Zinc in PDB 8pg6: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2754

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2754, PDB code: 8pg6 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)	34.65 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.493, 68.21, 40.304, 90, 93.42, 90
R / Rfree (%)	11.9 / 13.9

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2754 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 2754 (pdb code 8pg6). 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 2754, PDB code: 8pg6:
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 2754


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 2754 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.7 occ:0.86 O A:HOH482 1.9 7.7 0.7 NE2 A:HIS179 2.0 11.6 1.0 ND1 A:HIS116 2.0 12.3 1.0 NE2 A:HIS114 2.1 10.3 1.0 HB2 A:HIS116 2.9 10.8 1.0 CE1 A:HIS179 2.9 12.1 1.0 CE1 A:HIS116 3.0 12.4 1.0 CD2 A:HIS179 3.0 11.0 1.0 CG A:HIS116 3.0 9.8 1.0 CE1 A:HIS114 3.0 9.0 1.0 CD2 A:HIS114 3.0 10.3 1.0 O29 A:YSX303 3.1 17.8 0.5 HE1 A:HIS179 3.1 14.4 1.0 HE1 A:HIS116 3.1 14.9 1.0 HD2 A:HIS179 3.2 13.2 1.0 HE1 A:HIS114 3.2 10.8 1.0 O29 A:YSX303 3.2 14.5 0.6 HD2 A:HIS114 3.2 12.3 1.0 H051 A:YSX303 3.2 13.7 0.6 H051 A:YSX303 3.2 17.4 0.5 CB A:HIS116 3.4 9.0 1.0 H021 A:YSX303 3.4 14.9 0.6 ZN A:ZN302 3.5 10.0 0.8 H021 A:YSX303 3.6 18.4 0.5 HB3 A:HIS116 3.6 10.8 1.0 OD1 A:ASP118 3.8 12.1 1.0 HB2 A:CYS198 3.9 13.1 1.0 O09 A:YSX303 3.9 12.3 0.6 O09 A:YSX303 4.0 12.1 0.5 C28 A:YSX303 4.0 17.1 0.5 ND1 A:HIS179 4.0 12.3 1.0 C28 A:YSX303 4.1 14.3 0.6 NE2 A:HIS116 4.1 13.0 1.0 CG A:HIS179 4.1 11.7 1.0 CD2 A:HIS116 4.1 11.9 1.0 HB3 A:CYS198 4.1 13.1 1.0 ND1 A:HIS114 4.1 8.5 1.0 CG A:HIS114 4.2 8.5 1.0 N05 A:YSX303 4.2 11.4 0.6 N05 A:YSX303 4.2 14.5 0.5 CB A:CYS198 4.3 10.9 1.0 SG A:CYS198 4.4 10.3 1.0 C02 A:YSX303 4.5 12.4 0.6 H A:HIS116 4.5 9.6 1.0 OD2 A:ASP118 4.5 11.4 1.0 C02 A:YSX303 4.6 15.4 0.5 CG A:ASP118 4.6 10.6 1.0 N27 A:YSX303 4.7 13.6 0.6 N27 A:YSX303 4.7 16.4 0.5 HB3 A:SER180 4.7 14.1 1.0 HG2 A:ARG119 4.7 9.2 1.0 C07 A:YSX303 4.8 12.6 0.6 HE A:ARG119 4.8 9.6 1.0 CA A:HIS116 4.8 8.5 1.0 HD1 A:HIS179 4.8 14.7 1.0 H302 A:YSX303 4.8 21.6 0.5 C07 A:YSX303 4.8 11.6 0.5 H302 A:YSX303 4.9 19.9 0.6 HE2 A:HIS116 4.9 15.5 1.0 HD1 A:HIS114 4.9 10.2 1.0 O A:HOH541 5.0 14.2 0.9 H012 A:YSX303 5.0 13.9 0.6 HG3 A:ARG119 5.0 9.2 1.0 HD2 A:HIS116 5.0 14.3 1.0 H012 A:YSX303 5.0 17.5 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2754


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 2754 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.0 occ:0.81 O09 A:YSX303 2.0 12.3 0.6 O A:HOH482 2.0 7.7 0.7 NE2 A:HIS240 2.1 11.1 1.0 O09 A:YSX303 2.3 12.1 0.5 SG A:CYS198 2.3 10.3 1.0 OD2 A:ASP118 2.4 11.4 1.0 H051 A:YSX303 2.7 13.7 0.6 H051 A:YSX303 2.8 17.4 0.5 C07 A:YSX303 2.9 12.6 0.6 CD2 A:HIS240 3.0 11.3 1.0 HB3 A:CYS198 3.1 13.1 1.0 HD2 A:HIS240 3.1 13.6 1.0 N05 A:YSX303 3.2 11.4 0.6 CE1 A:HIS240 3.2 12.2 1.0 C07 A:YSX303 3.2 11.6 0.5 N05 A:YSX303 3.2 14.5 0.5 HH21 A:ARG119 3.3 12.2 1.0 CB A:CYS198 3.3 10.9 1.0 C06 A:YSX303 3.3 11.2 0.6 CG A:ASP118 3.4 10.6 1.0 C06 A:YSX303 3.4 12.8 0.5 HE1 A:HIS240 3.4 14.6 1.0 ZN A:ZN301 3.5 10.7 0.9 HE A:ARG119 3.5 9.6 1.0 HE1 A:HIS114 3.5 10.8 1.0 HB2 A:CYS198 3.7 13.1 1.0 OD1 A:ASP118 3.7 12.1 1.0 NH2 A:ARG119 3.9 10.2 1.0 H021 A:YSX303 4.0 18.4 0.5 O08 A:YSX303 4.1 12.8 0.6 H021 A:YSX303 4.1 14.9 0.6 NE2 A:HIS179 4.1 11.6 1.0 HE1 A:HIS179 4.2 14.4 1.0 NE A:ARG119 4.2 8.0 1.0 CG A:HIS240 4.2 11.1 1.0 CE1 A:HIS114 4.2 9.0 1.0 O A:HOH510 4.2 9.6 0.6 ND1 A:HIS240 4.2 11.1 1.0 CE1 A:HIS179 4.3 12.1 1.0 C04 A:YSX303 4.3 14.8 0.5 C04 A:YSX303 4.3 12.0 0.6 NE2 A:HIS114 4.3 10.3 1.0 O08 A:YSX303 4.4 13.1 0.5 HH22 A:ARG119 4.4 12.2 1.0 H221 A:YSX303 4.4 18.3 0.5 H121 A:YSX303 4.4 17.4 0.6 HA A:CYS198 4.4 12.1 1.0 CZ A:ARG119 4.5 8.7 1.0 CA A:CYS198 4.5 10.1 1.0 C10 A:YSX303 4.5 13.8 0.5 C10 A:YSX303 4.6 11.6 0.6 HA3 A:GLY239 4.6 10.8 1.0 CB A:ASP118 4.7 10.1 1.0 HB2 A:ASP118 4.8 12.1 1.0 O29 A:YSX303 4.8 17.8 0.5 CD2 A:HIS179 4.9 11.0 1.0 O29 A:YSX303 4.9 14.5 0.6 C02 A:YSX303 5.0 12.4 0.6 HB3 A:ASP118 5.0 12.1 1.0 C02 A:YSX303 5.0 15.4 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 2754 To Be Published.