Zinc in PDB 8pgs: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3380

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3380, PDB code: 8pgs 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)	29.10 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.47, 67.95, 40.26, 90, 93.78, 90
R / Rfree (%)	12.2 / 14.2

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3380 (pdb code 8pgs). 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 3380, PDB code: 8pgs:
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 3380


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 3380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.9 occ:0.88 O A:HOH496 1.9 6.1 0.5 NE2 A:HIS179 2.0 12.1 1.0 ND1 A:HIS116 2.1 11.9 1.0 NE2 A:HIS114 2.1 12.1 1.0 O35 A:YRC303 2.9 14.4 1.0 HB2 A:HIS116 3.0 12.2 1.0 CE1 A:HIS116 3.0 11.9 1.0 CE1 A:HIS179 3.0 11.8 1.0 CD2 A:HIS179 3.0 11.9 1.0 CE1 A:HIS114 3.0 10.9 1.0 CG A:HIS116 3.1 10.9 1.0 HE1 A:HIS116 3.1 14.2 1.0 CD2 A:HIS114 3.1 11.3 1.0 HE1 A:HIS179 3.2 14.2 1.0 HE1 A:HIS114 3.2 13.1 1.0 HD2 A:HIS179 3.2 14.3 1.0 H051 A:YRC303 3.3 16.5 1.0 HD2 A:HIS114 3.3 13.5 1.0 CB A:HIS116 3.4 10.1 1.0 H021 A:YRC303 3.4 17.0 1.0 ZN A:ZN302 3.6 11.2 0.8 HB3 A:HIS116 3.6 12.2 1.0 C34 A:YRC303 3.8 14.9 1.0 OD1 A:ASP118 3.8 12.8 1.0 HB2 A:CYS198 4.0 16.3 1.0 O09 A:YRC303 4.0 13.6 1.0 ND1 A:HIS179 4.1 12.7 1.0 NE2 A:HIS116 4.1 12.8 1.0 CG A:HIS179 4.1 12.6 1.0 CD2 A:HIS116 4.2 12.5 1.0 ND1 A:HIS114 4.2 11.5 1.0 HB3 A:CYS198 4.2 16.3 1.0 N05 A:YRC303 4.2 13.8 1.0 CG A:HIS114 4.2 10.9 1.0 CB A:CYS198 4.4 13.6 1.0 N25 A:YRC303 4.4 14.8 1.0 C02 A:YRC303 4.4 14.2 1.0 SG A:CYS198 4.5 12.0 1.0 OD2 A:ASP118 4.5 12.3 1.0 CG A:ASP118 4.6 11.3 1.0 H A:HIS116 4.6 12.0 1.0 O33 A:YRC303 4.7 15.0 1.0 HB3 A:SER180 4.7 14.6 1.0 C07 A:YRC303 4.8 13.8 1.0 HG2 A:ARG119 4.8 12.2 1.0 HE A:ARG119 4.8 13.3 1.0 CA A:HIS116 4.9 10.1 1.0 HE2 A:HIS116 4.9 15.4 1.0 HD1 A:HIS179 4.9 15.3 1.0 O A:HOH541 4.9 13.3 0.8 H012 A:YRC303 4.9 16.9 1.0 HD1 A:HIS114 4.9 13.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3380


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 3380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.2 occ:0.77 O A:HOH496 2.1 6.1 0.5 O09 A:YRC303 2.1 13.6 1.0 NE2 A:HIS240 2.2 12.1 1.0 SG A:CYS198 2.3 12.0 1.0 OD2 A:ASP118 2.4 12.3 1.0 H051 A:YRC303 2.7 16.5 1.0 CD2 A:HIS240 3.0 13.0 1.0 HB3 A:CYS198 3.0 16.3 1.0 C07 A:YRC303 3.1 13.8 1.0 HD2 A:HIS240 3.1 15.6 1.0 N05 A:YRC303 3.2 13.8 1.0 CE1 A:HIS240 3.2 13.1 1.0 CB A:CYS198 3.2 13.6 1.0 HH21 A:ARG119 3.3 15.6 1.0 C06 A:YRC303 3.4 13.8 1.0 CG A:ASP118 3.4 11.3 1.0 HE1 A:HIS240 3.5 15.8 1.0 HE1 A:HIS114 3.5 13.1 1.0 HE A:ARG119 3.6 13.3 1.0 ZN A:ZN301 3.6 11.9 0.9 HB2 A:CYS198 3.7 16.3 1.0 OD1 A:ASP118 3.7 12.8 1.0 H021 A:YRC303 3.8 17.0 1.0 NH2 A:ARG119 3.9 13.0 1.0 NE2 A:HIS179 4.2 12.1 1.0 CE1 A:HIS114 4.2 10.9 1.0 CG A:HIS240 4.2 11.9 1.0 NE A:ARG119 4.2 11.1 1.0 HE1 A:HIS179 4.2 14.2 1.0 O08 A:YRC303 4.2 15.7 1.0 ND1 A:HIS240 4.3 13.1 1.0 CE1 A:HIS179 4.3 11.8 1.0 C04 A:YRC303 4.3 14.4 1.0 O A:HOH493 4.4 12.0 0.6 HA A:CYS198 4.4 14.5 1.0 NE2 A:HIS114 4.4 12.1 1.0 HH22 A:ARG119 4.4 15.6 1.0 CZ A:ARG119 4.5 11.4 1.0 CA A:CYS198 4.5 12.1 1.0 H121 A:YRC303 4.6 23.3 1.0 C10 A:YRC303 4.6 14.6 1.0 HA3 A:GLY239 4.6 13.6 1.0 O35 A:YRC303 4.6 14.4 1.0 CB A:ASP118 4.7 10.6 1.0 HB2 A:ASP118 4.8 12.7 1.0 C02 A:YRC303 4.9 14.2 1.0 CD2 A:HIS179 4.9 11.9 1.0 HB3 A:ASP118 5.0 12.7 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 3380 To Be Published.