Zinc in PDB 8pa8: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551, PDB code: 8pa8 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)	40.19 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.38, 67.74, 40.27, 90, 93.56, 90
R / Rfree (%)	14.2 / 16.8

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551 (pdb code 8pa8). 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 2551, PDB code: 8pa8:
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 2551


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 2551 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.2 occ:0.81 O A:HOH476 1.8 15.7 1.0 NE2 A:HIS179 2.1 13.8 1.0 ND1 A:HIS116 2.1 14.7 1.0 NE2 A:HIS114 2.2 14.3 1.0 HB2 A:HIS116 2.9 13.3 1.0 CE1 A:HIS179 3.0 14.4 1.0 CD2 A:HIS179 3.0 14.1 1.0 CE1 A:HIS116 3.1 14.6 1.0 CE1 A:HIS114 3.1 12.8 1.0 CG A:HIS116 3.1 12.9 1.0 CD2 A:HIS114 3.1 13.7 1.0 H251 A:XLZ303 3.2 17.7 0.8 HD2 A:HIS179 3.2 16.9 1.0 HE1 A:HIS179 3.2 17.3 1.0 HE1 A:HIS116 3.3 17.4 1.0 HE1 A:HIS114 3.3 15.3 1.0 HD2 A:HIS114 3.3 16.4 1.0 CB A:HIS116 3.4 11.1 1.0 ZN A:ZN302 3.5 13.3 0.6 HB3 A:HIS116 3.6 13.3 1.0 H021 A:XLZ303 3.7 22.4 0.8 N35 A:XLZ303 3.7 23.1 0.8 OD1 A:ASP118 3.9 15.0 1.0 HB2 A:CYS198 4.0 19.7 1.0 O24 A:XLZ303 4.0 15.5 0.8 ND1 A:HIS179 4.1 14.8 1.0 CG A:HIS179 4.2 14.0 1.0 HB3 A:CYS198 4.2 19.7 1.0 N25 A:XLZ303 4.2 14.7 0.8 ND1 A:HIS114 4.2 13.6 1.0 NE2 A:HIS116 4.2 16.2 1.0 CD2 A:HIS116 4.2 15.2 1.0 CG A:HIS114 4.3 13.0 1.0 CB A:CYS198 4.4 16.4 1.0 SG A:CYS198 4.4 16.7 1.0 N27 A:XLZ303 4.4 21.8 0.8 H A:HIS116 4.5 12.5 1.0 OD2 A:ASP118 4.5 15.8 1.0 N34 A:XLZ303 4.5 23.8 0.8 C02 A:XLZ303 4.5 18.6 0.8 CG A:ASP118 4.6 14.0 1.0 HB3 A:SER180 4.7 17.2 1.0 C22 A:XLZ303 4.8 15.4 0.8 HG2 A:ARG119 4.8 13.6 1.0 CA A:HIS116 4.8 10.7 1.0 HE A:ARG119 4.8 13.9 1.0 HD1 A:HIS179 4.9 17.8 1.0 C21 A:XLZ303 4.9 14.6 0.8 HD1 A:HIS114 5.0 16.3 1.0 O A:HOH507 5.0 20.4 0.7 HE2 A:HIS116 5.0 19.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551


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 2551 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.3 occ:0.61 O24 A:XLZ303 2.1 15.5 0.8 O A:HOH476 2.1 15.7 1.0 NE2 A:HIS240 2.2 16.1 1.0 SG A:CYS198 2.3 16.7 1.0 OD2 A:ASP118 2.4 15.8 1.0 H251 A:XLZ303 2.8 17.7 0.8 HB3 A:CYS198 3.0 19.7 1.0 C22 A:XLZ303 3.1 15.4 0.8 CD2 A:HIS240 3.2 15.7 1.0 CB A:CYS198 3.2 16.4 1.0 CE1 A:HIS240 3.2 17.3 1.0 HH21 A:ARG119 3.2 18.5 1.0 N25 A:XLZ303 3.2 14.7 0.8 HD2 A:HIS240 3.3 18.8 1.0 C21 A:XLZ303 3.4 14.6 0.8 HE1 A:HIS240 3.4 20.7 1.0 CG A:ASP118 3.5 14.0 1.0 ZN A:ZN301 3.5 13.2 0.8 HE A:ARG119 3.5 13.9 1.0 HE1 A:HIS114 3.6 15.3 1.0 HB2 A:CYS198 3.7 19.7 1.0 OD1 A:ASP118 3.8 15.0 1.0 NH2 A:ARG119 3.9 15.4 1.0 H021 A:XLZ303 4.0 22.4 0.8 NE2 A:HIS179 4.1 13.8 1.0 HE1 A:HIS179 4.1 17.3 1.0 NE A:ARG119 4.2 11.6 1.0 CE1 A:HIS179 4.2 14.4 1.0 CE1 A:HIS114 4.2 12.8 1.0 O23 A:XLZ303 4.2 16.7 0.8 ND1 A:HIS240 4.3 17.0 1.0 O A:HOH463 4.3 11.7 0.4 CG A:HIS240 4.3 15.9 1.0 C26 A:XLZ303 4.3 15.4 0.8 NE2 A:HIS114 4.4 14.3 1.0 HA A:CYS198 4.4 17.0 1.0 H101 A:XLZ303 4.5 22.1 0.8 CA A:CYS198 4.5 14.2 1.0 HH22 A:ARG119 4.5 18.5 1.0 CZ A:ARG119 4.5 12.4 1.0 C08 A:XLZ303 4.6 15.5 0.8 HA3 A:GLY239 4.7 15.0 1.0 CB A:ASP118 4.8 13.5 1.0 HB2 A:ASP118 4.8 16.2 1.0 CD2 A:HIS179 4.9 14.1 1.0 C02 A:XLZ303 5.0 18.6 0.8

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2551 To Be Published.