Zinc in PDB 8pg5: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2731

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2731, PDB code: 8pg5 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)	28.98 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.515, 67.992, 40.245, 90, 93.25, 90
R / Rfree (%)	11.7 / 14

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2731 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 2731 (pdb code 8pg5). 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 2731, PDB code: 8pg5:
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 2731


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 2731 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.8 occ:0.76 O A:HOH487 1.9 2.9 0.4 NE2 A:HIS179 2.0 11.4 1.0 ND1 A:HIS116 2.0 11.1 1.0 NE2 A:HIS114 2.1 10.8 1.0 HB2 A:HIS116 2.9 11.4 1.0 CD2 A:HIS179 3.0 11.2 1.0 CE1 A:HIS179 3.0 11.8 1.0 CE1 A:HIS116 3.0 11.2 1.0 CE1 A:HIS114 3.0 9.0 1.0 CG A:HIS116 3.1 10.0 1.0 CD2 A:HIS114 3.1 9.8 1.0 H131 A:YR8303 3.1 15.0 0.8 H131 A:YR8303 3.2 17.0 0.2 HE1 A:HIS116 3.2 13.4 1.0 HD2 A:HIS179 3.2 13.5 1.0 HE1 A:HIS179 3.2 14.2 1.0 HE1 A:HIS114 3.2 10.8 1.0 HD2 A:HIS114 3.3 11.8 1.0 CB A:HIS116 3.4 9.5 1.0 H021 A:YR8303 3.5 15.4 0.8 ZN A:ZN302 3.5 9.2 0.7 H021 A:YR8303 3.6 17.4 0.2 HB3 A:HIS116 3.7 11.4 1.0 HB2 A:CYS198 3.8 14.1 1.0 O16 A:YR8303 3.8 12.8 0.8 OD1 A:ASP118 3.8 11.8 1.0 O16 A:YR8303 4.0 14.2 0.2 H041 A:YR8303 4.0 19.0 0.8 H041 A:YR8303 4.0 20.7 0.2 HB3 A:CYS198 4.1 14.1 1.0 ND1 A:HIS179 4.1 12.0 1.0 CG A:HIS179 4.1 11.6 1.0 NE2 A:HIS116 4.1 11.9 1.0 N13 A:YR8303 4.1 12.5 0.8 ND1 A:HIS114 4.1 9.2 1.0 N13 A:YR8303 4.1 14.2 0.2 CD2 A:HIS116 4.2 12.1 1.0 CG A:HIS114 4.2 9.6 1.0 CB A:CYS198 4.2 11.7 1.0 SG A:CYS198 4.3 11.3 1.0 H A:HIS116 4.5 10.3 1.0 OD2 A:ASP118 4.5 12.1 1.0 C02 A:YR8303 4.6 12.8 0.8 CG A:ASP118 4.6 10.7 1.0 C15 A:YR8303 4.6 12.8 0.8 C02 A:YR8303 4.7 14.5 0.2 C15 A:YR8303 4.7 14.4 0.2 HE A:ARG119 4.7 10.5 1.0 HB3 A:SER180 4.7 14.2 1.0 HG2 A:ARG119 4.8 10.0 1.0 CA A:HIS116 4.8 9.0 1.0 H011 A:YR8303 4.9 16.4 0.2 HD1 A:HIS179 4.9 14.4 1.0 C14 A:YR8303 4.9 12.7 0.8 C14 A:YR8303 4.9 14.4 0.2 HE2 A:HIS116 4.9 14.3 1.0 HG3 A:ARG119 4.9 10.0 1.0 HD1 A:HIS114 4.9 11.0 1.0 H011 A:YR8303 5.0 13.7 0.8 C04 A:YR8303 5.0 15.8 0.8

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2731


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 2731 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.2 occ:0.68 O A:HOH487 2.0 2.9 0.4 O16 A:YR8303 2.0 14.2 0.2 O16 A:YR8303 2.1 12.8 0.8 NE2 A:HIS240 2.1 11.5 1.0 OD2 A:ASP118 2.3 12.1 1.0 SG A:CYS198 2.3 11.3 1.0 H131 A:YR8303 2.8 15.0 0.8 H131 A:YR8303 2.9 17.0 0.2 C15 A:YR8303 3.0 14.4 0.2 C15 A:YR8303 3.0 12.8 0.8 CD2 A:HIS240 3.0 11.8 1.0 HB3 A:CYS198 3.1 14.1 1.0 HD2 A:HIS240 3.1 14.2 1.0 CE1 A:HIS240 3.2 12.8 1.0 HH21 A:ARG119 3.2 12.5 1.0 N13 A:YR8303 3.3 14.2 0.2 N13 A:YR8303 3.3 12.5 0.8 CB A:CYS198 3.3 11.7 1.0 CG A:ASP118 3.3 10.7 1.0 C14 A:YR8303 3.3 14.4 0.2 C14 A:YR8303 3.4 12.7 0.8 HE1 A:HIS240 3.4 15.3 1.0 HE A:ARG119 3.5 10.5 1.0 ZN A:ZN301 3.5 9.8 0.8 OD1 A:ASP118 3.6 11.8 1.0 HE1 A:HIS114 3.7 10.8 1.0 HB2 A:CYS198 3.7 14.1 1.0 NH2 A:ARG119 3.9 10.4 1.0 O17 A:YR8303 4.1 15.2 0.2 NE2 A:HIS179 4.2 11.4 1.0 O17 A:YR8303 4.2 13.7 0.8 NE A:ARG119 4.2 8.8 1.0 CG A:HIS240 4.2 11.6 1.0 O A:HOH552 4.2 9.0 0.5 ND1 A:HIS240 4.3 12.2 1.0 HE1 A:HIS179 4.3 14.2 1.0 H201 A:YR8303 4.3 21.6 0.2 H301 A:YR8303 4.3 20.3 0.8 CE1 A:HIS114 4.3 9.0 1.0 C12 A:YR8303 4.4 14.8 0.2 CE1 A:HIS179 4.4 11.8 1.0 H021 A:YR8303 4.4 17.4 0.2 HH22 A:ARG119 4.4 12.5 1.0 C12 A:YR8303 4.4 13.1 0.8 NE2 A:HIS114 4.4 10.8 1.0 H021 A:YR8303 4.4 15.4 0.8 HA A:CYS198 4.5 13.5 1.0 CZ A:ARG119 4.5 9.2 1.0 C18 A:YR8303 4.5 15.3 0.2 C18 A:YR8303 4.5 13.3 0.8 CA A:CYS198 4.5 11.3 1.0 HA3 A:GLY239 4.6 11.5 1.0 CB A:ASP118 4.7 10.0 1.0 H012 A:YR8303 4.7 13.7 0.8 HB2 A:ASP118 4.8 12.0 1.0 H012 A:YR8303 4.8 16.4 0.2 HB3 A:ASP118 4.9 12.0 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 2731 To Be Published.