Zinc in PDB 8pam: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2652

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2652, PDB code: 8pam 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)	29.06 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.477, 67.903, 40.284, 90, 93.58, 90
R / Rfree (%)	11.1 / 13.2

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2652 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 2652 (pdb code 8pam). 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 2652, PDB code: 8pam:
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 2652


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 2652 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.1 occ:0.85 O A:HOH532 1.9 7.1 0.7 NE2 A:HIS179 2.0 11.3 1.0 ND1 A:HIS116 2.0 11.3 1.0 NE2 A:HIS114 2.1 10.4 1.0 HB2 A:HIS116 2.9 10.8 1.0 CE1 A:HIS116 3.0 11.9 1.0 CD2 A:HIS179 3.0 10.5 1.0 CE1 A:HIS179 3.0 11.5 1.0 CE1 A:HIS114 3.0 8.9 1.0 CG A:HIS116 3.0 10.3 1.0 CD2 A:HIS114 3.1 9.9 1.0 HE1 A:HIS116 3.1 14.2 1.0 HD2 A:HIS179 3.2 12.6 1.0 HE1 A:HIS179 3.2 13.8 1.0 HE1 A:HIS114 3.2 10.7 1.0 H051 A:XZR303 3.2 13.0 0.7 H051 A:XZR303 3.2 20.3 0.3 HD2 A:HIS114 3.3 11.9 1.0 CB A:HIS116 3.4 9.1 1.0 ZN A:ZN302 3.5 10.7 0.8 HB3 A:HIS116 3.6 10.8 1.0 O27 A:XZR303 3.7 19.1 0.7 H282 A:XZR303 3.8 25.3 0.3 HB2 A:CYS198 3.8 14.1 1.0 H282 A:XZR303 3.8 23.2 0.7 OD1 A:ASP118 3.9 11.6 1.0 O09 A:XZR303 3.9 13.9 0.3 O27 A:XZR303 3.9 20.9 0.3 O09 A:XZR303 3.9 12.3 0.7 ND1 A:HIS179 4.1 12.1 1.0 NE2 A:HIS116 4.1 13.0 1.0 CG A:HIS179 4.1 11.6 1.0 HB3 A:CYS198 4.1 14.1 1.0 CD2 A:HIS116 4.2 12.6 1.0 ND1 A:HIS114 4.2 9.3 1.0 CG A:HIS114 4.2 9.1 1.0 N05 A:XZR303 4.2 16.9 0.3 N05 A:XZR303 4.2 10.9 0.7 CB A:CYS198 4.3 11.8 1.0 SG A:CYS198 4.3 11.0 1.0 C28 A:XZR303 4.4 21.1 0.3 C28 A:XZR303 4.4 19.4 0.7 H A:HIS116 4.5 10.2 1.0 OD2 A:ASP118 4.5 12.2 1.0 CG A:ASP118 4.6 10.1 1.0 C07 A:XZR303 4.6 14.2 0.3 HB3 A:SER180 4.7 13.2 1.0 H013 A:XZR303 4.7 22.1 0.3 C07 A:XZR303 4.7 12.1 0.7 HE A:ARG119 4.7 10.4 1.0 H011 A:XZR303 4.7 22.1 0.3 H013 A:XZR303 4.7 17.2 0.7 HG2 A:ARG119 4.8 9.8 1.0 CA A:HIS116 4.8 9.2 1.0 H011 A:XZR303 4.9 17.2 0.7 HD1 A:HIS179 4.9 14.5 1.0 HE2 A:HIS116 4.9 15.6 1.0 C02 A:XZR303 4.9 16.0 0.7 C06 A:XZR303 4.9 16.2 0.3 O A:HOH563 4.9 15.2 0.9 HD1 A:HIS114 4.9 11.2 1.0 HG3 A:ARG119 4.9 9.8 1.0 C06 A:XZR303 4.9 11.5 0.7 H281 A:XZR303 5.0 25.3 0.3 C02 A:XZR303 5.0 19.3 0.3

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2652


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 2652 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.7 occ:0.84 O09 A:XZR303 2.0 12.3 0.7 O A:HOH532 2.0 7.1 0.7 NE2 A:HIS240 2.1 11.2 1.0 O09 A:XZR303 2.1 13.9 0.3 SG A:CYS198 2.3 11.0 1.0 OD2 A:ASP118 2.3 12.2 1.0 H051 A:XZR303 2.8 13.0 0.7 C07 A:XZR303 3.0 12.1 0.7 CD2 A:HIS240 3.0 11.1 1.0 HB3 A:CYS198 3.0 14.1 1.0 HD2 A:HIS240 3.1 13.3 1.0 H051 A:XZR303 3.1 20.3 0.3 C07 A:XZR303 3.1 14.2 0.3 CE1 A:HIS240 3.2 12.3 1.0 HH21 A:ARG119 3.2 13.2 1.0 N05 A:XZR303 3.2 10.9 0.7 CB A:CYS198 3.3 11.8 1.0 C06 A:XZR303 3.3 11.5 0.7 CG A:ASP118 3.4 10.1 1.0 HE1 A:HIS240 3.4 14.7 1.0 N05 A:XZR303 3.5 16.9 0.3 C06 A:XZR303 3.5 16.2 0.3 ZN A:ZN301 3.5 10.1 0.8 HE A:ARG119 3.5 10.4 1.0 HE1 A:HIS114 3.6 10.7 1.0 HB2 A:CYS198 3.7 14.1 1.0 OD1 A:ASP118 3.7 11.6 1.0 NH2 A:ARG119 3.9 11.0 1.0 NE2 A:HIS179 4.1 11.3 1.0 HE1 A:HIS179 4.2 13.8 1.0 O08 A:XZR303 4.2 14.2 0.7 CG A:HIS240 4.2 11.2 1.0 NE A:ARG119 4.2 8.7 1.0 ND1 A:HIS240 4.2 12.2 1.0 H011 A:XZR303 4.3 22.1 0.3 O A:HOH527 4.3 10.9 0.7 CE1 A:HIS179 4.3 11.5 1.0 O08 A:XZR303 4.3 14.2 0.3 CE1 A:HIS114 4.3 8.9 1.0 H011 A:XZR303 4.3 17.2 0.7 C04 A:XZR303 4.4 12.0 0.7 NE2 A:HIS114 4.4 10.4 1.0 H121 A:XZR303 4.4 27.1 0.3 HH22 A:ARG119 4.4 13.2 1.0 H221 A:XZR303 4.4 20.5 0.7 HA A:CYS198 4.4 12.6 1.0 CZ A:ARG119 4.5 9.1 1.0 C04 A:XZR303 4.5 17.3 0.3 C10 A:XZR303 4.5 12.7 0.7 CA A:CYS198 4.5 10.6 1.0 C10 A:XZR303 4.6 17.7 0.3 HA3 A:GLY239 4.6 12.1 1.0 CB A:ASP118 4.7 9.5 1.0 HB2 A:ASP118 4.8 11.4 1.0 O27 A:XZR303 4.9 19.1 0.7 HB3 A:ASP118 4.9 11.4 1.0 CD2 A:HIS179 4.9 10.5 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 2652 To Be Published.