Zinc in PDB 8pgw: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3460

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3460, PDB code: 8pgw 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)	40.26 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.43, 68.04, 40.34, 90, 93.53, 90
R / Rfree (%)	15.1 / 17.8

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3460 (pdb code 8pgw). 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 3460, PDB code: 8pgw:
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 3460


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 3460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.4 occ:0.74 O A:HOH459 1.9 3.8 0.5 NE2 A:HIS179 2.1 13.4 1.0 ND1 A:HIS116 2.1 14.9 1.0 NE2 A:HIS114 2.2 13.1 1.0 O26 A:YRK303 2.8 20.0 1.0 HB2 A:HIS116 3.0 15.6 1.0 CD2 A:HIS179 3.0 13.6 1.0 CE1 A:HIS116 3.1 16.3 1.0 CE1 A:HIS179 3.1 15.0 1.0 CE1 A:HIS114 3.1 13.0 1.0 CG A:HIS116 3.1 14.3 1.0 CD2 A:HIS114 3.2 12.8 1.0 HE1 A:HIS116 3.2 19.5 1.0 HD2 A:HIS179 3.2 16.4 1.0 H111 A:YRK303 3.2 24.1 1.0 HE1 A:HIS179 3.3 18.0 1.0 HE1 A:HIS114 3.3 15.6 1.0 HD2 A:HIS114 3.3 15.4 1.0 CB A:HIS116 3.5 13.0 1.0 H141 A:YRK303 3.5 24.1 1.0 ZN A:ZN302 3.5 8.4 0.5 C25 A:YRK303 3.7 20.1 1.0 HB3 A:HIS116 3.7 15.6 1.0 OD1 A:ASP118 3.9 15.0 1.0 HB2 A:CYS198 4.0 18.6 1.0 O10 A:YRK303 4.1 20.1 1.0 ND1 A:HIS179 4.2 14.6 1.0 CG A:HIS179 4.2 13.8 1.0 NE2 A:HIS116 4.2 15.6 1.0 HB3 A:CYS198 4.2 18.6 1.0 N11 A:YRK303 4.2 20.1 1.0 ND1 A:HIS114 4.2 12.8 1.0 CD2 A:HIS116 4.2 15.2 1.0 CG A:HIS114 4.3 12.3 1.0 N16 A:YRK303 4.4 20.1 1.0 CB A:CYS198 4.4 15.5 1.0 C14 A:YRK303 4.4 20.1 1.0 SG A:CYS198 4.5 13.4 1.0 OD2 A:ASP118 4.5 15.2 1.0 H A:HIS116 4.6 13.8 1.0 CG A:ASP118 4.6 14.4 1.0 O24 A:YRK303 4.6 20.1 1.0 HB3 A:SER180 4.7 15.9 1.0 HE A:ARG119 4.8 14.5 1.0 HG2 A:ARG119 4.8 14.3 1.0 C08 A:YRK303 4.8 20.1 1.0 O A:HOH538 4.9 11.8 0.7 CA A:HIS116 4.9 12.4 1.0 HD1 A:HIS179 4.9 17.5 1.0 HE2 A:HIS116 4.9 18.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3460


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 3460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.4 occ:0.53 O A:HOH459 2.1 3.8 0.5 O10 A:YRK303 2.1 20.1 1.0 NE2 A:HIS240 2.2 12.5 1.0 SG A:CYS198 2.3 13.4 1.0 OD2 A:ASP118 2.5 15.2 1.0 H111 A:YRK303 2.8 24.1 1.0 HB3 A:CYS198 3.0 18.6 1.0 CD2 A:HIS240 3.1 12.4 1.0 C08 A:YRK303 3.1 20.1 1.0 HD2 A:HIS240 3.2 14.9 1.0 HH21 A:ARG119 3.2 18.2 1.0 CB A:CYS198 3.2 15.5 1.0 N11 A:YRK303 3.2 20.1 1.0 CE1 A:HIS240 3.3 12.9 1.0 C07 A:YRK303 3.4 20.1 1.0 HE1 A:HIS240 3.5 15.4 1.0 CG A:ASP118 3.5 14.4 1.0 HE1 A:HIS114 3.5 15.6 1.0 ZN A:ZN301 3.5 10.4 0.7 HE A:ARG119 3.6 14.5 1.0 HB2 A:CYS198 3.7 18.6 1.0 OD1 A:ASP118 3.8 15.0 1.0 NH2 A:ARG119 3.9 15.2 1.0 H141 A:YRK303 4.0 24.1 1.0 NE2 A:HIS179 4.2 13.4 1.0 CE1 A:HIS114 4.2 13.0 1.0 O09 A:YRK303 4.2 20.1 1.0 NE A:ARG119 4.2 12.1 1.0 HE1 A:HIS179 4.3 18.0 1.0 CG A:HIS240 4.3 12.9 1.0 C12 A:YRK303 4.3 20.1 1.0 ND1 A:HIS240 4.3 12.9 1.0 O A:HOH540 4.3 7.4 0.5 CE1 A:HIS179 4.3 15.0 1.0 HH22 A:ARG119 4.4 18.2 1.0 NE2 A:HIS114 4.4 13.1 1.0 HA A:CYS198 4.4 16.9 1.0 CZ A:ARG119 4.5 13.6 1.0 CA A:CYS198 4.5 14.1 1.0 HA3 A:GLY239 4.6 16.4 1.0 O26 A:YRK303 4.6 20.0 1.0 C06 A:YRK303 4.7 20.1 1.0 CB A:ASP118 4.8 13.3 1.0 CD2 A:HIS179 4.9 13.6 1.0 H311 A:YRK303 4.9 24.1 1.0 HB2 A:ASP118 4.9 16.0 1.0 C14 A:YRK303 4.9 20.1 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 3460 To Be Published.