Zinc in PDB 8pal: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2651

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2651, PDB code: 8pal 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)	28.98 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.5, 67.885, 40.253, 90, 93.24, 90
R / Rfree (%)	11.7 / 14

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2651 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2651 (pdb code 8pal). 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 2651, PDB code: 8pal:
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 2651


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 2651 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.6 occ:0.85 O A:HOH478 1.9 7.5 0.6 NE2 A:HIS179 2.0 12.8 1.0 ND1 A:HIS116 2.1 11.9 1.0 NE2 A:HIS114 2.1 12.6 1.0 HB2 A:HIS116 2.9 12.8 1.0 CD2 A:HIS179 3.0 11.9 1.0 CE1 A:HIS179 3.0 12.7 1.0 CE1 A:HIS116 3.0 12.4 1.0 CE1 A:HIS114 3.0 10.0 1.0 CD2 A:HIS114 3.1 11.7 1.0 CG A:HIS116 3.1 11.1 1.0 HD2 A:HIS179 3.2 14.3 1.0 HE1 A:HIS116 3.2 14.8 1.0 H151 A:XM8303 3.2 17.6 0.5 HE1 A:HIS179 3.2 15.2 1.0 H151 A:XM8303 3.2 14.3 0.5 HE1 A:HIS114 3.2 12.0 1.0 HD2 A:HIS114 3.2 14.1 1.0 CB A:HIS116 3.4 10.7 1.0 ZN A:ZN302 3.5 11.3 0.8 H021 A:XM8303 3.6 18.7 0.5 H021 A:XM8303 3.6 15.7 0.5 HB3 A:HIS116 3.6 12.8 1.0 HB2 A:CYS198 3.8 15.8 1.0 O19 A:XM8303 3.8 10.8 0.5 H042 A:XM8303 3.8 18.1 0.5 H042 A:XM8303 3.8 20.2 0.5 OD1 A:ASP118 3.9 12.7 1.0 O19 A:XM8303 4.0 15.7 0.5 HB3 A:CYS198 4.0 15.8 1.0 ND1 A:HIS179 4.1 13.2 1.0 CG A:HIS179 4.1 12.8 1.0 NE2 A:HIS116 4.1 13.4 1.0 ND1 A:HIS114 4.1 10.6 1.0 N15 A:XM8303 4.2 14.7 0.5 CG A:HIS114 4.2 10.8 1.0 CD2 A:HIS116 4.2 13.4 1.0 N15 A:XM8303 4.2 11.9 0.5 CB A:CYS198 4.2 13.1 1.0 SG A:CYS198 4.3 12.6 1.0 H A:HIS116 4.5 12.1 1.0 OD2 A:ASP118 4.5 12.7 1.0 CG A:ASP118 4.6 11.4 1.0 C17 A:XM8303 4.6 15.0 0.5 C02 A:XM8303 4.7 15.6 0.5 C17 A:XM8303 4.7 11.9 0.5 C02 A:XM8303 4.7 13.1 0.5 HE A:ARG119 4.7 12.8 1.0 HB3 A:SER180 4.7 15.9 1.0 C04 A:XM8303 4.7 15.1 0.5 HG2 A:ARG119 4.8 11.6 1.0 C04 A:XM8303 4.8 16.8 0.5 CA A:HIS116 4.8 10.6 1.0 C16 A:XM8303 4.9 15.3 0.5 HD1 A:HIS179 4.9 15.9 1.0 HG3 A:ARG119 4.9 11.6 1.0 C16 A:XM8303 4.9 12.4 0.5 HE2 A:HIS116 4.9 16.1 1.0 HD1 A:HIS114 4.9 12.7 1.0 H041 A:XM8303 5.0 20.2 0.5 O A:HOH545 5.0 12.6 0.8 H041 A:XM8303 5.0 18.1 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2651


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 2651 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.3 occ:0.79 O19 A:XM8303 2.0 15.7 0.5 O A:HOH478 2.1 7.5 0.6 NE2 A:HIS240 2.1 12.5 1.0 O19 A:XM8303 2.2 10.8 0.5 OD2 A:ASP118 2.3 12.7 1.0 SG A:CYS198 2.3 12.6 1.0 H151 A:XM8303 2.8 17.6 0.5 H151 A:XM8303 2.8 14.3 0.5 CD2 A:HIS240 3.0 13.1 1.0 C17 A:XM8303 3.0 11.9 0.5 C17 A:XM8303 3.1 15.0 0.5 HB3 A:CYS198 3.1 15.8 1.0 HD2 A:HIS240 3.1 15.7 1.0 HH21 A:ARG119 3.2 14.5 1.0 CE1 A:HIS240 3.2 14.1 1.0 N15 A:XM8303 3.2 11.9 0.5 CB A:CYS198 3.3 13.1 1.0 N15 A:XM8303 3.3 14.7 0.5 CG A:ASP118 3.3 11.4 1.0 C16 A:XM8303 3.3 12.4 0.5 HE1 A:HIS240 3.4 17.0 1.0 C16 A:XM8303 3.4 15.3 0.5 HE A:ARG119 3.5 12.8 1.0 ZN A:ZN301 3.5 11.6 0.8 OD1 A:ASP118 3.6 12.7 1.0 HB2 A:CYS198 3.7 15.8 1.0 HE1 A:HIS114 3.7 12.0 1.0 NH2 A:ARG119 3.9 12.1 1.0 HE1 A:HIS179 4.2 15.2 1.0 NE2 A:HIS179 4.2 12.8 1.0 CG A:HIS240 4.2 12.6 1.0 O18 A:XM8303 4.2 15.5 0.5 NE A:ARG119 4.2 10.7 1.0 H021 A:XM8303 4.2 15.7 0.5 O18 A:XM8303 4.2 13.8 0.5 O A:HOH539 4.2 12.9 0.7 ND1 A:HIS240 4.3 13.3 1.0 H021 A:XM8303 4.3 18.7 0.5 C14 A:XM8303 4.3 13.5 0.5 H321 A:XM8303 4.3 19.2 0.5 CE1 A:HIS179 4.3 12.7 1.0 CE1 A:HIS114 4.4 10.0 1.0 HH22 A:ARG119 4.4 14.5 1.0 C14 A:XM8303 4.4 14.4 0.5 NE2 A:HIS114 4.4 12.6 1.0 HA A:CYS198 4.4 15.6 1.0 CZ A:ARG119 4.5 10.8 1.0 C20 A:XM8303 4.5 12.7 0.5 CA A:CYS198 4.5 13.0 1.0 HA3 A:GLY239 4.6 13.4 1.0 C20 A:XM8303 4.6 15.7 0.5 CB A:ASP118 4.7 11.2 1.0 H221 A:XM8303 4.7 23.0 0.5 HB2 A:ASP118 4.7 13.4 1.0 HB3 A:ASP118 4.9 13.4 1.0 H013 A:XM8303 4.9 17.4 0.5 H013 A:XM8303 5.0 14.5 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 2651 To Be Published.