Zinc in PDB 8p9s: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2482

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2482, PDB code: 8p9s 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)	40.32 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.652, 67.949, 40.398, 90, 93.46, 90
R / Rfree (%)	12 / 13.7

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2482 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 2482 (pdb code 8p9s). 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 2482, PDB code: 8p9s:
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 2482


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 2482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.0 occ:0.79 O A:HOH483 1.9 5.7 0.6 NE2 A:HIS179 2.0 11.7 1.0 ND1 A:HIS116 2.0 11.2 1.0 NE2 A:HIS114 2.1 10.6 1.0 HB2 A:HIS116 2.9 10.5 1.0 CE1 A:HIS116 3.0 12.4 1.0 CE1 A:HIS179 3.0 11.9 1.0 CD2 A:HIS179 3.0 11.2 1.0 CE1 A:HIS114 3.0 9.6 1.0 CG A:HIS116 3.0 10.0 1.0 CD2 A:HIS114 3.1 9.9 1.0 HE1 A:HIS116 3.2 14.8 1.0 HE1 A:HIS114 3.2 11.6 1.0 HE1 A:HIS179 3.2 14.3 1.0 HD2 A:HIS179 3.2 13.4 1.0 H161 A:XCB303 3.2 15.1 1.0 HD2 A:HIS114 3.3 11.8 1.0 CB A:HIS116 3.4 8.8 1.0 ZN A:ZN302 3.5 9.9 0.8 H021 A:XCB303 3.6 15.1 1.0 HB3 A:HIS116 3.6 10.5 1.0 OD1 A:ASP118 3.8 11.1 1.0 O05 A:XCB303 3.8 16.6 1.0 HB2 A:CYS198 3.9 13.4 1.0 O19 A:XCB303 4.0 12.9 1.0 ND1 A:HIS179 4.1 12.7 1.0 NE2 A:HIS116 4.1 12.6 1.0 CG A:HIS179 4.1 11.8 1.0 ND1 A:HIS114 4.1 8.9 1.0 HB3 A:CYS198 4.1 13.4 1.0 CD2 A:HIS116 4.2 11.4 1.0 CG A:HIS114 4.2 8.7 1.0 N16 A:XCB303 4.2 12.6 1.0 CB A:CYS198 4.3 11.2 1.0 SG A:CYS198 4.4 10.5 1.0 H A:HIS116 4.5 10.4 1.0 OD2 A:ASP118 4.5 11.5 1.0 CG A:ASP118 4.6 10.2 1.0 C02 A:XCB303 4.6 12.6 1.0 C04 A:XCB303 4.6 15.2 1.0 HB3 A:SER180 4.7 14.6 1.0 HG2 A:ARG119 4.7 10.1 1.0 C18 A:XCB303 4.7 12.9 1.0 HE A:ARG119 4.8 10.9 1.0 CA A:HIS116 4.8 8.8 1.0 HD1 A:HIS179 4.9 15.3 1.0 HE2 A:HIS116 4.9 15.2 1.0 HD1 A:HIS114 4.9 10.6 1.0 HG3 A:ARG119 4.9 10.1 1.0 O A:HOH532 5.0 13.8 0.8 C17 A:XCB303 5.0 12.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2482


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 2482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.9 occ:0.77 O A:HOH483 2.0 5.7 0.6 O19 A:XCB303 2.1 12.9 1.0 NE2 A:HIS240 2.1 10.8 1.0 SG A:CYS198 2.3 10.5 1.0 OD2 A:ASP118 2.4 11.5 1.0 H161 A:XCB303 2.7 15.1 1.0 CD2 A:HIS240 3.0 10.8 1.0 C18 A:XCB303 3.1 12.9 1.0 HB3 A:CYS198 3.1 13.4 1.0 HD2 A:HIS240 3.1 13.0 1.0 CE1 A:HIS240 3.2 12.1 1.0 N16 A:XCB303 3.2 12.6 1.0 HH21 A:ARG119 3.3 13.2 1.0 CB A:CYS198 3.3 11.2 1.0 CG A:ASP118 3.4 10.2 1.0 C17 A:XCB303 3.4 12.6 1.0 HE1 A:HIS240 3.4 14.5 1.0 ZN A:ZN301 3.5 10.0 0.8 HE A:ARG119 3.5 10.9 1.0 HE1 A:HIS114 3.6 11.6 1.0 OD1 A:ASP118 3.7 11.1 1.0 HB2 A:CYS198 3.7 13.4 1.0 NH2 A:ARG119 3.9 11.0 1.0 H021 A:XCB303 4.1 15.1 1.0 NE2 A:HIS179 4.1 11.7 1.0 HE1 A:HIS179 4.2 14.3 1.0 NE A:ARG119 4.2 9.1 1.0 CG A:HIS240 4.2 11.2 1.0 ND1 A:HIS240 4.2 11.6 1.0 O20 A:XCB303 4.2 14.5 1.0 O A:HOH511 4.3 10.3 0.6 CE1 A:HIS114 4.3 9.6 1.0 CE1 A:HIS179 4.3 11.9 1.0 C15 A:XCB303 4.3 12.5 1.0 NE2 A:HIS114 4.4 10.6 1.0 HA A:CYS198 4.4 12.9 1.0 HH22 A:ARG119 4.4 13.2 1.0 CZ A:ARG119 4.5 9.5 1.0 H231 A:XCB303 4.5 19.9 1.0 CA A:CYS198 4.5 10.8 1.0 C21 A:XCB303 4.6 13.2 1.0 HA3 A:GLY239 4.6 12.7 1.0 CB A:ASP118 4.7 9.7 1.0 HB2 A:ASP118 4.8 11.7 1.0 CD2 A:HIS179 4.9 11.2 1.0 HB3 A:ASP118 5.0 11.7 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 2482 To Be Published.