Zinc in PDB 8pgp: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3193

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3193, PDB code: 8pgp 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)	28.93 / 0.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.26, 67.47, 40.09, 90, 93.66, 90
R / Rfree (%)	12.7 / 13.4

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3193 (pdb code 8pgp). 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 3193, PDB code: 8pgp:
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 3193


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 3193 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.4 occ:0.75 O A:HOH503 1.9 8.1 0.9 NE2 A:HIS179 2.0 9.0 1.0 ND1 A:HIS116 2.0 9.0 1.0 NE2 A:HIS114 2.1 8.5 1.0 O39 A:YSR303 2.9 12.4 1.0 HB2 A:HIS116 2.9 9.2 1.0 CE1 A:HIS116 2.9 9.7 1.0 CE1 A:HIS179 3.0 9.6 1.0 CD2 A:HIS179 3.0 9.3 1.0 CE1 A:HIS114 3.0 8.3 1.0 CG A:HIS116 3.1 8.8 1.0 CD2 A:HIS114 3.1 8.6 1.0 HE1 A:HIS116 3.1 11.6 1.0 HE1 A:HIS179 3.2 11.6 1.0 HD2 A:HIS179 3.2 11.1 1.0 HE1 A:HIS114 3.2 9.9 1.0 H051 A:YSR303 3.2 11.7 1.0 HD2 A:HIS114 3.3 10.3 1.0 CB A:HIS116 3.4 7.7 1.0 H021 A:YSR303 3.5 13.2 1.0 ZN A:ZN302 3.5 6.7 0.7 HB3 A:HIS116 3.6 9.2 1.0 C38 A:YSR303 3.7 12.3 1.0 OD1 A:ASP118 3.8 9.6 1.0 HB2 A:CYS198 3.9 11.4 1.0 O08 A:YSR303 4.0 9.4 1.0 ND1 A:HIS179 4.1 9.4 1.0 NE2 A:HIS116 4.1 10.5 1.0 CG A:HIS179 4.1 9.2 1.0 HB3 A:CYS198 4.1 11.4 1.0 ND1 A:HIS114 4.1 7.7 1.0 CD2 A:HIS116 4.2 10.3 1.0 N05 A:YSR303 4.2 9.7 1.0 CG A:HIS114 4.2 7.8 1.0 CB A:CYS198 4.3 9.5 1.0 N28 A:YSR303 4.4 12.2 1.0 C02 A:YSR303 4.4 11.0 1.0 SG A:CYS198 4.4 8.5 1.0 OD2 A:ASP118 4.5 9.1 1.0 H A:HIS116 4.5 8.4 1.0 CG A:ASP118 4.6 8.6 1.0 O37 A:YSR303 4.6 14.4 1.0 HB3 A:SER180 4.7 11.3 1.0 HG2 A:ARG119 4.8 8.5 1.0 C07 A:YSR303 4.8 10.0 1.0 HE A:ARG119 4.8 8.9 1.0 CA A:HIS116 4.8 7.5 1.0 O A:HOH560 4.8 12.0 0.8 HD1 A:HIS179 4.8 11.3 1.0 HE2 A:HIS116 4.8 12.6 1.0 HD1 A:HIS114 4.9 9.2 1.0 H013 A:YSR303 5.0 13.7 1.0 HG3 A:ARG119 5.0 8.5 1.0 C06 A:YSR303 5.0 9.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3193


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 3193 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:6.7 occ:0.66 O A:HOH503 2.0 8.1 0.9 NE2 A:HIS240 2.1 9.2 1.0 O08 A:YSR303 2.1 9.4 1.0 SG A:CYS198 2.3 8.5 1.0 OD2 A:ASP118 2.3 9.1 1.0 H051 A:YSR303 2.6 11.7 1.0 CD2 A:HIS240 3.0 9.2 1.0 HB3 A:CYS198 3.0 11.4 1.0 C07 A:YSR303 3.1 10.0 1.0 HD2 A:HIS240 3.1 11.1 1.0 N05 A:YSR303 3.1 9.7 1.0 CE1 A:HIS240 3.2 9.5 1.0 CB A:CYS198 3.2 9.5 1.0 HH21 A:ARG119 3.2 10.9 1.0 C06 A:YSR303 3.4 9.7 1.0 CG A:ASP118 3.4 8.6 1.0 HE1 A:HIS240 3.4 11.4 1.0 HE1 A:HIS114 3.5 9.9 1.0 HE A:ARG119 3.5 8.9 1.0 ZN A:ZN301 3.5 7.4 0.8 HB2 A:CYS198 3.7 11.4 1.0 OD1 A:ASP118 3.7 9.6 1.0 NH2 A:ARG119 3.9 9.1 1.0 H021 A:YSR303 4.0 13.2 1.0 NE2 A:HIS179 4.1 9.0 1.0 HE1 A:HIS179 4.1 11.6 1.0 CE1 A:HIS114 4.2 8.3 1.0 CG A:HIS240 4.2 9.2 1.0 NE A:ARG119 4.2 7.4 1.0 O09 A:YSR303 4.2 11.8 1.0 ND1 A:HIS240 4.2 9.3 1.0 CE1 A:HIS179 4.2 9.6 1.0 C04 A:YSR303 4.3 10.2 1.0 O A:HOH530 4.3 8.0 0.5 NE2 A:HIS114 4.4 8.5 1.0 HA A:CYS198 4.4 10.6 1.0 HH22 A:ARG119 4.4 10.9 1.0 CZ A:ARG119 4.4 7.7 1.0 CA A:CYS198 4.5 8.8 1.0 HA3 A:GLY239 4.6 10.3 1.0 C10 A:YSR303 4.6 10.6 1.0 O39 A:YSR303 4.6 12.4 1.0 CB A:ASP118 4.7 8.2 1.0 HB2 A:ASP118 4.8 9.9 1.0 H121 A:YSR303 4.8 18.9 1.0 CD2 A:HIS179 4.9 9.3 1.0 HB3 A:ASP118 5.0 9.9 1.0 C02 A:YSR303 5.0 11.0 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 3193 To Be Published.