Zinc in PDB 8pao: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2654

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2654, PDB code: 8pao 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)	34.55 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.433, 67.883, 40.202, 90, 93.29, 90
R / Rfree (%)	13.4 / 16.4

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2654 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 2654 (pdb code 8pao). 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 2654, PDB code: 8pao:
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 2654


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 2654 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.6 occ:0.98 O A:HOH493 1.9 12.3 0.8 NE2 A:HIS179 2.1 15.6 1.0 ND1 A:HIS116 2.2 14.9 1.0 NE2 A:HIS114 2.2 14.5 1.0 HB2 A:HIS116 2.9 15.5 1.0 CD2 A:HIS179 3.0 14.6 1.0 CE1 A:HIS114 3.1 14.2 1.0 CG A:HIS116 3.1 12.9 1.0 CE1 A:HIS116 3.1 15.3 1.0 CD2 A:HIS114 3.1 13.4 1.0 CE1 A:HIS179 3.1 15.8 1.0 HD2 A:HIS179 3.2 17.5 1.0 H391 A:XZH303 3.2 18.7 0.5 H391 A:XZH303 3.2 21.0 0.5 HE1 A:HIS114 3.3 17.1 1.0 HE1 A:HIS116 3.3 18.4 1.0 HD2 A:HIS114 3.3 16.0 1.0 HE1 A:HIS179 3.4 18.9 1.0 CB A:HIS116 3.4 12.9 1.0 ZN A:ZN302 3.5 16.5 1.0 HB3 A:HIS116 3.6 15.5 1.0 H231 A:XZH303 3.7 20.4 0.5 N25 A:XZH303 3.8 25.0 0.5 H231 A:XZH303 3.8 24.4 0.5 OD1 A:ASP118 3.8 16.6 1.0 N25 A:XZH303 3.9 22.3 0.5 O01 A:XZH303 3.9 14.0 0.5 HB2 A:CYS198 3.9 18.5 1.0 HB3 A:CYS198 4.1 18.5 1.0 O01 A:XZH303 4.1 20.7 0.5 CG A:HIS179 4.2 15.1 1.0 ND1 A:HIS114 4.2 14.3 1.0 ND1 A:HIS179 4.2 16.4 1.0 N39 A:XZH303 4.2 15.6 0.5 NE2 A:HIS116 4.2 16.5 1.0 N39 A:XZH303 4.2 17.5 0.5 CG A:HIS114 4.2 13.8 1.0 CD2 A:HIS116 4.3 15.8 1.0 CB A:CYS198 4.3 15.4 1.0 N26 A:XZH303 4.3 26.8 0.5 SG A:CYS198 4.3 15.4 1.0 N24 A:XZH303 4.4 23.4 0.5 H A:HIS116 4.5 16.2 1.0 OD2 A:ASP118 4.5 17.3 1.0 N24 A:XZH303 4.5 19.8 0.5 N26 A:XZH303 4.5 24.1 0.5 C23 A:XZH303 4.6 17.0 0.5 CG A:ASP118 4.6 15.4 1.0 C23 A:XZH303 4.6 20.4 0.5 HG2 A:ARG119 4.7 16.3 1.0 C02 A:XZH303 4.7 16.1 0.5 HB3 A:SER180 4.7 20.5 1.0 HE A:ARG119 4.7 17.4 1.0 C02 A:XZH303 4.8 19.5 0.5 CA A:HIS116 4.8 13.1 1.0 HG3 A:ARG119 4.9 16.3 1.0 O A:HOH522 4.9 19.2 0.7 C04 A:XZH303 4.9 16.8 0.5 C04 A:XZH303 5.0 16.8 0.5 HD1 A:HIS114 5.0 17.1 1.0 HD1 A:HIS179 5.0 19.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2654


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 2654 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.5 occ:0.97 O A:HOH493 2.0 12.3 0.8 O01 A:XZH303 2.0 20.7 0.5 O01 A:XZH303 2.2 14.0 0.5 NE2 A:HIS240 2.2 16.5 1.0 SG A:CYS198 2.3 15.4 1.0 OD2 A:ASP118 2.4 17.3 1.0 H391 A:XZH303 2.8 18.7 0.5 H391 A:XZH303 2.9 21.0 0.5 C02 A:XZH303 3.0 19.5 0.5 HB3 A:CYS198 3.1 18.5 1.0 C02 A:XZH303 3.1 16.1 0.5 CD2 A:HIS240 3.1 16.5 1.0 CE1 A:HIS240 3.2 16.7 1.0 HH21 A:ARG119 3.2 20.4 1.0 HD2 A:HIS240 3.2 19.8 1.0 N39 A:XZH303 3.2 15.6 0.5 CB A:CYS198 3.3 15.4 1.0 N39 A:XZH303 3.3 17.5 0.5 C04 A:XZH303 3.4 16.8 0.5 CG A:ASP118 3.4 15.4 1.0 C04 A:XZH303 3.4 16.8 0.5 HE1 A:HIS240 3.4 20.0 1.0 ZN A:ZN301 3.5 15.6 1.0 HE A:ARG119 3.5 17.4 1.0 HE1 A:HIS114 3.6 17.1 1.0 HB2 A:CYS198 3.7 18.5 1.0 OD1 A:ASP118 3.7 16.6 1.0 NH2 A:ARG119 3.9 17.0 1.0 H231 A:XZH303 4.0 24.4 0.5 H231 A:XZH303 4.0 20.4 0.5 NE2 A:HIS179 4.1 15.6 1.0 NE A:ARG119 4.2 14.5 1.0 O03 A:XZH303 4.2 20.7 0.5 O03 A:XZH303 4.3 17.2 0.5 HE1 A:HIS179 4.3 18.9 1.0 O A:HOH492 4.3 12.7 0.6 CG A:HIS240 4.3 16.4 1.0 CE1 A:HIS114 4.3 14.2 1.0 ND1 A:HIS240 4.3 16.1 1.0 C38 A:XZH303 4.3 17.8 0.5 C38 A:XZH303 4.3 15.3 0.5 CE1 A:HIS179 4.3 15.8 1.0 NE2 A:HIS114 4.4 14.5 1.0 HH22 A:ARG119 4.4 20.4 1.0 CZ A:ARG119 4.4 15.3 1.0 HA A:CYS198 4.4 18.9 1.0 H171 A:XZH303 4.5 24.3 0.5 H071 A:XZH303 4.5 23.3 0.5 CA A:CYS198 4.5 15.8 1.0 C05 A:XZH303 4.6 17.0 0.5 C05 A:XZH303 4.6 18.1 0.5 HA3 A:GLY239 4.6 18.3 1.0 CB A:ASP118 4.7 15.5 1.0 HB2 A:ASP118 4.7 18.5 1.0 CD2 A:HIS179 4.9 14.6 1.0 HB3 A:ASP118 5.0 18.5 1.0 C23 A:XZH303 5.0 20.4 0.5 HG2 A:ARG119 5.0 16.3 1.0 C23 A:XZH303 5.0 17.0 0.5

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2654 To Be Published.