3.6 16.3 1.0 HE1 A:HIS240 3.6 16.5 1.0 HE1 A:HIS114 3.6 16.3 1.0 HB2 A:CYS198 3.7 18.5 1.0 OD1 A:ASP118 3.9 15.4 1.0 NH2 A:ARG119 3.9 15.1 1.0 H021 A:YUH303 3.9 23.9 1.0 NE2 A:HIS179 4.1 14.5 1.0 O A:HOH481 4.2 12.8 0.7 HE1 A:HIS179 4.3 18.0 1.0 NE A:ARG119 4.3 13.6 1.0 O18 A:YUH303 4.3 19.9 1.0 CE1 A:HIS114 4.3 13.6 1.0 CG A:HIS240 4.3 14.0 1.0 CE1 A:HIS179 4.3 15.0 1.0 C21 A:YUH303 4.3 20.0 1.0 ND1 A:HIS240 4.4 13.8 1.0 HH22 A:ARG119 4.4 18.1 1.0 HA A:CYS198 4.5 17.6 1.0 NE2 A:HIS114 4.5 13.8 1.0 CZ A:ARG119 4.5 14.2 1.0 CA A:CYS198 4.5 14.7 1.0 HA3 A:GLY239 4.6 16.6 1.0 O32 A:YUH303 4.6 19.9 1.0 C08 A:YUH303 4.6 20.0 1.0 H101 A:YUH303 4.8 24.0 1.0 CB A:ASP118 4.8 13.9 1.0 CD2 A:HIS179 4.8 14.4 1.0 HB2 A:ASP118 4.8 16.7 1.0 C02 A:YUH303 4.9 20.0 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 3394 To Be Published.