Zinc in PDB 8p95: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2407

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2407, PDB code: 8p95 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)	39.44 / 1.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.52, 68.03, 40.27, 90, 93.55, 90
R / Rfree (%)	12 / 13.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2407 (pdb code 8p95). 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 2407, PDB code: 8p95:
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 2407


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 2407 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.4 occ:0.96 NE2 A:HIS179 2.0 9.9 1.0 NE2 A:HIS114 2.0 9.1 1.0 ND1 A:HIS116 2.0 10.5 1.0 HB2 A:HIS116 2.9 10.4 1.0 CE1 A:HIS116 3.0 11.6 1.0 CE1 A:HIS114 3.0 8.8 1.0 CE1 A:HIS179 3.0 10.2 1.0 CD2 A:HIS179 3.0 9.3 1.0 CG A:HIS116 3.0 9.4 1.0 CD2 A:HIS114 3.1 8.6 1.0 HE1 A:HIS116 3.1 13.9 1.0 HE1 A:HIS114 3.1 10.6 1.0 HE1 A:HIS179 3.2 12.2 1.0 HD2 A:HIS179 3.2 11.2 1.0 H151 A:XA9303 3.2 12.4 1.0 HD2 A:HIS114 3.3 10.3 1.0 CB A:HIS116 3.4 8.7 1.0 ZN A:ZN302 3.5 9.2 0.8 HB3 A:HIS116 3.7 10.4 1.0 H181 A:XA9303 3.7 14.2 1.0 H191 A:XA9303 3.8 16.9 1.0 HB2 A:CYS198 3.8 13.3 1.0 OD1 A:ASP118 3.9 10.1 1.0 O14 A:XA9303 3.9 10.6 1.0 NE2 A:HIS116 4.1 12.5 1.0 ND1 A:HIS114 4.1 8.9 1.0 ND1 A:HIS179 4.1 10.8 1.0 CG A:HIS179 4.1 9.9 1.0 CD2 A:HIS116 4.2 11.8 1.0 N15 A:XA9303 4.2 10.3 1.0 CG A:HIS114 4.2 8.2 1.0 HB3 A:CYS198 4.2 13.3 1.0 CB A:CYS198 4.3 11.1 1.0 SG A:CYS198 4.3 9.4 1.0 H A:HIS116 4.5 10.1 1.0 OD2 A:ASP118 4.5 10.3 1.0 CG A:ASP118 4.6 9.1 1.0 C18 A:XA9303 4.6 11.8 1.0 C19 A:XA9303 4.7 14.1 1.0 HB3 A:SER180 4.7 13.4 1.0 HG2 A:ARG119 4.7 10.2 1.0 C12 A:XA9303 4.7 10.6 1.0 HE A:ARG119 4.8 10.9 1.0 CA A:HIS116 4.8 8.7 1.0 HD1 A:HIS114 4.9 10.7 1.0 HE2 A:HIS116 4.9 15.0 1.0 HG3 A:ARG119 4.9 10.2 1.0 HD1 A:HIS179 4.9 12.9 1.0 O A:HOH533 5.0 12.3 0.9 C11 A:XA9303 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2407


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 2407 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.2 occ:0.85 NE2 A:HIS240 2.1 9.6 1.0 O14 A:XA9303 2.1 10.6 1.0 OD2 A:ASP118 2.3 10.3 1.0 SG A:CYS198 2.3 9.4 1.0 H151 A:XA9303 2.7 12.4 1.0 CD2 A:HIS240 3.0 9.4 1.0 HB3 A:CYS198 3.1 13.3 1.0 C12 A:XA9303 3.1 10.6 1.0 CE1 A:HIS240 3.1 10.2 1.0 HD2 A:HIS240 3.2 11.3 1.0 N15 A:XA9303 3.2 10.3 1.0 HH21 A:ARG119 3.2 12.9 1.0 CB A:CYS198 3.3 11.1 1.0 CG A:ASP118 3.3 9.1 1.0 HE1 A:HIS240 3.4 12.3 1.0 C11 A:XA9303 3.4 10.5 1.0 HE A:ARG119 3.5 10.9 1.0 ZN A:ZN301 3.5 9.4 1.0 HB2 A:CYS198 3.6 13.3 1.0 HE1 A:HIS114 3.6 10.6 1.0 OD1 A:ASP118 3.6 10.1 1.0 NH2 A:ARG119 3.9 10.8 1.0 H181 A:XA9303 4.1 14.2 1.0 NE2 A:HIS179 4.2 9.9 1.0 HE1 A:HIS179 4.2 12.2 1.0 NE A:ARG119 4.2 9.1 1.0 CG A:HIS240 4.2 9.4 1.0 ND1 A:HIS240 4.2 10.4 1.0 O13 A:XA9303 4.3 12.5 1.0 CE1 A:HIS179 4.3 10.2 1.0 CE1 A:HIS114 4.3 8.8 1.0 C16 A:XA9303 4.4 11.0 1.0 O A:HOH517 4.4 10.1 0.7 NE2 A:HIS114 4.4 9.1 1.0 CZ A:ARG119 4.4 9.0 1.0 HH22 A:ARG119 4.5 12.9 1.0 HA A:CYS198 4.5 12.5 1.0 CA A:CYS198 4.5 10.4 1.0 H081 A:XA9303 4.6 16.7 1.0 HA3 A:GLY239 4.6 11.9 1.0 C10 A:XA9303 4.6 11.1 1.0 CB A:ASP118 4.6 9.6 1.0 HB2 A:ASP118 4.7 11.5 1.0 HB3 A:ASP118 4.9 11.5 1.0 HG2 A:ARG119 5.0 10.2 1.0 CD2 A:HIS179 5.0 9.3 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 2407 To Be Published.