Zinc in PDB 8pgt: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3393

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3393, PDB code: 8pgt 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)	40.21 / 1.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.49, 68.01, 40.3, 90, 93.75, 90
R / Rfree (%)	11.9 / 13.7

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3393 (pdb code 8pgt). 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 3393, PDB code: 8pgt:
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 3393


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 3393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.2 occ:0.89 O A:HOH475 1.9 6.2 0.6 NE2 A:HIS179 2.0 11.0 1.0 ND1 A:HIS116 2.0 11.1 1.0 NE2 A:HIS114 2.1 10.7 1.0 O32 A:YKZ303 2.9 12.9 0.6 O32 A:YKZ303 2.9 13.1 0.4 HB2 A:HIS116 2.9 11.8 1.0 CE1 A:HIS116 3.0 11.4 1.0 CE1 A:HIS179 3.0 11.1 1.0 CD2 A:HIS179 3.0 10.4 1.0 CE1 A:HIS114 3.0 9.8 1.0 CG A:HIS116 3.1 9.9 1.0 CD2 A:HIS114 3.1 9.9 1.0 HE1 A:HIS116 3.1 13.7 1.0 HE1 A:HIS179 3.2 13.3 1.0 HE1 A:HIS114 3.2 11.8 1.0 H201 A:YKZ303 3.2 15.8 0.4 H201 A:YKZ303 3.2 14.9 0.6 HD2 A:HIS179 3.2 12.5 1.0 HD2 A:HIS114 3.3 11.9 1.0 CB A:HIS116 3.4 9.8 1.0 H021 A:YKZ303 3.5 16.3 0.4 H021 A:YKZ303 3.5 16.0 0.6 ZN A:ZN302 3.6 9.5 0.7 HB3 A:HIS116 3.6 11.8 1.0 C31 A:YKZ303 3.7 13.3 0.6 C31 A:YKZ303 3.8 13.8 0.4 OD1 A:ASP118 3.9 12.1 1.0 O18 A:YKZ303 4.0 13.3 0.6 HB2 A:CYS198 4.0 14.4 1.0 NE2 A:HIS116 4.1 11.9 1.0 O18 A:YKZ303 4.1 13.9 0.4 ND1 A:HIS179 4.1 11.6 1.0 CG A:HIS179 4.1 11.5 1.0 CD2 A:HIS116 4.1 11.8 1.0 ND1 A:HIS114 4.2 9.8 1.0 CG A:HIS114 4.2 9.8 1.0 N20 A:YKZ303 4.2 13.2 0.4 N20 A:YKZ303 4.2 12.5 0.6 HB3 A:CYS198 4.3 14.4 1.0 N22 A:YKZ303 4.4 13.5 0.6 C02 A:YKZ303 4.4 13.6 0.4 C02 A:YKZ303 4.4 13.3 0.6 N22 A:YKZ303 4.4 14.1 0.4 CB A:CYS198 4.4 12.0 1.0 SG A:CYS198 4.5 11.3 1.0 OD2 A:ASP118 4.5 12.0 1.0 H A:HIS116 4.6 11.5 1.0 CG A:ASP118 4.6 10.9 1.0 O30 A:YKZ303 4.6 13.6 0.6 HB3 A:SER180 4.7 14.2 1.0 O30 A:YKZ303 4.7 14.8 0.4 HG2 A:ARG119 4.8 11.3 1.0 C17 A:YKZ303 4.8 13.5 0.4 CA A:HIS116 4.8 9.8 1.0 HE A:ARG119 4.8 12.0 1.0 HE2 A:HIS116 4.9 14.3 1.0 C17 A:YKZ303 4.9 12.9 0.6 HD1 A:HIS179 4.9 13.8 1.0 O A:HOH541 4.9 11.2 0.7 HD1 A:HIS114 4.9 11.8 1.0 H012 A:YKZ303 4.9 15.9 0.4 H012 A:YKZ303 5.0 15.5 0.6

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3393


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 3393 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.5 occ:0.68 O A:HOH475 2.0 6.2 0.6 NE2 A:HIS240 2.1 11.4 1.0 O18 A:YKZ303 2.1 13.9 0.4 O18 A:YKZ303 2.1 13.3 0.6 SG A:CYS198 2.3 11.3 1.0 OD2 A:ASP118 2.4 12.0 1.0 H201 A:YKZ303 2.6 14.9 0.6 H201 A:YKZ303 2.7 15.8 0.4 CD2 A:HIS240 3.0 11.8 1.0 C17 A:YKZ303 3.1 12.9 0.6 HB3 A:CYS198 3.1 14.4 1.0 C17 A:YKZ303 3.1 13.5 0.4 HD2 A:HIS240 3.1 14.2 1.0 N20 A:YKZ303 3.2 12.5 0.6 CE1 A:HIS240 3.2 12.1 1.0 N20 A:YKZ303 3.2 13.2 0.4 HH21 A:ARG119 3.2 14.2 1.0 CB A:CYS198 3.3 12.0 1.0 C16 A:YKZ303 3.4 12.4 0.6 CG A:ASP118 3.4 10.9 1.0 HE1 A:HIS240 3.4 14.5 1.0 C16 A:YKZ303 3.4 13.2 0.4 HE1 A:HIS114 3.5 11.8 1.0 HE A:ARG119 3.5 12.0 1.0 ZN A:ZN301 3.6 10.2 0.9 HB2 A:CYS198 3.7 14.4 1.0 OD1 A:ASP118 3.7 12.1 1.0 H021 A:YKZ303 3.9 16.0 0.6 NH2 A:ARG119 3.9 11.8 1.0 H021 A:YKZ303 3.9 16.3 0.4 NE2 A:HIS179 4.1 11.0 1.0 CG A:HIS240 4.2 11.6 1.0 NE A:ARG119 4.2 10.0 1.0 CE1 A:HIS114 4.2 9.8 1.0 O19 A:YKZ303 4.2 14.8 0.6 HE1 A:HIS179 4.2 13.3 1.0 ND1 A:HIS240 4.2 12.5 1.0 O19 A:YKZ303 4.3 15.0 0.4 C21 A:YKZ303 4.3 13.1 0.6 CE1 A:HIS179 4.3 11.1 1.0 C21 A:YKZ303 4.3 13.6 0.4 O A:HOH489 4.4 9.1 0.4 NE2 A:HIS114 4.4 10.7 1.0 HH22 A:ARG119 4.4 14.2 1.0 HA A:CYS198 4.4 13.4 1.0 CZ A:ARG119 4.5 10.5 1.0 CA A:CYS198 4.5 11.2 1.0 H151 A:YKZ303 4.6 22.7 0.4 HA3 A:GLY239 4.6 12.9 1.0 C08 A:YKZ303 4.6 12.7 0.6 O32 A:YKZ303 4.6 12.9 0.6 C08 A:YKZ303 4.6 13.8 0.4 H101 A:YKZ303 4.7 20.7 0.6 O32 A:YKZ303 4.7 13.1 0.4 CB A:ASP118 4.7 10.2 1.0 HB2 A:ASP118 4.8 12.2 1.0 C02 A:YKZ303 4.9 13.3 0.6 CD2 A:HIS179 4.9 10.4 1.0 C02 A:YKZ303 4.9 13.6 0.4 HB3 A:ASP118 5.0 12.2 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 3393 To Be Published.