Zinc in PDB 8pb0: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2696

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2696, PDB code: 8pb0 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)	28.99 / 1.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.49, 67.91, 40.22, 90, 93.37, 90
R / Rfree (%)	13.5 / 16

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2696 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 2696 (pdb code 8pb0). 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 2696, PDB code: 8pb0:
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 2696


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 2696 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.4 occ:0.89 O A:HOH483 1.9 4.3 0.5 NE2 A:HIS179 2.1 12.2 1.0 ND1 A:HIS116 2.1 12.7 1.0 NE2 A:HIS114 2.1 11.1 1.0 HB2 A:HIS116 2.9 12.8 1.0 CE1 A:HIS179 3.0 13.0 1.0 CE1 A:HIS114 3.0 9.9 1.0 CE1 A:HIS116 3.0 13.1 1.0 CD2 A:HIS179 3.0 11.9 1.0 CG A:HIS116 3.1 11.1 1.0 CD2 A:HIS114 3.1 10.2 1.0 HE1 A:HIS114 3.2 11.9 1.0 HE1 A:HIS179 3.2 15.6 1.0 HE1 A:HIS116 3.2 15.7 1.0 H051 A:XQE303 3.2 13.8 0.8 H051 A:XQE303 3.2 19.8 0.2 HD2 A:HIS179 3.2 14.3 1.0 HD2 A:HIS114 3.3 12.2 1.0 CB A:HIS116 3.4 10.6 1.0 ZN A:ZN302 3.5 12.1 0.9 H021 A:XQE303 3.6 21.7 0.2 H021 A:XQE303 3.6 14.9 0.8 HB3 A:HIS116 3.7 12.8 1.0 HB2 A:CYS198 3.8 14.1 1.0 OD1 A:ASP118 3.8 11.8 1.0 O09 A:XQE303 3.9 11.4 0.8 H281 A:XQE303 4.0 25.1 0.2 HB3 A:CYS198 4.1 14.1 1.0 H281 A:XQE303 4.1 22.3 0.8 ND1 A:HIS179 4.1 12.8 1.0 ND1 A:HIS114 4.1 10.5 1.0 NE2 A:HIS116 4.1 13.1 1.0 CG A:HIS179 4.2 13.0 1.0 CD2 A:HIS116 4.2 12.4 1.0 CG A:HIS114 4.2 9.6 1.0 N05 A:XQE303 4.2 11.5 0.8 N05 A:XQE303 4.2 16.5 0.2 CB A:CYS198 4.3 11.8 1.0 O09 A:XQE303 4.3 17.4 0.2 SG A:CYS198 4.3 11.7 1.0 H A:HIS116 4.4 11.8 1.0 OD2 A:ASP118 4.5 12.9 1.0 C28 A:XQE303 4.5 18.6 0.8 C28 A:XQE303 4.6 20.9 0.2 C02 A:XQE303 4.6 12.4 0.8 CG A:ASP118 4.6 11.3 1.0 C02 A:XQE303 4.6 18.1 0.2 HB3 A:SER180 4.7 15.4 1.0 HG2 A:ARG119 4.7 11.7 1.0 N27 A:XQE303 4.7 14.4 0.8 C07 A:XQE303 4.7 11.9 0.8 HE A:ARG119 4.8 13.0 1.0 CA A:HIS116 4.8 10.5 1.0 N27 A:XQE303 4.8 19.6 0.2 C07 A:XQE303 4.9 17.2 0.2 HD1 A:HIS179 4.9 15.3 1.0 HD1 A:HIS114 4.9 12.6 1.0 HG3 A:ARG119 4.9 11.7 1.0 HE2 A:HIS116 4.9 15.8 1.0 O A:HOH558 4.9 16.4 0.9 C06 A:XQE303 4.9 11.4 0.8 C06 A:XQE303 5.0 16.6 0.2

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2696


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 2696 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.1 occ:0.88 O A:HOH483 2.0 4.3 0.5 O09 A:XQE303 2.0 17.4 0.2 O09 A:XQE303 2.1 11.4 0.8 NE2 A:HIS240 2.1 11.5 1.0 SG A:CYS198 2.3 11.7 1.0 OD2 A:ASP118 2.3 12.9 1.0 H051 A:XQE303 2.7 19.8 0.2 H051 A:XQE303 2.8 13.8 0.8 C07 A:XQE303 3.0 17.2 0.2 HB3 A:CYS198 3.0 14.1 1.0 CD2 A:HIS240 3.0 12.0 1.0 C07 A:XQE303 3.1 11.9 0.8 HD2 A:HIS240 3.1 14.4 1.0 N05 A:XQE303 3.2 16.5 0.2 CE1 A:HIS240 3.2 12.5 1.0 CB A:CYS198 3.2 11.8 1.0 HH21 A:ARG119 3.2 15.0 1.0 N05 A:XQE303 3.3 11.5 0.8 C06 A:XQE303 3.3 16.6 0.2 CG A:ASP118 3.3 11.3 1.0 C06 A:XQE303 3.4 11.4 0.8 HE1 A:HIS240 3.5 15.0 1.0 ZN A:ZN301 3.5 11.4 0.9 HE A:ARG119 3.5 13.0 1.0 HE1 A:HIS114 3.6 11.9 1.0 HB2 A:CYS198 3.6 14.1 1.0 OD1 A:ASP118 3.7 11.8 1.0 NH2 A:ARG119 3.9 12.5 1.0 H021 A:XQE303 4.0 14.9 0.8 H021 A:XQE303 4.1 21.7 0.2 NE2 A:HIS179 4.2 12.2 1.0 O08 A:XQE303 4.2 18.0 0.2 HE1 A:HIS179 4.2 15.6 1.0 NE A:ARG119 4.2 10.8 1.0 CG A:HIS240 4.2 11.8 1.0 O A:HOH457 4.2 11.9 0.7 O08 A:XQE303 4.2 13.5 0.8 ND1 A:HIS240 4.3 12.0 1.0 CE1 A:HIS114 4.3 9.9 1.0 CE1 A:HIS179 4.3 13.0 1.0 C04 A:XQE303 4.3 16.5 0.2 C04 A:XQE303 4.4 10.9 0.8 H221 A:XQE303 4.4 20.0 0.8 NE2 A:HIS114 4.4 11.1 1.0 HA A:CYS198 4.4 14.0 1.0 H121 A:XQE303 4.4 19.8 0.2 HH22 A:ARG119 4.4 15.0 1.0 CZ A:ARG119 4.4 11.0 1.0 CA A:CYS198 4.5 11.6 1.0 C10 A:XQE303 4.5 16.3 0.2 HA3 A:GLY239 4.6 12.2 1.0 C10 A:XQE303 4.6 12.3 0.8 CB A:ASP118 4.7 10.7 1.0 HB2 A:ASP118 4.7 12.8 1.0 HB3 A:ASP118 4.9 12.8 1.0 CD2 A:HIS179 5.0 11.9 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 2696 To Be Published.