Zinc in PDB 8pgh: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2955

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2955, PDB code: 8pgh 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)	34.13 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.547, 67.886, 40.208, 90, 93.07, 90
R / Rfree (%)	11.8 / 13.7

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2955 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 2955 (pdb code 8pgh). 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 2955, PDB code: 8pgh:
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 2955


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 2955 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.7 occ:0.89 O A:HOH464 1.9 7.9 0.6 NE2 A:HIS179 2.0 12.3 1.0 ND1 A:HIS116 2.0 11.8 1.0 NE2 A:HIS114 2.1 11.5 1.0 HB2 A:HIS116 2.9 13.0 1.0 CE1 A:HIS179 3.0 13.1 1.0 CE1 A:HIS116 3.0 12.4 1.0 CE1 A:HIS114 3.0 10.6 1.0 CD2 A:HIS179 3.0 12.1 1.0 CG A:HIS116 3.0 11.1 1.0 CD2 A:HIS114 3.1 10.8 1.0 HE1 A:HIS179 3.2 15.7 1.0 HE1 A:HIS116 3.2 14.8 1.0 HE1 A:HIS114 3.2 12.7 1.0 HD2 A:HIS179 3.2 14.5 1.0 H181 A:YUZ303 3.2 21.7 0.4 HD2 A:HIS114 3.3 12.9 1.0 H181 A:YUZ303 3.3 16.0 0.6 CB A:HIS116 3.4 10.8 1.0 ZN A:ZN302 3.5 11.4 0.8 H111 A:YUZ303 3.5 25.7 0.6 HB3 A:HIS116 3.6 13.0 1.0 H021 A:YUZ303 3.6 18.8 0.6 H021 A:YUZ303 3.7 21.2 0.4 HB2 A:CYS198 3.8 15.8 1.0 OD1 A:ASP118 3.8 13.7 1.0 O22 A:YUZ303 3.9 15.2 0.4 O22 A:YUZ303 3.9 14.2 0.6 ND1 A:HIS179 4.1 13.3 1.0 NE2 A:HIS116 4.1 13.3 1.0 H041 A:YUZ303 4.1 18.2 0.4 CG A:HIS179 4.1 13.0 1.0 ND1 A:HIS114 4.1 10.2 1.0 HB3 A:CYS198 4.1 15.8 1.0 CD2 A:HIS116 4.2 13.4 1.0 C11 A:YUZ303 4.2 21.4 0.6 CG A:HIS114 4.2 10.4 1.0 N18 A:YUZ303 4.2 18.1 0.4 CB A:CYS198 4.3 13.2 1.0 N18 A:YUZ303 4.3 13.3 0.6 SG A:CYS198 4.3 12.5 1.0 H A:HIS116 4.5 12.2 1.0 OD2 A:ASP118 4.5 13.5 1.0 CG A:ASP118 4.6 12.7 1.0 C20 A:YUZ303 4.7 15.0 0.6 C02 A:YUZ303 4.7 15.7 0.6 HB3 A:SER180 4.7 15.3 1.0 C20 A:YUZ303 4.7 16.0 0.4 C02 A:YUZ303 4.7 17.7 0.4 HG2 A:ARG119 4.8 11.5 1.0 HE A:ARG119 4.8 12.3 1.0 CA A:HIS116 4.8 10.3 1.0 C04 A:YUZ303 4.8 15.2 0.4 C03 A:YUZ303 4.8 18.9 0.6 HD1 A:HIS179 4.9 15.9 1.0 HE2 A:HIS116 4.9 16.0 1.0 HD1 A:HIS114 4.9 12.3 1.0 O A:HOH543 4.9 17.0 0.8 N10 A:YUZ303 4.9 22.4 0.6 C19 A:YUZ303 4.9 17.4 0.4 HG3 A:ARG119 4.9 11.5 1.0 C19 A:YUZ303 5.0 13.9 0.6

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2955


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 2955 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.4 occ:0.77 O22 A:YUZ303 2.0 14.2 0.6 O A:HOH464 2.0 7.9 0.6 NE2 A:HIS240 2.1 13.1 1.0 O22 A:YUZ303 2.2 15.2 0.4 SG A:CYS198 2.3 12.5 1.0 OD2 A:ASP118 2.3 13.5 1.0 H181 A:YUZ303 2.7 16.0 0.6 C20 A:YUZ303 2.9 15.0 0.6 H181 A:YUZ303 3.0 21.7 0.4 CD2 A:HIS240 3.0 12.8 1.0 HB3 A:CYS198 3.1 15.8 1.0 HD2 A:HIS240 3.1 15.4 1.0 C20 A:YUZ303 3.2 16.0 0.4 CE1 A:HIS240 3.2 13.8 1.0 N18 A:YUZ303 3.2 13.3 0.6 CB A:CYS198 3.3 13.2 1.0 HH21 A:ARG119 3.3 15.0 1.0 N18 A:YUZ303 3.3 18.1 0.4 C19 A:YUZ303 3.3 13.9 0.6 CG A:ASP118 3.3 12.7 1.0 C19 A:YUZ303 3.4 17.4 0.4 HE1 A:HIS240 3.4 16.6 1.0 ZN A:ZN301 3.5 11.7 0.9 HE A:ARG119 3.5 12.3 1.0 HE1 A:HIS114 3.6 12.7 1.0 OD1 A:ASP118 3.6 13.7 1.0 HB2 A:CYS198 3.7 15.8 1.0 NH2 A:ARG119 3.9 12.5 1.0 HE1 A:HIS179 4.1 15.7 1.0 NE2 A:HIS179 4.1 12.3 1.0 O21 A:YUZ303 4.1 15.3 0.6 H021 A:YUZ303 4.2 18.8 0.6 NE A:ARG119 4.2 10.3 1.0 O A:HOH534 4.2 11.5 0.6 CE1 A:HIS179 4.2 13.1 1.0 CG A:HIS240 4.2 13.1 1.0 ND1 A:HIS240 4.3 13.9 1.0 CE1 A:HIS114 4.3 10.6 1.0 C17 A:YUZ303 4.3 18.1 0.4 O21 A:YUZ303 4.3 16.6 0.4 H021 A:YUZ303 4.4 21.2 0.4 C17 A:YUZ303 4.4 12.9 0.6 NE2 A:HIS114 4.4 11.5 1.0 H251 A:YUZ303 4.4 24.7 0.4 H351 A:YUZ303 4.4 20.4 0.6 HA A:CYS198 4.4 14.3 1.0 HH22 A:ARG119 4.5 15.0 1.0 CZ A:ARG119 4.5 10.3 1.0 C23 A:YUZ303 4.5 18.4 0.4 C23 A:YUZ303 4.5 13.9 0.6 CA A:CYS198 4.5 12.0 1.0 HA3 A:GLY239 4.6 13.8 1.0 CB A:ASP118 4.7 12.2 1.0 HB2 A:ASP118 4.7 14.7 1.0 HB3 A:ASP118 4.9 14.7 1.0 H111 A:YUZ303 4.9 25.7 0.6 C16 A:YUZ303 4.9 18.4 0.4 CD2 A:HIS179 5.0 12.1 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 2955 To Be Published.