Zinc in PDB 8pan: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2653

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2653, PDB code: 8pan 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)	34.57 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.381, 67.896, 40.242, 90, 93.48, 90
R / Rfree (%)	12.8 / 14.8

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2653 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 2653 (pdb code 8pan). 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 2653, PDB code: 8pan:
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 2653


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 2653 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.4 occ:0.72 O A:HOH536 1.9 10.3 0.7 NE2 A:HIS179 2.0 14.0 1.0 ND1 A:HIS116 2.1 15.0 1.0 NE2 A:HIS114 2.1 14.1 1.0 HB2 A:HIS116 2.9 13.8 1.0 CD2 A:HIS179 3.0 13.2 1.0 CE1 A:HIS179 3.0 13.9 1.0 CE1 A:HIS116 3.0 15.4 1.0 CE1 A:HIS114 3.1 12.3 1.0 CD2 A:HIS114 3.1 13.3 1.0 CG A:HIS116 3.1 12.5 1.0 HD2 A:HIS179 3.2 15.8 1.0 HE1 A:HIS116 3.2 18.4 1.0 HE1 A:HIS179 3.2 16.6 1.0 H141 A:XZL303 3.2 16.5 0.6 HE1 A:HIS114 3.2 14.7 1.0 HD2 A:HIS114 3.3 15.9 1.0 H141 A:XZL303 3.3 23.3 0.5 CB A:HIS116 3.4 11.5 1.0 ZN A:ZN302 3.5 13.1 0.8 HB3 A:HIS116 3.7 13.8 1.0 HB2 A:CYS198 3.8 17.9 1.0 O18 A:XZL303 3.8 12.0 0.6 OD1 A:ASP118 3.9 14.5 1.0 H021 A:XZL303 3.9 20.1 0.6 H051 A:XZL303 3.9 25.5 0.5 HB3 A:CYS198 4.0 17.9 1.0 H013 A:XZL303 4.0 14.4 0.6 H051 A:XZL303 4.0 29.0 0.6 O03 A:XZL303 4.0 18.8 0.5 O18 A:XZL303 4.1 21.4 0.5 ND1 A:HIS179 4.1 14.6 1.0 CG A:HIS179 4.1 13.8 1.0 NE2 A:HIS116 4.1 16.7 1.0 ND1 A:HIS114 4.2 12.3 1.0 CB A:CYS198 4.2 14.9 1.0 CD2 A:HIS116 4.2 16.0 1.0 CG A:HIS114 4.2 12.3 1.0 N14 A:XZL303 4.2 13.8 0.6 H021 A:XZL303 4.2 25.4 0.5 SG A:CYS198 4.3 14.7 1.0 N14 A:XZL303 4.3 19.5 0.5 H A:HIS116 4.5 12.9 1.0 OD2 A:ASP118 4.5 15.0 1.0 C16 A:XZL303 4.6 12.5 0.6 CG A:ASP118 4.6 12.9 1.0 HE A:ARG119 4.7 13.7 1.0 C16 A:XZL303 4.7 21.3 0.5 C05 A:XZL303 4.7 21.3 0.5 HG2 A:ARG119 4.7 13.0 1.0 C02 A:XZL303 4.7 16.8 0.6 HB3 A:SER180 4.7 16.9 1.0 C02 A:XZL303 4.8 21.3 0.5 CA A:HIS116 4.8 11.3 1.0 HD1 A:HIS179 4.9 17.4 1.0 C04 A:XZL303 4.9 20.6 0.5 C01 A:XZL303 4.9 12.1 0.6 C15 A:XZL303 4.9 13.1 0.6 HE2 A:HIS116 4.9 20.0 1.0 HD1 A:HIS114 4.9 14.6 1.0 C05 A:XZL303 4.9 24.2 0.6 C15 A:XZL303 4.9 19.9 0.5 HG3 A:ARG119 5.0 13.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2653


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 2653 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.1 occ:0.76 O18 A:XZL303 1.7 21.4 0.5 O A:HOH536 2.0 10.3 0.7 NE2 A:HIS240 2.2 14.9 1.0 O18 A:XZL303 2.2 12.0 0.6 SG A:CYS198 2.3 14.7 1.0 OD2 A:ASP118 2.3 15.0 1.0 H141 A:XZL303 2.7 23.3 0.5 C16 A:XZL303 2.8 21.3 0.5 H141 A:XZL303 3.0 16.5 0.6 CD2 A:HIS240 3.1 13.5 1.0 HB3 A:CYS198 3.1 17.9 1.0 C16 A:XZL303 3.1 12.5 0.6 CE1 A:HIS240 3.2 14.8 1.0 HH21 A:ARG119 3.2 16.6 1.0 HD2 A:HIS240 3.2 16.1 1.0 N14 A:XZL303 3.2 19.5 0.5 CB A:CYS198 3.3 14.9 1.0 C15 A:XZL303 3.3 19.9 0.5 CG A:ASP118 3.4 12.9 1.0 N14 A:XZL303 3.4 13.8 0.6 HE1 A:HIS240 3.4 17.6 1.0 C15 A:XZL303 3.5 13.1 0.6 ZN A:ZN301 3.5 12.4 0.7 HE A:ARG119 3.5 13.7 1.0 OD1 A:ASP118 3.7 14.5 1.0 HE1 A:HIS114 3.7 14.7 1.0 HB2 A:CYS198 3.7 17.9 1.0 NH2 A:ARG119 3.9 13.9 1.0 O17 A:XZL303 3.9 22.3 0.5 H013 A:XZL303 4.0 14.4 0.6 H021 A:XZL303 4.2 25.4 0.5 NE2 A:HIS179 4.2 14.0 1.0 HE1 A:HIS179 4.2 16.6 1.0 NE A:ARG119 4.2 11.5 1.0 O A:HOH511 4.2 11.9 0.5 CG A:HIS240 4.3 13.4 1.0 ND1 A:HIS240 4.3 14.5 1.0 H211 A:XZL303 4.3 24.4 0.5 O17 A:XZL303 4.3 13.3 0.6 CE1 A:HIS179 4.3 13.9 1.0 CE1 A:HIS114 4.3 12.3 1.0 H211 A:XZL303 4.3 24.4 0.6 HH22 A:ARG119 4.4 16.6 1.0 NE2 A:HIS114 4.4 14.1 1.0 C13 A:XZL303 4.4 19.9 0.5 HA A:CYS198 4.4 16.6 1.0 C13 A:XZL303 4.4 15.4 0.6 CZ A:ARG119 4.5 12.0 1.0 CA A:CYS198 4.5 13.9 1.0 C19 A:XZL303 4.6 19.7 0.5 C19 A:XZL303 4.6 15.3 0.6 HA3 A:GLY239 4.6 15.4 1.0 CB A:ASP118 4.7 12.5 1.0 HB2 A:ASP118 4.8 15.0 1.0 H021 A:XZL303 4.8 20.1 0.6 C01 A:XZL303 4.8 12.1 0.6 HB3 A:ASP118 4.9 15.0 1.0 H011 A:XZL303 4.9 14.4 0.6 CD2 A:HIS179 5.0 13.2 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 2653 To Be Published.