Zinc in PDB 8p8z: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1963

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1963, PDB code: 8p8z 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)	34.51 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.444, 67.805, 40.174, 90, 93.58, 90
R / Rfree (%)	12.6 / 14.2

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1963 (pdb code 8p8z). 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 1963, PDB code: 8p8z:
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 1963


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 1963 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.0 occ:0.96 O A:HOH464 1.9 39.0 1.0 NE2 A:HIS179 2.0 9.3 1.0 ND1 A:HIS116 2.0 9.8 1.0 NE2 A:HIS114 2.0 8.6 1.0 HB2 A:HIS116 2.9 10.3 1.0 CE1 A:HIS114 3.0 8.3 1.0 CE1 A:HIS116 3.0 10.4 1.0 CE1 A:HIS179 3.0 10.0 1.0 CD2 A:HIS179 3.0 9.3 1.0 CD2 A:HIS114 3.1 8.0 1.0 CG A:HIS116 3.1 9.0 1.0 HE1 A:HIS114 3.1 10.0 1.0 HE1 A:HIS116 3.1 12.5 1.0 HE1 A:HIS179 3.2 12.0 1.0 HD2 A:HIS179 3.2 11.2 1.0 H101 A:X6U303 3.2 14.5 0.4 H101 A:X6U303 3.2 12.4 0.7 HD2 A:HIS114 3.3 9.6 1.0 CB A:HIS116 3.4 8.5 1.0 ZN A:ZN302 3.5 8.7 0.8 H021 A:X6U303 3.6 14.8 0.4 HB3 A:HIS116 3.7 10.3 1.0 H021 A:X6U303 3.7 13.2 0.7 HB2 A:CYS198 3.8 12.3 1.0 OD1 A:ASP118 3.8 9.3 1.0 O14 A:X6U303 3.9 12.0 0.4 O14 A:X6U303 3.9 10.3 0.7 ND1 A:HIS114 4.1 7.8 1.0 NE2 A:HIS116 4.1 11.1 1.0 ND1 A:HIS179 4.1 10.3 1.0 CG A:HIS179 4.1 9.9 1.0 CG A:HIS114 4.2 7.7 1.0 H012 A:X6U303 4.2 14.3 0.7 N10 A:X6U303 4.2 12.1 0.4 CD2 A:HIS116 4.2 10.3 1.0 N10 A:X6U303 4.2 10.3 0.7 HB3 A:CYS198 4.2 12.3 1.0 CB A:CYS198 4.3 10.3 1.0 H011 A:X6U303 4.3 14.3 0.7 SG A:CYS198 4.3 9.3 1.0 H012 A:X6U303 4.4 15.1 0.4 H A:HIS116 4.5 9.6 1.0 OD2 A:ASP118 4.5 9.8 1.0 H011 A:X6U303 4.6 15.1 0.4 C01 A:X6U303 4.6 12.0 0.7 C02 A:X6U303 4.6 11.0 0.7 CG A:ASP118 4.6 9.0 1.0 HB3 A:SER180 4.6 12.7 1.0 C02 A:X6U303 4.6 12.3 0.4 HG2 A:ARG119 4.7 9.3 1.0 C12 A:X6U303 4.7 10.3 0.7 C12 A:X6U303 4.7 12.6 0.4 HE A:ARG119 4.7 10.0 1.0 C01 A:X6U303 4.8 12.6 0.4 CA A:HIS116 4.8 8.2 1.0 HD1 A:HIS114 4.9 9.4 1.0 HE2 A:HIS116 4.9 13.4 1.0 HD1 A:HIS179 4.9 12.4 1.0 C11 A:X6U303 4.9 12.5 0.4 HG3 A:ARG119 4.9 9.3 1.0 C11 A:X6U303 4.9 10.7 0.7 O A:HOH548 4.9 12.1 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1963


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 1963 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.7 occ:0.85 O14 A:X6U303 2.0 12.0 0.4 O A:HOH464 2.0 39.0 1.0 NE2 A:HIS240 2.1 9.7 1.0 O14 A:X6U303 2.2 10.3 0.7 SG A:CYS198 2.3 9.3 1.0 OD2 A:ASP118 2.3 9.8 1.0 H101 A:X6U303 2.7 12.4 0.7 H101 A:X6U303 2.8 14.5 0.4 C12 A:X6U303 3.0 12.6 0.4 CD2 A:HIS240 3.0 9.7 1.0 HB3 A:CYS198 3.0 12.3 1.0 C12 A:X6U303 3.1 10.3 0.7 HD2 A:HIS240 3.2 11.7 1.0 CE1 A:HIS240 3.2 10.1 1.0 N10 A:X6U303 3.2 10.3 0.7 N10 A:X6U303 3.2 12.1 0.4 CB A:CYS198 3.2 10.3 1.0 HH21 A:ARG119 3.3 11.5 1.0 C11 A:X6U303 3.3 12.5 0.4 CG A:ASP118 3.3 9.0 1.0 C11 A:X6U303 3.4 10.7 0.7 HE1 A:HIS240 3.4 12.1 1.0 HE A:ARG119 3.5 10.0 1.0 ZN A:ZN301 3.5 9.0 1.0 HE1 A:HIS114 3.6 10.0 1.0 HB2 A:CYS198 3.6 12.3 1.0 OD1 A:ASP118 3.6 9.3 1.0 NH2 A:ARG119 3.9 9.6 1.0 H021 A:X6U303 4.1 13.2 0.7 O13 A:X6U303 4.1 13.4 0.4 NE2 A:HIS179 4.1 9.3 1.0 H021 A:X6U303 4.1 14.8 0.4 NE A:ARG119 4.2 8.3 1.0 HE1 A:HIS179 4.2 12.0 1.0 CG A:HIS240 4.2 9.4 1.0 ND1 A:HIS240 4.3 9.8 1.0 O13 A:X6U303 4.3 11.3 0.7 CE1 A:HIS114 4.3 8.3 1.0 CE1 A:HIS179 4.3 10.0 1.0 O A:HOH511 4.3 8.6 0.6 C09 A:X6U303 4.3 12.1 0.4 C09 A:X6U303 4.4 10.5 0.7 NE2 A:HIS114 4.4 8.6 1.0 H171 A:X6U303 4.4 17.7 0.7 CZ A:ARG119 4.4 8.1 1.0 HH22 A:ARG119 4.4 11.5 1.0 HA A:CYS198 4.5 11.7 1.0 C15 A:X6U303 4.5 13.1 0.4 CA A:CYS198 4.5 9.7 1.0 HA3 A:GLY239 4.6 11.0 1.0 C15 A:X6U303 4.6 11.4 0.7 CB A:ASP118 4.6 8.8 1.0 H171 A:X6U303 4.6 19.4 0.4 HB2 A:ASP118 4.7 10.6 1.0 HB3 A:ASP118 4.9 10.6 1.0 CD2 A:HIS179 4.9 9.3 1.0 HG2 A:ARG119 5.0 9.3 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 1963 To Be Published.