Zinc in PDB 8p92: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2117

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2117, PDB code: 8p92 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)	28.90 / 1.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.45, 67.82, 40.11, 90, 93.2, 90
R / Rfree (%)	13 / 15

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2117 (pdb code 8p92). 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 2117, PDB code: 8p92:
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 2117


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 2117 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:6.5 occ:0.94 O A:HOH474 1.9 6.0 0.9 NE2 A:HIS179 2.0 7.7 1.0 ND1 A:HIS116 2.0 7.2 1.0 NE2 A:HIS114 2.1 6.3 1.0 HB2 A:HIS116 2.9 7.7 1.0 CE1 A:HIS116 3.0 8.1 1.0 CD2 A:HIS179 3.0 6.8 1.0 CE1 A:HIS114 3.0 6.3 1.0 CE1 A:HIS179 3.0 8.0 1.0 CG A:HIS116 3.0 7.1 1.0 CD2 A:HIS114 3.1 6.2 1.0 HE1 A:HIS116 3.1 9.7 1.0 HD2 A:HIS179 3.2 8.2 1.0 HE1 A:HIS114 3.2 7.6 1.0 H061 A:XB0303 3.2 9.2 1.0 HE1 A:HIS179 3.2 9.7 1.0 HD2 A:HIS114 3.3 7.4 1.0 CB A:HIS116 3.4 6.4 1.0 ZN A:ZN302 3.5 6.5 0.9 HB3 A:HIS116 3.6 7.7 1.0 H012 A:XB0303 3.7 12.5 1.0 HB2 A:CYS198 3.8 9.2 1.0 H021 A:XB0303 3.8 10.2 1.0 O09 A:XB0303 3.8 7.4 1.0 OD1 A:ASP118 3.9 7.1 1.0 ND1 A:HIS114 4.1 6.0 1.0 NE2 A:HIS116 4.1 8.8 1.0 ND1 A:HIS179 4.1 7.6 1.0 CG A:HIS179 4.1 7.4 1.0 N06 A:XB0303 4.2 7.6 1.0 CD2 A:HIS116 4.2 8.1 1.0 CG A:HIS114 4.2 6.0 1.0 HB3 A:CYS198 4.2 9.2 1.0 CB A:CYS198 4.3 7.6 1.0 SG A:CYS198 4.4 6.6 1.0 H A:HIS116 4.4 8.2 1.0 OD2 A:ASP118 4.5 7.3 1.0 C01 A:XB0303 4.6 10.4 1.0 CG A:ASP118 4.6 6.6 1.0 C08 A:XB0303 4.7 8.1 1.0 HB3 A:SER180 4.7 9.3 1.0 C02 A:XB0303 4.7 8.5 1.0 HG2 A:ARG119 4.7 7.3 1.0 CA A:HIS116 4.8 6.7 1.0 HE A:ARG119 4.8 7.4 1.0 HD1 A:HIS114 4.9 7.2 1.0 HG3 A:ARG119 4.9 7.3 1.0 HE2 A:HIS116 4.9 10.5 1.0 C07 A:XB0303 4.9 7.7 1.0 HD1 A:HIS179 4.9 9.2 1.0 O A:HOH563 4.9 9.0 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2117


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 2117 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:6.5 occ:0.89 O A:HOH474 2.0 6.0 0.9 NE2 A:HIS240 2.1 7.2 1.0 O09 A:XB0303 2.1 7.4 1.0 SG A:CYS198 2.3 6.6 1.0 OD2 A:ASP118 2.3 7.3 1.0 H061 A:XB0303 2.7 9.2 1.0 CD2 A:HIS240 3.0 7.6 1.0 HB3 A:CYS198 3.0 9.2 1.0 C08 A:XB0303 3.0 8.1 1.0 CE1 A:HIS240 3.1 7.4 1.0 HD2 A:HIS240 3.1 9.1 1.0 N06 A:XB0303 3.2 7.6 1.0 CB A:CYS198 3.2 7.6 1.0 HH21 A:ARG119 3.3 9.2 1.0 HE1 A:HIS240 3.3 8.8 1.0 CG A:ASP118 3.4 6.6 1.0 C07 A:XB0303 3.4 7.7 1.0 ZN A:ZN301 3.5 6.5 0.9 HE A:ARG119 3.6 7.4 1.0 HB2 A:CYS198 3.6 9.2 1.0 HE1 A:HIS114 3.6 7.6 1.0 OD1 A:ASP118 3.7 7.1 1.0 NH2 A:ARG119 3.9 7.7 1.0 NE2 A:HIS179 4.1 7.7 1.0 H021 A:XB0303 4.1 10.2 1.0 HE1 A:HIS179 4.2 9.7 1.0 NE A:ARG119 4.2 6.2 1.0 CG A:HIS240 4.2 7.2 1.0 O10 A:XB0303 4.2 9.3 1.0 ND1 A:HIS240 4.2 7.4 1.0 CE1 A:HIS114 4.3 6.3 1.0 CE1 A:HIS179 4.3 8.0 1.0 C05 A:XB0303 4.3 8.4 1.0 O A:HOH535 4.4 7.7 0.9 NE2 A:HIS114 4.4 6.3 1.0 CZ A:ARG119 4.4 6.1 1.0 HH22 A:ARG119 4.4 9.2 1.0 HA A:CYS198 4.5 8.1 1.0 H131 A:XB0303 4.5 11.6 1.0 CA A:CYS198 4.5 6.7 1.0 HA3 A:GLY239 4.5 7.9 1.0 C11 A:XB0303 4.6 8.4 1.0 CB A:ASP118 4.6 6.8 1.0 HB2 A:ASP118 4.7 8.2 1.0 HB3 A:ASP118 4.9 8.2 1.0 CD2 A:HIS179 4.9 6.8 1.0 HG2 A:ARG119 5.0 7.3 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 2117 To Be Published.