Zinc in PDB 8pg4: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2730

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2730, PDB code: 8pg4 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)	39.52 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.59, 68.1, 40.36, 90, 93.32, 90
R / Rfree (%)	14.3 / 16.3

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2730 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 2730 (pdb code 8pg4). 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 2730, PDB code: 8pg4:
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 2730


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 2730 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.2 occ:0.83 O A:HOH440 1.9 10.4 0.7 NE2 A:HIS179 2.1 14.5 1.0 ND1 A:HIS116 2.1 14.1 1.0 NE2 A:HIS114 2.1 13.9 1.0 HB2 A:HIS116 2.9 14.9 1.0 CE1 A:HIS116 3.0 14.4 1.0 CD2 A:HIS179 3.0 14.3 1.0 CE1 A:HIS179 3.0 15.1 1.0 CE1 A:HIS114 3.1 12.4 1.0 CG A:HIS116 3.1 13.1 1.0 CD2 A:HIS114 3.1 13.1 1.0 HE1 A:HIS116 3.1 17.3 1.0 HD2 A:HIS179 3.2 17.1 1.0 H121 A:YTO303 3.2 24.0 0.5 HE1 A:HIS114 3.2 14.9 1.0 H121 A:YTO303 3.2 24.0 0.5 HE1 A:HIS179 3.2 18.1 1.0 HD2 A:HIS114 3.3 15.7 1.0 CB A:HIS116 3.4 12.5 1.0 ZN A:ZN302 3.5 13.0 0.8 O03 A:YTO303 3.6 20.0 0.5 H041 A:YTO303 3.6 24.0 0.5 HB3 A:HIS116 3.7 14.9 1.0 O15 A:YTO303 3.8 20.0 0.5 OD1 A:ASP118 3.8 14.8 1.0 HB2 A:CYS198 3.8 17.5 1.0 O15 A:YTO303 3.9 20.0 0.5 NE2 A:HIS116 4.1 15.2 1.0 ND1 A:HIS179 4.1 15.1 1.0 C04 A:YTO303 4.1 20.0 0.5 CG A:HIS179 4.1 14.7 1.0 ND1 A:HIS114 4.2 12.3 1.0 HB3 A:CYS198 4.2 17.5 1.0 CD2 A:HIS116 4.2 15.3 1.0 N12 A:YTO303 4.2 20.0 0.5 N12 A:YTO303 4.2 20.0 0.5 H041 A:YTO303 4.2 24.0 0.5 CG A:HIS114 4.2 12.7 1.0 CB A:CYS198 4.3 14.6 1.0 SG A:CYS198 4.4 14.0 1.0 H011 A:YTO303 4.4 24.0 0.5 O03 A:YTO303 4.5 20.0 0.5 H A:HIS116 4.5 14.0 1.0 OD2 A:ASP118 4.6 15.1 1.0 C14 A:YTO303 4.6 20.0 0.5 CG A:ASP118 4.7 13.7 1.0 C14 A:YTO303 4.7 20.0 0.5 HE A:ARG119 4.7 14.3 1.0 HB3 A:SER180 4.7 18.1 1.0 HG2 A:ARG119 4.8 13.9 1.0 C02 A:YTO303 4.8 20.0 0.5 CA A:HIS116 4.9 12.0 1.0 O A:HOH531 4.9 14.5 0.7 HE2 A:HIS116 4.9 18.2 1.0 C04 A:YTO303 4.9 20.0 0.5 C13 A:YTO303 4.9 20.0 0.5 C13 A:YTO303 4.9 20.0 0.5 HD1 A:HIS179 4.9 18.1 1.0 HD1 A:HIS114 4.9 14.8 1.0 HG3 A:ARG119 4.9 13.9 1.0 C05 A:YTO303 4.9 20.0 0.5 H013 A:YTO303 5.0 24.0 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2730


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 2730 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.0 occ:0.78 O A:HOH440 2.1 10.4 0.7 O15 A:YTO303 2.1 20.0 0.5 O15 A:YTO303 2.1 20.0 0.5 NE2 A:HIS240 2.2 14.7 1.0 SG A:CYS198 2.3 14.0 1.0 OD2 A:ASP118 2.4 15.1 1.0 H121 A:YTO303 2.8 24.0 0.5 H121 A:YTO303 3.0 24.0 0.5 C14 A:YTO303 3.0 20.0 0.5 C14 A:YTO303 3.0 20.0 0.5 CD2 A:HIS240 3.1 14.8 1.0 HB3 A:CYS198 3.1 17.5 1.0 HH21 A:ARG119 3.1 16.0 1.0 CE1 A:HIS240 3.2 15.8 1.0 HD2 A:HIS240 3.2 17.8 1.0 N12 A:YTO303 3.3 20.0 0.5 CB A:CYS198 3.3 14.6 1.0 N12 A:YTO303 3.3 20.0 0.5 C13 A:YTO303 3.4 20.0 0.5 HE1 A:HIS240 3.4 19.0 1.0 CG A:ASP118 3.4 13.7 1.0 C13 A:YTO303 3.4 20.0 0.5 HE A:ARG119 3.5 14.3 1.0 ZN A:ZN301 3.5 13.2 0.8 HE1 A:HIS114 3.6 14.9 1.0 OD1 A:ASP118 3.7 14.8 1.0 HB2 A:CYS198 3.7 17.5 1.0 NH2 A:ARG119 3.8 13.4 1.0 NE A:ARG119 4.2 11.9 1.0 O16 A:YTO303 4.2 20.0 0.5 NE2 A:HIS179 4.2 14.5 1.0 O16 A:YTO303 4.2 20.0 0.5 O A:HOH533 4.2 6.8 0.4 HE1 A:HIS179 4.2 18.1 1.0 CG A:HIS240 4.3 14.8 1.0 CE1 A:HIS114 4.3 12.4 1.0 ND1 A:HIS240 4.3 15.4 1.0 CE1 A:HIS179 4.3 15.1 1.0 H191 A:YTO303 4.4 24.0 0.5 HH22 A:ARG119 4.4 16.0 1.0 C11 A:YTO303 4.4 20.0 0.5 NE2 A:HIS114 4.4 13.9 1.0 H291 A:YTO303 4.4 24.0 0.5 CZ A:ARG119 4.4 12.5 1.0 C11 A:YTO303 4.4 20.0 0.5 HA A:CYS198 4.5 17.3 1.0 H013 A:YTO303 4.5 24.0 0.5 C17 A:YTO303 4.6 20.0 0.5 C17 A:YTO303 4.6 20.0 0.5 CA A:CYS198 4.6 14.4 1.0 HA3 A:GLY239 4.6 15.4 1.0 CB A:ASP118 4.7 12.9 1.0 HG A:SER69 4.7 13.7 0.3 H011 A:YTO303 4.8 24.0 0.5 O03 A:YTO303 4.8 20.0 0.5 HB2 A:ASP118 4.8 15.5 1.0 HB3 A:ASP118 5.0 15.5 1.0 CD2 A:HIS179 5.0 14.3 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 2730 To Be Published.