Zinc in PDB 8p93: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2163

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2163, PDB code: 8p93 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)	34.48 / 1.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.43, 67.67, 40.15, 90, 93.42, 90
R / Rfree (%)	12.8 / 14.2

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2163 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 2163 (pdb code 8p93). 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 2163, PDB code: 8p93:
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 2163


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 2163 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.4 occ:0.76 O A:HOH481 1.9 8.7 0.7 NE2 A:HIS179 1.9 11.8 1.0 NE2 A:HIS114 2.0 11.9 1.0 ND1 A:HIS116 2.0 12.4 1.0 HB2 A:HIS116 2.9 12.7 1.0 CE1 A:HIS179 2.9 11.7 1.0 CD2 A:HIS179 2.9 10.8 1.0 CE1 A:HIS116 3.0 13.0 1.0 CE1 A:HIS114 3.0 11.0 1.0 CD2 A:HIS114 3.0 11.1 1.0 CG A:HIS116 3.1 11.7 1.0 HE1 A:HIS116 3.1 15.6 1.0 HD2 A:HIS179 3.1 13.0 1.0 HE1 A:HIS114 3.2 13.2 1.0 HE1 A:HIS179 3.2 14.1 1.0 H061 A:XAQ303 3.2 17.7 0.5 H061 A:XAQ303 3.2 14.8 0.5 HD2 A:HIS114 3.2 13.3 1.0 CB A:HIS116 3.4 10.6 1.0 ZN A:ZN302 3.5 9.8 0.7 H021 A:XAQ303 3.6 18.3 0.5 H021 A:XAQ303 3.6 16.4 0.5 HB3 A:HIS116 3.7 12.7 1.0 HB2 A:CYS198 3.8 15.6 1.0 O09 A:XAQ303 3.8 12.6 0.5 OD1 A:ASP118 3.9 12.6 1.0 O09 A:XAQ303 4.0 14.7 0.5 H031 A:XAQ303 4.0 18.1 0.5 H031 A:XAQ303 4.0 19.3 0.5 ND1 A:HIS179 4.1 12.3 1.0 CG A:HIS179 4.1 11.1 1.0 ND1 A:HIS114 4.1 10.7 1.0 NE2 A:HIS116 4.1 13.3 1.0 CD2 A:HIS116 4.1 13.4 1.0 N06 A:XAQ303 4.2 14.7 0.5 CG A:HIS114 4.2 10.2 1.0 N06 A:XAQ303 4.2 12.3 0.5 HB3 A:CYS198 4.2 15.6 1.0 CB A:CYS198 4.3 12.9 1.0 SG A:CYS198 4.3 12.0 1.0 H A:HIS116 4.5 11.8 1.0 OD2 A:ASP118 4.5 12.8 1.0 C02 A:XAQ303 4.6 15.2 0.5 C02 A:XAQ303 4.6 13.7 0.5 CG A:ASP118 4.6 11.5 1.0 C03 A:XAQ303 4.6 15.1 0.5 HB3 A:SER180 4.6 13.7 1.0 C08 A:XAQ303 4.6 13.2 0.5 C03 A:XAQ303 4.7 16.1 0.5 H032 A:XAQ303 4.7 18.1 0.5 C08 A:XAQ303 4.7 13.4 0.5 HG2 A:ARG119 4.7 11.3 1.0 HE A:ARG119 4.7 12.2 1.0 H032 A:XAQ303 4.8 19.3 0.5 CA A:HIS116 4.8 10.2 1.0 HD1 A:HIS179 4.8 14.8 1.0 HD1 A:HIS114 4.9 12.9 1.0 HG3 A:ARG119 4.9 11.3 1.0 HE2 A:HIS116 4.9 16.0 1.0 C07 A:XAQ303 4.9 14.3 0.5 C07 A:XAQ303 4.9 12.4 0.5 O A:HOH551 4.9 13.1 0.8

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2163


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 2163 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.8 occ:0.68 O09 A:XAQ303 1.9 14.7 0.5 O A:HOH481 2.0 8.7 0.7 NE2 A:HIS240 2.1 12.3 1.0 O09 A:XAQ303 2.2 12.6 0.5 SG A:CYS198 2.3 12.0 1.0 OD2 A:ASP118 2.3 12.8 1.0 H061 A:XAQ303 2.7 14.8 0.5 H061 A:XAQ303 2.8 17.7 0.5 C08 A:XAQ303 2.9 13.2 0.5 CD2 A:HIS240 3.0 12.4 1.0 HB3 A:CYS198 3.0 15.6 1.0 C08 A:XAQ303 3.1 13.4 0.5 HD2 A:HIS240 3.1 14.9 1.0 CE1 A:HIS240 3.2 13.4 1.0 N06 A:XAQ303 3.2 12.3 0.5 HH21 A:ARG119 3.2 15.4 1.0 CB A:CYS198 3.2 12.9 1.0 N06 A:XAQ303 3.2 14.7 0.5 C07 A:XAQ303 3.3 12.4 0.5 CG A:ASP118 3.4 11.5 1.0 C07 A:XAQ303 3.4 14.3 0.5 HE1 A:HIS240 3.4 16.1 1.0 HE A:ARG119 3.5 12.2 1.0 ZN A:ZN301 3.5 10.4 0.8 HE1 A:HIS114 3.6 13.2 1.0 HB2 A:CYS198 3.6 15.6 1.0 OD1 A:ASP118 3.7 12.6 1.0 NH2 A:ARG119 3.9 12.8 1.0 NE2 A:HIS179 4.1 11.8 1.0 O10 A:XAQ303 4.1 13.4 0.5 NE A:ARG119 4.1 10.1 1.0 H021 A:XAQ303 4.2 18.3 0.5 HE1 A:HIS179 4.2 14.1 1.0 H021 A:XAQ303 4.2 16.4 0.5 CG A:HIS240 4.2 12.2 1.0 ND1 A:HIS240 4.2 12.8 1.0 O10 A:XAQ303 4.3 14.6 0.5 CE1 A:HIS179 4.3 11.7 1.0 CE1 A:HIS114 4.3 11.0 1.0 O A:HOH515 4.3 10.3 0.5 C05 A:XAQ303 4.3 15.2 0.5 C05 A:XAQ303 4.4 13.0 0.5 NE2 A:HIS114 4.4 11.9 1.0 H291 A:XAQ303 4.4 21.3 0.5 HH22 A:ARG119 4.4 15.4 1.0 HA A:CYS198 4.4 14.4 1.0 CZ A:ARG119 4.4 10.6 1.0 H131 A:XAQ303 4.5 16.4 0.5 CA A:CYS198 4.5 12.0 1.0 C11 A:XAQ303 4.5 15.5 0.5 C11 A:XAQ303 4.6 12.8 0.5 HA3 A:GLY239 4.6 12.8 1.0 CB A:ASP118 4.7 10.9 1.0 HB2 A:ASP118 4.7 13.1 1.0 HB3 A:ASP118 4.9 13.1 1.0 CD2 A:HIS179 4.9 10.8 1.0 HG2 A:ARG119 5.0 11.3 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 2163 To Be Published.