Zinc in PDB 8pge: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2936

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2936, PDB code: 8pge 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)	40.27 / 1.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.48, 68.08, 40.35, 90, 93.53, 90
R / Rfree (%)	13 / 15.8

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2936 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 2936 (pdb code 8pge). 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 2936, PDB code: 8pge:
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 2936


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 2936 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.2 occ:0.96 O A:HOH481 2.0 16.6 1.0 O24 A:YU8303 2.1 14.5 0.2 O24 A:YU8303 2.2 11.9 0.8 NE2 A:HIS240 2.2 11.8 1.0 SG A:CYS198 2.3 11.4 1.0 OD2 A:ASP118 2.4 11.6 1.0 H251 A:YU8303 2.8 12.8 0.8 H251 A:YU8303 2.8 17.0 0.2 C22 A:YU8303 3.1 14.5 0.2 HB3 A:CYS198 3.1 14.2 1.0 CD2 A:HIS240 3.1 11.1 1.0 C22 A:YU8303 3.1 10.3 0.8 CE1 A:HIS240 3.2 11.1 1.0 HD2 A:HIS240 3.2 13.2 1.0 N25 A:YU8303 3.2 10.7 0.8 N25 A:YU8303 3.3 14.2 0.2 HH21 A:ARG119 3.3 13.6 1.0 CB A:CYS198 3.3 11.9 1.0 HE1 A:HIS240 3.4 13.2 1.0 C21 A:YU8303 3.4 14.5 0.2 CG A:ASP118 3.4 9.0 1.0 C21 A:YU8303 3.4 11.9 0.8 HE1 A:HIS114 3.5 11.1 1.0 HE A:ARG119 3.6 11.9 1.0 ZN A:ZN302 3.6 10.7 1.0 HB2 A:CYS198 3.7 14.2 1.0 OD1 A:ASP118 3.7 10.4 1.0 NH2 A:ARG119 3.9 11.4 1.0 H021 A:YU8303 3.9 14.3 0.8 H021 A:YU8303 4.0 17.8 0.2 NE2 A:HIS179 4.1 10.4 1.0 O23 A:YU8303 4.2 15.5 0.2 CE1 A:HIS114 4.2 9.3 1.0 NE A:ARG119 4.2 10.0 1.0 CG A:HIS240 4.3 10.7 1.0 ND1 A:HIS240 4.3 11.5 1.0 O23 A:YU8303 4.3 13.3 0.8 HE1 A:HIS179 4.3 12.3 1.0 O A:HOH479 4.3 10.6 0.6 CE1 A:HIS179 4.3 10.2 1.0 C26 A:YU8303 4.3 14.1 0.2 C26 A:YU8303 4.3 10.6 0.8 NE2 A:HIS114 4.4 10.2 1.0 H201 A:YU8303 4.4 19.9 0.2 HH22 A:ARG119 4.4 13.6 1.0 CZ A:ARG119 4.5 9.8 1.0 HA A:CYS198 4.5 13.3 1.0 H101 A:YU8303 4.5 16.9 0.8 CA A:CYS198 4.5 11.1 1.0 C08 A:YU8303 4.6 14.6 0.2 HA3 A:GLY239 4.6 12.6 1.0 C08 A:YU8303 4.6 10.8 0.8 O37 A:YU8303 4.7 14.5 0.2 O37 A:YU8303 4.7 11.1 0.8 CB A:ASP118 4.7 10.5 1.0 HB2 A:ASP118 4.8 12.6 1.0 CD2 A:HIS179 4.8 8.8 1.0 C02 A:YU8303 4.9 11.9 0.8 C02 A:YU8303 4.9 14.8 0.2

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2936


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 2936 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.7 occ:1.00 O A:HOH481 1.9 16.6 1.0 NE2 A:HIS179 2.1 10.4 1.0 ND1 A:HIS116 2.1 11.6 1.0 NE2 A:HIS114 2.1 10.2 1.0 HB2 A:HIS116 2.9 9.8 1.0 O37 A:YU8303 3.0 14.5 0.2 O37 A:YU8303 3.0 11.1 0.8 CE1 A:HIS116 3.0 11.1 1.0 CD2 A:HIS179 3.0 8.8 1.0 CE1 A:HIS179 3.0 10.2 1.0 CE1 A:HIS114 3.0 9.3 1.0 CG A:HIS116 3.1 8.5 1.0 CD2 A:HIS114 3.1 9.8 1.0 HE1 A:HIS116 3.2 13.2 1.0 HE1 A:HIS114 3.2 11.1 1.0 HD2 A:HIS179 3.2 10.5 1.0 HE1 A:HIS179 3.2 12.3 1.0 H251 A:YU8303 3.2 17.0 0.2 H251 A:YU8303 3.3 12.8 0.8 HD2 A:HIS114 3.3 11.7 1.0 CB A:HIS116 3.4 8.2 1.0 H021 A:YU8303 3.5 14.3 0.8 ZN A:ZN301 3.6 12.2 1.0 H021 A:YU8303 3.6 17.8 0.2 HB3 A:HIS116 3.6 9.8 1.0 C36 A:YU8303 3.8 15.1 0.2 C36 A:YU8303 3.8 11.7 0.8 OD1 A:ASP118 3.8 10.4 1.0 O24 A:YU8303 4.0 11.9 0.8 O24 A:YU8303 4.0 14.5 0.2 HB2 A:CYS198 4.1 14.2 1.0 ND1 A:HIS179 4.1 11.1 1.0 NE2 A:HIS116 4.1 11.3 1.0 CG A:HIS179 4.2 10.5 1.0 ND1 A:HIS114 4.2 8.8 1.0 CD2 A:HIS116 4.2 10.6 1.0 N25 A:YU8303 4.2 14.2 0.2 N25 A:YU8303 4.2 10.7 0.8 HB3 A:CYS198 4.2 14.2 1.0 CG A:HIS114 4.3 8.3 1.0 C02 A:YU8303 4.4 11.9 0.8 N27 A:YU8303 4.4 12.8 0.8 CB A:CYS198 4.5 11.9 1.0 N27 A:YU8303 4.5 15.7 0.2 C02 A:YU8303 4.5 14.8 0.2 SG A:CYS198 4.5 11.4 1.0 H A:HIS116 4.5 10.9 1.0 OD2 A:ASP118 4.5 11.6 1.0 CG A:ASP118 4.6 9.0 1.0 HB3 A:SER180 4.7 14.1 1.0 HG2 A:ARG119 4.7 11.5 1.0 O35 A:YU8303 4.8 15.7 0.2 O35 A:YU8303 4.8 12.3 0.8 C22 A:YU8303 4.8 14.5 0.2 C22 A:YU8303 4.8 10.3 0.8 CA A:HIS116 4.8 8.6 1.0 HE A:ARG119 4.9 11.9 1.0 O A:HOH533 4.9 10.5 0.8 HD1 A:HIS179 4.9 13.3 1.0 HE2 A:HIS116 4.9 13.5 1.0 HD1 A:HIS114 4.9 10.5 1.0 H013 A:YU8303 5.0 14.5 0.8

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2936 To Be Published.