Zinc in PDB 8pgb: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2850

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2850, PDB code: 8pgb 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)	34.66 / 1.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.55, 68.126, 40.335, 90, 93.62, 90
R / Rfree (%)	12.7 / 15.5

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2850 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2850 (pdb code 8pgb). 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 2850, PDB code: 8pgb:
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 2850


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 2850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.0 occ:0.73 O A:HOH492 2.0 11.7 0.8 NE2 A:HIS179 2.0 15.4 1.0 ND1 A:HIS116 2.1 15.3 1.0 NE2 A:HIS114 2.1 14.6 1.0 HB2 A:HIS116 2.9 15.4 1.0 CE1 A:HIS179 3.0 16.0 1.0 CD2 A:HIS179 3.0 15.0 1.0 CE1 A:HIS116 3.0 16.1 1.0 CE1 A:HIS114 3.1 12.9 1.0 CG A:HIS116 3.1 14.0 1.0 CD2 A:HIS114 3.1 14.0 1.0 HE1 A:HIS116 3.2 19.4 1.0 HE1 A:HIS179 3.2 19.2 1.0 HD2 A:HIS179 3.2 18.0 1.0 H131 A:YSK303 3.2 19.9 0.5 HE1 A:HIS114 3.2 15.5 1.0 H131 A:YSK303 3.2 20.2 0.5 HD2 A:HIS114 3.3 16.8 1.0 CB A:HIS116 3.4 12.8 1.0 H051 A:YSK303 3.5 22.0 0.5 ZN A:ZN302 3.5 14.7 0.8 H051 A:YSK303 3.7 21.5 0.5 HB3 A:HIS116 3.7 15.4 1.0 N31 A:YSK303 3.7 21.6 0.5 O17 A:YSK303 3.9 15.1 0.5 OD1 A:ASP118 3.9 15.6 1.0 N31 A:YSK303 3.9 20.5 0.5 HB2 A:CYS198 4.0 19.1 1.0 ND1 A:HIS179 4.1 16.1 1.0 CG A:HIS179 4.1 15.3 1.0 NE2 A:HIS116 4.1 16.5 1.0 ND1 A:HIS114 4.2 13.4 1.0 CD2 A:HIS116 4.2 15.7 1.0 HB3 A:CYS198 4.2 19.1 1.0 N13 A:YSK303 4.2 16.6 0.5 O17 A:YSK303 4.2 18.0 0.5 CG A:HIS114 4.2 13.3 1.0 N13 A:YSK303 4.2 16.8 0.5 C04 A:YSK303 4.3 19.8 0.5 C05 A:YSK303 4.4 18.3 0.5 CB A:CYS198 4.4 15.9 1.0 H A:HIS116 4.5 13.8 1.0 SG A:CYS198 4.5 15.4 1.0 OD2 A:ASP118 4.5 16.7 1.0 C04 A:YSK303 4.5 17.5 0.5 O32 A:YSK303 4.6 23.0 0.5 C05 A:YSK303 4.6 17.9 0.5 CG A:ASP118 4.7 14.9 1.0 C15 A:YSK303 4.7 15.0 0.5 HB3 A:SER180 4.7 19.4 1.0 O32 A:YSK303 4.7 18.6 0.5 HG2 A:ARG119 4.8 14.9 1.0 CA A:HIS116 4.8 12.2 1.0 HD1 A:HIS179 4.9 19.3 1.0 O A:HOH533 4.9 17.7 0.9 HE A:ARG119 4.9 16.6 1.0 HE2 A:HIS116 4.9 19.8 1.0 HD1 A:HIS114 4.9 16.1 1.0 C14 A:YSK303 4.9 16.5 0.5 C15 A:YSK303 5.0 17.4 0.5 HG3 A:ARG119 5.0 14.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2850


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 2850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.7 occ:0.78 O A:HOH492 2.0 11.7 0.8 O17 A:YSK303 2.1 15.1 0.5 NE2 A:HIS240 2.2 15.6 1.0 O17 A:YSK303 2.2 18.0 0.5 SG A:CYS198 2.3 15.4 1.0 OD2 A:ASP118 2.4 16.7 1.0 H131 A:YSK303 2.6 20.2 0.5 H131 A:YSK303 2.8 19.9 0.5 C15 A:YSK303 3.0 15.0 0.5 HB3 A:CYS198 3.0 19.1 1.0 CD2 A:HIS240 3.1 15.3 1.0 C15 A:YSK303 3.1 17.4 0.5 HD2 A:HIS240 3.1 18.4 1.0 N13 A:YSK303 3.2 16.8 0.5 CE1 A:HIS240 3.2 16.0 1.0 N13 A:YSK303 3.3 16.6 0.5 CB A:CYS198 3.3 15.9 1.0 HH21 A:ARG119 3.3 18.4 1.0 C14 A:YSK303 3.4 16.5 0.5 C14 A:YSK303 3.4 16.5 0.5 CG A:ASP118 3.4 14.9 1.0 HE1 A:HIS240 3.4 19.1 1.0 HE1 A:HIS114 3.5 15.5 1.0 HE A:ARG119 3.5 16.6 1.0 ZN A:ZN301 3.5 14.0 0.7 HB2 A:CYS198 3.7 19.1 1.0 OD1 A:ASP118 3.7 15.6 1.0 H051 A:YSK303 3.8 22.0 0.5 NH2 A:ARG119 3.9 15.4 1.0 H051 A:YSK303 4.0 21.5 0.5 NE2 A:HIS179 4.2 15.4 1.0 NE A:ARG119 4.2 13.9 1.0 O16 A:YSK303 4.2 14.7 0.5 CE1 A:HIS114 4.2 12.9 1.0 CG A:HIS240 4.2 16.1 1.0 ND1 A:HIS240 4.3 15.0 1.0 O A:HOH467 4.3 13.6 0.5 C12 A:YSK303 4.3 16.7 0.5 O16 A:YSK303 4.3 18.2 0.5 HE1 A:HIS179 4.3 19.2 1.0 C12 A:YSK303 4.4 16.8 0.5 CE1 A:HIS179 4.4 16.0 1.0 NE2 A:HIS114 4.4 14.6 1.0 HA A:CYS198 4.4 17.8 1.0 CZ A:ARG119 4.4 13.7 1.0 H301 A:YSK303 4.5 24.6 0.5 HH22 A:ARG119 4.5 18.4 1.0 CA A:CYS198 4.5 14.8 1.0 C18 A:YSK303 4.6 17.3 0.5 H201 A:YSK303 4.6 22.0 0.5 C18 A:YSK303 4.6 16.6 0.5 HA3 A:GLY239 4.7 17.0 1.0 CB A:ASP118 4.7 14.5 1.0 HB2 A:ASP118 4.8 17.4 1.0 C05 A:YSK303 4.8 18.3 0.5 CD2 A:HIS179 4.9 15.0 1.0 HB3 A:ASP118 5.0 17.4 1.0 HG2 A:ARG119 5.0 14.9 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 2850 To Be Published.