Zinc in PDB 8p8y: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1657

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1657, PDB code: 8p8y 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)	39.90 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.31, 67.25, 39.96, 90, 93.16, 90
R / Rfree (%)	12.4 / 14.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1657 (pdb code 8p8y). 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 1657, PDB code: 8p8y:
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 1657


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 1657 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.7 occ:0.86 O A:HOH495 1.9 6.5 0.6 ND1 A:HIS116 2.0 14.7 1.0 NE2 A:HIS179 2.0 11.5 1.0 NE2 A:HIS114 2.1 11.4 1.0 CE1 A:HIS116 2.9 13.1 1.0 HB2 A:HIS116 2.9 12.8 1.0 CD2 A:HIS179 3.0 11.1 1.0 CE1 A:HIS114 3.0 11.0 1.0 CE1 A:HIS179 3.0 11.0 1.0 CG A:HIS116 3.0 11.8 1.0 HE1 A:HIS116 3.0 15.7 1.0 CD2 A:HIS114 3.1 10.5 1.0 HD2 A:HIS179 3.1 13.3 1.0 H171 A:X78303 3.2 16.1 1.0 HE1 A:HIS114 3.2 13.2 1.0 HE1 A:HIS179 3.2 13.2 1.0 HD2 A:HIS114 3.3 12.6 1.0 CB A:HIS116 3.4 10.6 1.0 ZN A:ZN302 3.5 8.8 0.6 H201 A:X78303 3.6 17.7 1.0 HB3 A:HIS116 3.7 12.8 1.0 HB2 A:CYS198 3.8 16.3 1.0 OD1 A:ASP118 3.9 12.3 1.0 O15 A:X78303 3.9 14.0 1.0 NE2 A:HIS116 4.0 13.1 1.0 CG A:HIS179 4.1 11.0 1.0 ND1 A:HIS179 4.1 11.4 1.0 CD2 A:HIS116 4.1 12.8 1.0 ND1 A:HIS114 4.1 10.7 1.0 N17 A:X78303 4.1 13.4 1.0 CG A:HIS114 4.2 9.9 1.0 H223 A:X78303 4.2 19.3 1.0 HB3 A:CYS198 4.2 16.3 1.0 CB A:CYS198 4.3 13.6 1.0 H221 A:X78303 4.3 19.3 1.0 SG A:CYS198 4.4 12.5 1.0 H A:HIS116 4.5 11.5 1.0 OD2 A:ASP118 4.5 12.2 1.0 C20 A:X78303 4.5 14.8 1.0 C22 A:X78303 4.6 16.1 1.0 CG A:ASP118 4.6 11.1 1.0 HB3 A:SER180 4.7 13.1 1.0 C14 A:X78303 4.7 13.2 1.0 HG2 A:ARG119 4.7 12.2 1.0 HE2 A:HIS116 4.8 15.7 1.0 HE A:ARG119 4.8 12.2 1.0 CA A:HIS116 4.8 10.3 1.0 HD1 A:HIS114 4.9 12.8 1.0 HD1 A:HIS179 4.9 13.7 1.0 C13 A:X78303 4.9 13.2 1.0 HG3 A:ARG119 4.9 12.2 1.0 O A:HOH527 5.0 11.6 0.8 HD2 A:HIS116 5.0 15.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1657


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 1657 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.8 occ:0.60 O A:HOH495 2.1 6.5 0.6 O15 A:X78303 2.1 14.0 1.0 NE2 A:HIS240 2.1 12.8 1.0 OD2 A:ASP118 2.3 12.2 1.0 SG A:CYS198 2.3 12.5 1.0 H171 A:X78303 2.8 16.1 1.0 HB3 A:CYS198 3.0 16.3 1.0 C14 A:X78303 3.0 13.2 1.0 CD2 A:HIS240 3.0 12.2 1.0 HD2 A:HIS240 3.1 14.7 1.0 N17 A:X78303 3.2 13.4 1.0 CE1 A:HIS240 3.2 12.8 1.0 CB A:CYS198 3.2 13.6 1.0 HH21 A:ARG119 3.3 16.8 1.0 C13 A:X78303 3.3 13.2 1.0 CG A:ASP118 3.4 11.1 1.0 HE1 A:HIS240 3.4 15.3 1.0 HE A:ARG119 3.5 12.2 1.0 ZN A:ZN301 3.5 10.7 0.9 HB2 A:CYS198 3.6 16.3 1.0 HE1 A:HIS114 3.6 13.2 1.0 OD1 A:ASP118 3.7 12.3 1.0 NH2 A:ARG119 3.9 14.0 1.0 H201 A:X78303 4.1 17.7 1.0 NE2 A:HIS179 4.1 11.5 1.0 NE A:ARG119 4.2 10.2 1.0 HE1 A:HIS179 4.2 13.2 1.0 O16 A:X78303 4.2 15.4 1.0 CG A:HIS240 4.2 12.4 1.0 ND1 A:HIS240 4.2 12.9 1.0 CE1 A:HIS114 4.3 11.0 1.0 C18 A:X78303 4.3 13.3 1.0 CE1 A:HIS179 4.3 11.0 1.0 O A:HOH489 4.3 7.7 0.4 NE2 A:HIS114 4.4 11.4 1.0 HA A:CYS198 4.4 15.0 1.0 HH22 A:ARG119 4.5 16.8 1.0 CZ A:ARG119 4.5 10.7 1.0 CA A:CYS198 4.5 12.5 1.0 C12 A:X78303 4.5 13.2 1.0 HA3 A:GLY239 4.6 13.6 1.0 H101 A:X78303 4.6 18.5 1.0 CB A:ASP118 4.7 11.3 1.0 HB2 A:ASP118 4.7 13.6 1.0 HB3 A:ASP118 4.9 13.6 1.0 CD2 A:HIS179 4.9 11.1 1.0 HG2 A:ARG119 5.0 12.2 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 1657 To Be Published.